{"diffoscope-json-version": 1, "source1": "/srv/reproducible-results/rbuild-debian/r-b-build.Pgo0yWXT/b1/apbs_3.0.0+dfsg1-3_arm64.changes", "source2": "/srv/reproducible-results/rbuild-debian/r-b-build.Pgo0yWXT/b2/apbs_3.0.0+dfsg1-3_arm64.changes", "unified_diff": null, "details": [{"source1": "Files", "source2": "Files", "unified_diff": "@@ -1,9 +1,9 @@\n \n- 1cb4d9ca52f47723550b5037ddf321c5 226062368 science optional apbs-data_3.0.0+dfsg1-3_all.deb\n+ b9e7b60083ab9d191a05c6e59ddaeaf6 226062112 science optional apbs-data_3.0.0+dfsg1-3_all.deb\n  a1790431dbdf79d58ffd8f90522b17c9 152044 debug optional apbs-dbgsym_3.0.0+dfsg1-3_arm64.deb\n  48397b26b31f8257d89cd616dcd85aab 80296 science optional apbs_3.0.0+dfsg1-3_arm64.deb\n  4f03b23209f75b4394f635db21801175 66316 libdevel optional libapbs-dev_3.0.0+dfsg1-3_arm64.deb\n  8782957a680d09db1a5a9e2c5302db7a 531172 debug optional libapbs3-dbgsym_3.0.0+dfsg1-3_arm64.deb\n  7bd67d942a606b6e2ed8c4e32c92ea61 220764 libs optional libapbs3_3.0.0+dfsg1-3_arm64.deb\n  af5a467de0cc0e18b75a68a3debed3f3 162928 debug optional python3-apbslib-dbgsym_3.0.0+dfsg1-3_arm64.deb\n  6cc09e35557aef4c4844ba890a6b27f8 101248 python optional python3-apbslib_3.0.0+dfsg1-3_arm64.deb\n"}, {"source1": "apbs-data_3.0.0+dfsg1-3_all.deb", "source2": "apbs-data_3.0.0+dfsg1-3_all.deb", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -1,3 +1,3 @@\n -rw-r--r--   0        0        0        4 2020-07-23 09:35:23.000000 debian-binary\n--rw-r--r--   0        0        0    13244 2020-07-23 09:35:23.000000 control.tar.xz\n--rw-r--r--   0        0        0 226048932 2020-07-23 09:35:23.000000 data.tar.xz\n+-rw-r--r--   0        0        0    13240 2020-07-23 09:35:23.000000 control.tar.xz\n+-rw-r--r--   0        0        0 226048680 2020-07-23 09:35:23.000000 data.tar.xz\n"}, {"source1": "control.tar.xz", "source2": "control.tar.xz", "unified_diff": null, "details": [{"source1": "control.tar", "source2": "control.tar", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "comments": ["Files differ"], "unified_diff": null}]}]}]}, {"source1": "data.tar.xz", "source2": "data.tar.xz", "unified_diff": null, "details": [{"source1": "data.tar", "source2": "data.tar", "unified_diff": null, "details": [{"source1": "./usr/share/apbs/examples/FKBP/io.mc", "source2": "./usr/share/apbs/examples/FKBP/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:33:09 2025\n+# Creation Date and Time:  Sun Jan  7 09:44:15 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path 1d7h-dmso-complex.pqr\n@@ -637,32 +637,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.581017\n+Vacc_SASA: Time elapsed: 0.510784\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.494940e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.671651e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.162000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.894000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.292760e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.684400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.742904e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.802977e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.211746e-02\n Vprtstp: contraction number = 6.211746e-02\n Vprtstp: iteration = 2\n@@ -736,30 +736,30 @@\n Vprtstp: contraction number = 6.956346e-01\n Vprtstp: iteration = 25\n Vprtstp: relative residual = 1.302234e-06\n Vprtstp: contraction number = 6.974500e-01\n Vprtstp: iteration = 26\n Vprtstp: relative residual = 9.101840e-07\n Vprtstp: contraction number = 6.989406e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.507652e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.702807e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 8.541841e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.650632e+00\n Vpmg_setPart:  lower corner = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  upper corner = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  actual minima = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  actual maxima = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.506409949028E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.550000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.770000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -807,30 +807,30 @@\n VPMG::extEnergy: extQfEnergy = 7766.58 kT\n VPMG::extEnergy: extDiEnergy = 3755.14 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.519322\n+Vacc_SASA: Time elapsed: 0.529531\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.499660e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.707010e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.137000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.116000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.453550e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.059190e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.013586e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.113834e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.221522e-01\n Vprtstp: contraction number = 1.221522e-01\n Vprtstp: iteration = 2\n@@ -862,32 +862,32 @@\n Vprtstp: contraction number = 4.471936e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.248629e-06\n Vprtstp: contraction number = 4.746468e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 6.237535e-07\n Vprtstp: contraction number = 4.995506e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.604067e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.833529e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.455798e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.575515e+00\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.428963535142E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.400000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.010000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -908,32 +908,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.517184\n+Vacc_SASA: Time elapsed: 0.505635\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.434794e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.675164e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.214000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.620000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.375580e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.167210e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.538357e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.644524e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.215755e-02\n Vprtstp: contraction number = 2.215755e-02\n Vprtstp: iteration = 2\n@@ -947,30 +947,30 @@\n Vprtstp: contraction number = 9.587608e-02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.603412e-06\n Vprtstp: contraction number = 9.909475e-02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.626039e-07\n Vprtstp: contraction number = 1.014112e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.735229e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.938587e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.528792e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.702475e+00\n Vpmg_setPart:  lower corner = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  upper corner = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  actual minima = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  actual maxima = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.121921918409E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.950000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.790000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -1018,30 +1018,30 @@\n VPMG::extEnergy: extQfEnergy = 10309.9 kT\n VPMG::extEnergy: extDiEnergy = 4985.22 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.538033\n+Vacc_SASA: Time elapsed: 0.516585\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.725300e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.419460e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.108000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.014000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.557710e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.160100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.802557e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.872352e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.329182e-01\n Vprtstp: contraction number = 1.329182e-01\n Vprtstp: iteration = 2\n@@ -1058,32 +1058,32 @@\n Vprtstp: contraction number = 1.009933e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.280625e-06\n Vprtstp: contraction number = 1.024328e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.326631e-07\n Vprtstp: contraction number = 1.035924e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.021944e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.252634e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.852958e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.965769e+00\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.696401888033E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.500000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.130000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.80966\n Vpbe_ctor2:  solute dimensions = 5.374 x 6.581 x 6.611\n Vpbe_ctor2:  solute charge = 2.77556e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.0328757\n@@ -1104,32 +1104,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.005038\n+Vacc_SASA: Time elapsed: 0.009663\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.207400e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.850500e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.141000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.081000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.164240e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.426500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.027895e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.079328e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.503042e-01\n Vprtstp: contraction number = 1.503042e-01\n Vprtstp: iteration = 2\n@@ -1146,32 +1146,32 @@\n Vprtstp: contraction number = 1.186135e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 3.304907e-06\n Vprtstp: contraction number = 1.191339e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.951730e-07\n Vprtstp: contraction number = 1.195716e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.946381e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.118835e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.237601e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.384759e+00\n Vpmg_setPart:  lower corner = (-30.249, -30.2305, -27.5085)\n Vpmg_setPart:  upper corner = (65.751, 65.7695, 68.4915)\n Vpmg_setPart:  actual minima = (-30.249, -30.2305, -27.5085)\n Vpmg_setPart:  actual maxima = (65.751, 65.7695, 68.4915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.176059394103E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.800000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.000000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.80966\n Vpbe_ctor2:  solute dimensions = 5.374 x 6.581 x 6.611\n Vpbe_ctor2:  solute charge = 2.77556e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.0328757\n@@ -1217,30 +1217,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00535489 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.007456\n+Vacc_SASA: Time elapsed: 0.011064\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.790000e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.786500e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.987000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.734000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.150710e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.450650e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.243195e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.330533e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.268584e-01\n Vprtstp: contraction number = 2.268584e-01\n Vprtstp: iteration = 2\n@@ -1269,32 +1269,32 @@\n Vprtstp: contraction number = 3.027355e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.523815e-06\n Vprtstp: contraction number = 3.032958e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 7.666858e-07\n Vprtstp: contraction number = 3.037805e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.974043e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.148024e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.287888e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.521285e+00\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.709734790786E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.800000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.200000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.80966\n Vpbe_ctor2:  solute dimensions = 5.374 x 6.581 x 6.611\n Vpbe_ctor2:  solute charge = 2.77556e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -1315,32 +1315,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.006083\n+Vacc_SASA: Time elapsed: 0.002802\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.073200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.759100e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.591000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.455600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.251050e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.829500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.565030e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.682088e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.197218e-01\n Vprtstp: contraction number = 1.197218e-01\n Vprtstp: iteration = 2\n@@ -1357,32 +1357,32 @@\n Vprtstp: contraction number = 1.080232e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.668171e-06\n Vprtstp: contraction number = 1.086670e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.821545e-07\n Vprtstp: contraction number = 1.091941e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.939171e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.137222e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.299659e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.481936e+00\n Vpmg_setPart:  lower corner = (-30.249, -30.2305, -27.5085)\n Vpmg_setPart:  upper corner = (65.751, 65.7695, 68.4915)\n Vpmg_setPart:  actual minima = (-30.249, -30.2305, -27.5085)\n Vpmg_setPart:  actual maxima = (65.751, 65.7695, 68.4915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.413483938867E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.500000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.80966\n Vpbe_ctor2:  solute dimensions = 5.374 x 6.581 x 6.611\n Vpbe_ctor2:  solute charge = 2.77556e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -1428,30 +1428,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0422608 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.006214\n+Vacc_SASA: Time elapsed: 0.010488\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.115600e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.066600e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.338900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.487000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.443040e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.413200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.785948e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.929449e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.511608e-01\n Vprtstp: contraction number = 1.511608e-01\n Vprtstp: iteration = 2\n@@ -1468,30 +1468,30 @@\n Vprtstp: contraction number = 1.062405e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.836009e-06\n Vprtstp: contraction number = 1.072929e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.984242e-07\n Vprtstp: contraction number = 1.080737e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.019460e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.246520e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.239973e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.364314e+00\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.884571864356E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.300000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -1514,32 +1514,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.520106\n+Vacc_SASA: Time elapsed: 0.562797\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.461280e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.717533e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.351000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.387000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.158600e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.591700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.152310e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.336624e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.148454e-02\n Vprtstp: contraction number = 6.148454e-02\n Vprtstp: iteration = 2\n@@ -1613,32 +1613,32 @@\n Vprtstp: contraction number = 7.027151e-01\n Vprtstp: iteration = 25\n Vprtstp: relative residual = 1.401142e-06\n Vprtstp: contraction number = 7.044026e-01\n Vprtstp: iteration = 26\n Vprtstp: relative residual = 9.889238e-07\n Vprtstp: contraction number = 7.057985e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.046805e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.224692e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.626933e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.739074e+00\n Vpmg_setPart:  lower corner = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  upper corner = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  actual minima = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  actual maxima = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.486452023042E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.500000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.840000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.0328757\n@@ -1684,30 +1684,30 @@\n VPMG::extEnergy: extQfEnergy = 7766.05 kT\n VPMG::extEnergy: extDiEnergy = 3755.1 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.494903\n+Vacc_SASA: Time elapsed: 0.502371\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.078940e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.313150e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.315000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.385000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.300040e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.537200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.938260e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.177450e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.211906e-01\n Vprtstp: contraction number = 1.211906e-01\n Vprtstp: iteration = 2\n@@ -1739,30 +1739,30 @@\n Vprtstp: contraction number = 4.581101e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.399352e-06\n Vprtstp: contraction number = 4.836226e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.075712e-07\n Vprtstp: contraction number = 5.056422e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.345576e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.547865e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.015951e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.167770e+00\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.371923967456E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.080000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.220000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -1785,32 +1785,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.506032\n+Vacc_SASA: Time elapsed: 0.505157\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.427679e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.660671e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.018000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.860000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.914100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.928500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.431497e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.760736e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.219671e-02\n Vprtstp: contraction number = 2.219671e-02\n Vprtstp: iteration = 2\n@@ -1824,32 +1824,32 @@\n Vprtstp: contraction number = 9.588702e-02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.611478e-06\n Vprtstp: contraction number = 9.903019e-02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.632204e-07\n Vprtstp: contraction number = 1.012861e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.500247e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.654887e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.843331e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.991657e+00\n Vpmg_setPart:  lower corner = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  upper corner = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  actual minima = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  actual maxima = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.119297547416E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.010000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.860000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -1895,30 +1895,30 @@\n VPMG::extEnergy: extQfEnergy = 10305.9 kT\n VPMG::extEnergy: extDiEnergy = 4984.29 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.492708\n+Vacc_SASA: Time elapsed: 0.504880\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.770090e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.237100e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.143000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.377000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.286050e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.380520e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.659839e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.030434e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.325279e-01\n Vprtstp: contraction number = 1.325279e-01\n Vprtstp: iteration = 2\n@@ -1935,44 +1935,44 @@\n Vprtstp: contraction number = 1.009444e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.272261e-06\n Vprtstp: contraction number = 1.024006e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.317723e-07\n Vprtstp: contraction number = 1.035733e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.946457e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.146752e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.984155e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.210391e+00\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.638817315582E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.110000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.120000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 4.857619e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.231772e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:33:26 2025\n+# Creation Date and Time:  Sun Jan  7 09:44:28 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path 1d7h-dmso-complex.pqr\n@@ -2605,32 +2605,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.565802\n+Vacc_SASA: Time elapsed: 0.535463\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.513613e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.718232e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.284000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.146000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.094520e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.220200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.742122e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.908704e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.251961e-02\n Vprtstp: contraction number = 3.251961e-02\n Vprtstp: iteration = 2\n@@ -2647,32 +2647,32 @@\n Vprtstp: contraction number = 1.569967e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.728368e-06\n Vprtstp: contraction number = 1.692265e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.127259e-07\n Vprtstp: contraction number = 1.809371e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.737732e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.911911e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.724087e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.858622e+00\n Vpmg_setPart:  lower corner = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  upper corner = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  actual minima = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  actual maxima = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.619056487019E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.170000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.650000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.0328757\n@@ -2718,30 +2718,30 @@\n VPMG::extEnergy: extQfEnergy = 7853.47 kT\n VPMG::extEnergy: extDiEnergy = 3800.32 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.506685\n+Vacc_SASA: Time elapsed: 0.512930\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.333160e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.631230e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.976000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.047000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.328560e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.958200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.332925e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.427450e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.054672e-01\n Vprtstp: contraction number = 1.054672e-01\n Vprtstp: iteration = 2\n@@ -2758,32 +2758,32 @@\n Vprtstp: contraction number = 1.551340e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 4.573968e-06\n Vprtstp: contraction number = 1.730130e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.440650e-07\n Vprtstp: contraction number = 1.845367e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.917035e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.130735e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.045921e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.175088e+00\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.439357878013E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.340000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.390000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -2804,32 +2804,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.507124\n+Vacc_SASA: Time elapsed: 0.509884\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.467065e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.715576e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.534000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.275000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.132270e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.144100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.901313e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.332134e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.215755e-02\n Vprtstp: contraction number = 2.215755e-02\n Vprtstp: iteration = 2\n@@ -2843,30 +2843,30 @@\n Vprtstp: contraction number = 9.587608e-02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.603412e-06\n Vprtstp: contraction number = 9.909475e-02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.626039e-07\n Vprtstp: contraction number = 1.014112e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.594430e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.774357e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.537512e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.677496e+00\n Vpmg_setPart:  lower corner = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  upper corner = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  actual minima = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  actual maxima = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.121921918409E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.240000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.060000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -2914,30 +2914,30 @@\n VPMG::extEnergy: extQfEnergy = 10309.9 kT\n VPMG::extEnergy: extDiEnergy = 4985.22 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.551746\n+Vacc_SASA: Time elapsed: 0.512209\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.733600e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.262560e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.076000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.777000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.285500e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.310080e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.035952e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.072288e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.329182e-01\n Vprtstp: contraction number = 1.329182e-01\n Vprtstp: iteration = 2\n@@ -2954,30 +2954,30 @@\n Vprtstp: contraction number = 1.009933e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.280625e-06\n Vprtstp: contraction number = 1.024328e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.326631e-07\n Vprtstp: contraction number = 1.035924e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.941439e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.129592e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.951454e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.167544e+00\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.696401888033E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.220000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.320000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.80966\n Vpbe_ctor2:  solute dimensions = 5.374 x 6.581 x 6.611\n Vpbe_ctor2:  solute charge = 2.77556e-17\n@@ -3000,32 +3000,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.005686\n+Vacc_SASA: Time elapsed: 0.009218\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.224400e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.503900e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.700000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.971000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.314840e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.425540e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.258338e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.295410e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.464441e-01\n Vprtstp: contraction number = 1.464441e-01\n Vprtstp: iteration = 2\n@@ -3042,30 +3042,30 @@\n Vprtstp: contraction number = 1.083801e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.974607e-06\n Vprtstp: contraction number = 1.096829e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.183173e-07\n Vprtstp: contraction number = 1.105624e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.929371e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.126082e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.111448e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.314064e+00\n Vpmg_setPart:  lower corner = (-30.249, -30.2305, -27.5085)\n Vpmg_setPart:  upper corner = (65.751, 65.7695, 68.4915)\n Vpmg_setPart:  actual minima = (-30.249, -30.2305, -27.5085)\n Vpmg_setPart:  actual maxima = (65.751, 65.7695, 68.4915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.982504155807E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.900000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.900000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.80966\n Vpbe_ctor2:  solute dimensions = 5.374 x 6.581 x 6.611\n Vpbe_ctor2:  solute charge = 2.77556e-17\n@@ -3113,30 +3113,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0085798 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.007589\n+Vacc_SASA: Time elapsed: 0.010986\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.204200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.506200e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.727000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.563000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.384260e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.412330e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.479782e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.536820e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.791557e-01\n Vprtstp: contraction number = 1.791557e-01\n Vprtstp: iteration = 2\n@@ -3156,32 +3156,32 @@\n Vprtstp: contraction number = 1.764760e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.223991e-06\n Vprtstp: contraction number = 1.794914e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.841505e-07\n Vprtstp: contraction number = 1.811887e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.153121e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.361180e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.241106e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.465264e+00\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.713502079454E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.400000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.700000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.80966\n Vpbe_ctor2:  solute dimensions = 5.374 x 6.581 x 6.611\n Vpbe_ctor2:  solute charge = 2.77556e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -3202,32 +3202,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.005023\n+Vacc_SASA: Time elapsed: 0.012327\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.579200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.352300e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.386000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.322000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.204790e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.219780e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.721857e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.783267e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.197218e-01\n Vprtstp: contraction number = 1.197218e-01\n Vprtstp: iteration = 2\n@@ -3244,30 +3244,30 @@\n Vprtstp: contraction number = 1.080232e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.668171e-06\n Vprtstp: contraction number = 1.086670e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.821545e-07\n Vprtstp: contraction number = 1.091941e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.865794e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.063993e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.140683e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.276951e+00\n Vpmg_setPart:  lower corner = (-30.249, -30.2305, -27.5085)\n Vpmg_setPart:  upper corner = (65.751, 65.7695, 68.4915)\n Vpmg_setPart:  actual minima = (-30.249, -30.2305, -27.5085)\n Vpmg_setPart:  actual maxima = (65.751, 65.7695, 68.4915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.413483938867E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.700000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.800000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.80966\n Vpbe_ctor2:  solute dimensions = 5.374 x 6.581 x 6.611\n Vpbe_ctor2:  solute charge = 2.77556e-17\n@@ -3315,30 +3315,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0422608 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.007843\n+Vacc_SASA: Time elapsed: 0.010938\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.674700e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.034500e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.327000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.817000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.304760e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.647600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.936149e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.018942e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.511608e-01\n Vprtstp: contraction number = 1.511608e-01\n Vprtstp: iteration = 2\n@@ -3355,30 +3355,30 @@\n Vprtstp: contraction number = 1.062405e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.836009e-06\n Vprtstp: contraction number = 1.072929e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.984242e-07\n Vprtstp: contraction number = 1.080737e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.805479e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.011541e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.286672e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.429118e+00\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.884571864356E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.700000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -3401,32 +3401,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.506127\n+Vacc_SASA: Time elapsed: 0.515476\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.431320e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.708961e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.121000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.928000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.083390e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.007790e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.276666e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.433997e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.257199e-02\n Vprtstp: contraction number = 3.257199e-02\n Vprtstp: iteration = 2\n@@ -3443,30 +3443,30 @@\n Vprtstp: contraction number = 1.541269e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.608808e-06\n Vprtstp: contraction number = 1.652212e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.820839e-07\n Vprtstp: contraction number = 1.753372e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.805706e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.971636e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.435388e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.586940e+00\n Vpmg_setPart:  lower corner = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  upper corner = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  actual minima = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  actual maxima = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.592645225811E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.530000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.730000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -3514,30 +3514,30 @@\n VPMG::extEnergy: extQfEnergy = 7853.32 kT\n VPMG::extEnergy: extDiEnergy = 3800.2 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.494968\n+Vacc_SASA: Time elapsed: 0.503461\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.295890e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.586120e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.025000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.911000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.261440e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.195600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.541430e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.755794e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051303e-01\n Vprtstp: contraction number = 1.051303e-01\n Vprtstp: iteration = 2\n@@ -3554,32 +3554,32 @@\n Vprtstp: contraction number = 1.566068e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 4.652962e-06\n Vprtstp: contraction number = 1.751224e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.683754e-07\n Vprtstp: contraction number = 1.866285e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.876977e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.084946e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.456048e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.576391e+00\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.382181498242E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.800000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.440000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -3600,32 +3600,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.502378\n+Vacc_SASA: Time elapsed: 0.512243\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.436410e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.697507e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.349000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.328000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.174880e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.224700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.890327e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.080973e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.219671e-02\n Vprtstp: contraction number = 2.219671e-02\n Vprtstp: iteration = 2\n@@ -3639,32 +3639,32 @@\n Vprtstp: contraction number = 9.588702e-02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.611478e-06\n Vprtstp: contraction number = 9.903019e-02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.632204e-07\n Vprtstp: contraction number = 1.012861e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.670227e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.842531e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.082117e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.204981e+00\n Vpmg_setPart:  lower corner = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  upper corner = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  actual minima = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  actual maxima = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.119297547416E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.460000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.400000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -3710,30 +3710,30 @@\n VPMG::extEnergy: extQfEnergy = 10305.9 kT\n VPMG::extEnergy: extDiEnergy = 4984.29 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.494610\n+Vacc_SASA: Time elapsed: 0.503519\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.174940e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.322720e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.224000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.084000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.289420e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.313270e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.139404e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.275061e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.325279e-01\n Vprtstp: contraction number = 1.325279e-01\n Vprtstp: iteration = 2\n@@ -3750,44 +3750,44 @@\n Vprtstp: contraction number = 1.009444e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.272261e-06\n Vprtstp: contraction number = 1.024006e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.317723e-07\n Vprtstp: contraction number = 1.035733e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.024861e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.223648e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.438361e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.651535e+00\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.638817315582E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.240000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.280000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.345060e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.423400e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:33:38 2025\n+# Creation Date and Time:  Sun Jan  7 09:44:38 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path 1d7i-dss-complex.pqr\n@@ -4420,32 +4420,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.519790\n+Vacc_SASA: Time elapsed: 0.532015\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.420932e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.696491e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.747000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.995000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.301460e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.365200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.673707e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.898063e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.573903e-02\n Vprtstp: contraction number = 6.573903e-02\n Vprtstp: iteration = 2\n@@ -4516,30 +4516,30 @@\n Vprtstp: contraction number = 6.827181e-01\n Vprtstp: iteration = 24\n Vprtstp: relative residual = 1.259903e-06\n Vprtstp: contraction number = 6.840214e-01\n Vprtstp: iteration = 25\n Vprtstp: relative residual = 8.633870e-07\n Vprtstp: contraction number = 6.852808e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.967510e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.171509e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.164443e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.309130e+00\n Vpmg_setPart:  lower corner = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  upper corner = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  actual minima = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  actual maxima = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.345051831139E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.640000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.970000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -4587,30 +4587,30 @@\n VPMG::extEnergy: extQfEnergy = 6529.57 kT\n VPMG::extEnergy: extDiEnergy = 2987.06 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.508069\n+Vacc_SASA: Time elapsed: 0.510474\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.303620e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.425040e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.528000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.035000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.343040e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.219800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.477785e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.811572e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.216933e-01\n Vprtstp: contraction number = 1.216933e-01\n Vprtstp: iteration = 2\n@@ -4639,30 +4639,30 @@\n Vprtstp: contraction number = 3.953520e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.724728e-06\n Vprtstp: contraction number = 4.218661e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 7.702114e-07\n Vprtstp: contraction number = 4.465699e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.201890e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.405100e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.519874e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.623327e+00\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.171725099545E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.400000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.110000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -4685,32 +4685,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.506006\n+Vacc_SASA: Time elapsed: 0.503442\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.437679e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.666685e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.123800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.484000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.386040e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.339700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.433719e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.309869e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.208737e-02\n Vprtstp: contraction number = 2.208737e-02\n Vprtstp: iteration = 2\n@@ -4724,32 +4724,32 @@\n Vprtstp: contraction number = 9.525881e-02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.554352e-06\n Vprtstp: contraction number = 9.854831e-02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.569345e-07\n Vprtstp: contraction number = 1.009646e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.709924e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.924689e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.474729e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.572262e+00\n Vpmg_setPart:  lower corner = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  upper corner = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  actual minima = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  actual maxima = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.014263549371E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.000000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.230000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -4795,30 +4795,30 @@\n VPMG::extEnergy: extQfEnergy = 9211.28 kT\n VPMG::extEnergy: extDiEnergy = 4239.53 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.514274\n+Vacc_SASA: Time elapsed: 0.503263\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.330750e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.065710e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.121000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.949000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.303430e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.326290e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.688523e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.538584e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.291558e-01\n Vprtstp: contraction number = 1.291558e-01\n Vprtstp: iteration = 2\n@@ -4835,32 +4835,32 @@\n Vprtstp: contraction number = 1.003267e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.195888e-06\n Vprtstp: contraction number = 1.018284e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.232544e-07\n Vprtstp: contraction number = 1.030651e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.866577e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.065496e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.979381e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.195129e+00\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.449231705544E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.010000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.230000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 5.02661\n Vpbe_ctor2:  solute dimensions = 5.303 x 9.299 x 6.49\n Vpbe_ctor2:  solute charge = -8.32667e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.0328757\n@@ -4881,32 +4881,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.006984\n+Vacc_SASA: Time elapsed: 0.011177\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.430800e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.963600e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.783000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.671000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.322400e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.478830e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.900667e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.764743e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.937868e-02\n Vprtstp: contraction number = 9.937868e-02\n Vprtstp: iteration = 2\n@@ -4923,32 +4923,32 @@\n Vprtstp: contraction number = 1.252714e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.602930e-06\n Vprtstp: contraction number = 1.287705e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.415857e-07\n Vprtstp: contraction number = 1.312312e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.928669e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.126422e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.089707e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.287993e+00\n Vpmg_setPart:  lower corner = (-30.6595, -28.789, -27.497)\n Vpmg_setPart:  upper corner = (65.3405, 67.211, 68.503)\n Vpmg_setPart:  actual minima = (-30.6595, -28.789, -27.497)\n Vpmg_setPart:  actual maxima = (65.3405, 67.211, 68.503)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.561986028141E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.800000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.300000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 5.02661\n Vpbe_ctor2:  solute dimensions = 5.303 x 9.299 x 6.49\n Vpbe_ctor2:  solute charge = -8.32667e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.0328757\n@@ -4994,30 +4994,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00497505 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.006760\n+Vacc_SASA: Time elapsed: 0.013364\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.900500e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.931100e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.631000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.481000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.403480e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.138080e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.117419e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.990403e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.636290e-01\n Vprtstp: contraction number = 2.636290e-01\n Vprtstp: iteration = 2\n@@ -5049,32 +5049,32 @@\n Vprtstp: contraction number = 3.506954e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.726432e-06\n Vprtstp: contraction number = 3.673674e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 6.664171e-07\n Vprtstp: contraction number = 3.860084e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.373166e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.576108e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.110464e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.235263e+00\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.344916094234E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.200000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 5.02661\n Vpbe_ctor2:  solute dimensions = 5.303 x 9.299 x 6.49\n Vpbe_ctor2:  solute charge = -8.32667e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -5095,32 +5095,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.008443\n+Vacc_SASA: Time elapsed: 0.011261\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.190900e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.629400e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.872000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.306900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.415240e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.537200e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.483410e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.328159e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.352196e-02\n Vprtstp: contraction number = 6.352196e-02\n Vprtstp: iteration = 2\n@@ -5134,30 +5134,30 @@\n Vprtstp: contraction number = 1.012293e-01\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.271886e-06\n Vprtstp: contraction number = 1.033361e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 6.595226e-07\n Vprtstp: contraction number = 1.051554e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.753412e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.981942e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.896448e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.093674e+00\n Vpmg_setPart:  lower corner = (-30.6595, -28.789, -27.497)\n Vpmg_setPart:  upper corner = (65.3405, 67.211, 68.503)\n Vpmg_setPart:  actual minima = (-30.6595, -28.789, -27.497)\n Vpmg_setPart:  actual maxima = (65.3405, 67.211, 68.503)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 9.389840581990E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.600000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.100000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 5.02661\n Vpbe_ctor2:  solute dimensions = 5.303 x 9.299 x 6.49\n Vpbe_ctor2:  solute charge = -8.32667e-17\n@@ -5205,30 +5205,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0518244 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.006679\n+Vacc_SASA: Time elapsed: 0.010535\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.398700e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.667400e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.290000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.080800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.251280e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.608800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.681280e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.536949e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.573900e-01\n Vprtstp: contraction number = 1.573900e-01\n Vprtstp: iteration = 2\n@@ -5245,30 +5245,30 @@\n Vprtstp: contraction number = 1.046499e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.765958e-06\n Vprtstp: contraction number = 1.060018e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.889858e-07\n Vprtstp: contraction number = 1.070160e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.901197e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.088432e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.059957e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.201804e+00\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.361370594878E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.200000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.400000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -5291,32 +5291,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.549147\n+Vacc_SASA: Time elapsed: 0.554270\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.457596e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.698550e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.445000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.337000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.144360e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.025310e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.034742e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.931787e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.573435e-02\n Vprtstp: contraction number = 6.573435e-02\n Vprtstp: iteration = 2\n@@ -5387,30 +5387,30 @@\n Vprtstp: contraction number = 6.841463e-01\n Vprtstp: iteration = 24\n Vprtstp: relative residual = 1.230794e-06\n Vprtstp: contraction number = 6.854643e-01\n Vprtstp: iteration = 25\n Vprtstp: relative residual = 8.453252e-07\n Vprtstp: contraction number = 6.868128e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.225612e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.397492e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.397084e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.583278e+00\n Vpmg_setPart:  lower corner = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  upper corner = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  actual minima = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  actual maxima = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.248457904492E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.030000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.770000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -5458,30 +5458,30 @@\n VPMG::extEnergy: extQfEnergy = 6529.31 kT\n VPMG::extEnergy: extDiEnergy = 2986.91 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.515719\n+Vacc_SASA: Time elapsed: 0.509747\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.614710e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.326340e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.362000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.141000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.496700e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.558700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.846694e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.648007e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.206113e-01\n Vprtstp: contraction number = 1.206113e-01\n Vprtstp: iteration = 2\n@@ -5510,32 +5510,32 @@\n Vprtstp: contraction number = 3.809962e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.385263e-06\n Vprtstp: contraction number = 4.084139e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.028523e-07\n Vprtstp: contraction number = 4.351898e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.295190e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.524744e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.001310e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.130472e+00\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.037057682028E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.030000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.300000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -5556,32 +5556,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.508392\n+Vacc_SASA: Time elapsed: 0.494061\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.416921e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.652170e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.409000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.127000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.370350e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.272270e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.338375e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.133015e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.233304e-02\n Vprtstp: contraction number = 2.233304e-02\n Vprtstp: iteration = 2\n@@ -5595,32 +5595,32 @@\n Vprtstp: contraction number = 9.522390e-02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.574058e-06\n Vprtstp: contraction number = 9.845638e-02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.587415e-07\n Vprtstp: contraction number = 1.008486e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.877922e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.076149e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.816099e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.011051e+00\n Vpmg_setPart:  lower corner = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  upper corner = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  actual minima = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  actual maxima = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.004264667397E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.880000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.120000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -5666,30 +5666,30 @@\n VPMG::extEnergy: extQfEnergy = 9208.92 kT\n VPMG::extEnergy: extDiEnergy = 4238.63 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.511205\n+Vacc_SASA: Time elapsed: 0.496474\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.270400e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.863130e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.579000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.243000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.499550e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.374450e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.611154e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.396479e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.281343e-01\n Vprtstp: contraction number = 1.281343e-01\n Vprtstp: iteration = 2\n@@ -5706,44 +5706,44 @@\n Vprtstp: contraction number = 1.003059e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.185212e-06\n Vprtstp: contraction number = 1.017952e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.220913e-07\n Vprtstp: contraction number = 1.030122e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.181989e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.400769e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.867381e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.091727e+00\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.314075450214E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.190000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.180000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 4.834022e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 4.586969e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:33:55 2025\n+# Creation Date and Time:  Sun Jan  7 09:44:51 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path 1d7i-dss-complex.pqr\n@@ -6376,32 +6376,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.579198\n+Vacc_SASA: Time elapsed: 0.564421\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.547630e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.753485e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.881000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.791000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.306600e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.391600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.791164e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.894076e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.298567e-02\n Vprtstp: contraction number = 3.298567e-02\n Vprtstp: iteration = 2\n@@ -6418,30 +6418,30 @@\n Vprtstp: contraction number = 1.536726e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.666279e-06\n Vprtstp: contraction number = 1.683668e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.055929e-07\n Vprtstp: contraction number = 1.833984e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.102734e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.297245e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.081373e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.165897e+00\n Vpmg_setPart:  lower corner = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  upper corner = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  actual minima = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  actual maxima = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.725356066403E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.970000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.290000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -6489,30 +6489,30 @@\n VPMG::extEnergy: extQfEnergy = 6899.51 kT\n VPMG::extEnergy: extDiEnergy = 3158.85 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.563728\n+Vacc_SASA: Time elapsed: 0.509846\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.505060e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.654380e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.428000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.131000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.496740e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.268800e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.876465e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.849034e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.032281e-01\n Vprtstp: contraction number = 1.032281e-01\n Vprtstp: iteration = 2\n@@ -6529,32 +6529,32 @@\n Vprtstp: contraction number = 1.485117e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 3.842446e-06\n Vprtstp: contraction number = 1.674805e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 6.939533e-07\n Vprtstp: contraction number = 1.806019e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.061033e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.287753e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.115649e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.319099e+00\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.209791610861E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.200000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.410000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -6575,32 +6575,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.517835\n+Vacc_SASA: Time elapsed: 0.507500\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.450932e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.720223e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.258000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.298000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.164330e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.184580e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.576247e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.869765e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.208737e-02\n Vprtstp: contraction number = 2.208737e-02\n Vprtstp: iteration = 2\n@@ -6614,32 +6614,32 @@\n Vprtstp: contraction number = 9.525881e-02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.554352e-06\n Vprtstp: contraction number = 9.854831e-02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.569345e-07\n Vprtstp: contraction number = 1.009646e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.705949e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.887220e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.844780e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.026956e+00\n Vpmg_setPart:  lower corner = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  upper corner = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  actual minima = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  actual maxima = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.014263549371E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.250000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.890000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -6685,30 +6685,30 @@\n VPMG::extEnergy: extQfEnergy = 9211.28 kT\n VPMG::extEnergy: extDiEnergy = 4239.53 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.519185\n+Vacc_SASA: Time elapsed: 0.508165\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.671810e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.507060e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.325000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.167000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.414100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.390300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.108445e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.147484e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.291558e-01\n Vprtstp: contraction number = 1.291558e-01\n Vprtstp: iteration = 2\n@@ -6725,32 +6725,32 @@\n Vprtstp: contraction number = 1.003267e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.195888e-06\n Vprtstp: contraction number = 1.018284e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.232544e-07\n Vprtstp: contraction number = 1.030651e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.287085e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.418932e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.137115e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.242925e+00\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.449231705544E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.090000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 5.02661\n Vpbe_ctor2:  solute dimensions = 5.303 x 9.299 x 6.49\n Vpbe_ctor2:  solute charge = -8.32667e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.0328757\n@@ -6771,32 +6771,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.002585\n+Vacc_SASA: Time elapsed: 0.008993\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.942800e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.313400e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.443000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.097000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.181200e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.186800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.258056e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.277974e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.464737e-02\n Vprtstp: contraction number = 8.464737e-02\n Vprtstp: iteration = 2\n@@ -6813,30 +6813,30 @@\n Vprtstp: contraction number = 1.071698e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.052787e-06\n Vprtstp: contraction number = 1.084632e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.152581e-07\n Vprtstp: contraction number = 1.094790e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.284021e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.410999e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 8.761620e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.520340e-01\n Vpmg_setPart:  lower corner = (-30.6595, -28.789, -27.497)\n Vpmg_setPart:  upper corner = (65.3405, 67.211, 68.503)\n Vpmg_setPart:  actual minima = (-30.6595, -28.789, -27.497)\n Vpmg_setPart:  actual maxima = (65.3405, 67.211, 68.503)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 6.368169150406E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.800000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.000000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 5.02661\n Vpbe_ctor2:  solute dimensions = 5.303 x 9.299 x 6.49\n Vpbe_ctor2:  solute charge = -8.32667e-17\n@@ -6884,30 +6884,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00594757 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001436\n+Vacc_SASA: Time elapsed: 0.011194\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.385400e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.708900e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.834000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.166000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.132900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.778000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.404736e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.378596e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.027171e-01\n Vprtstp: contraction number = 2.027171e-01\n Vprtstp: iteration = 2\n@@ -6927,32 +6927,32 @@\n Vprtstp: contraction number = 1.717621e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.164324e-06\n Vprtstp: contraction number = 1.754898e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.631488e-07\n Vprtstp: contraction number = 1.779681e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.450459e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.578048e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.187776e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.262397e+00\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.345277247759E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.900000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.800000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 5.02661\n Vpbe_ctor2:  solute dimensions = 5.303 x 9.299 x 6.49\n Vpbe_ctor2:  solute charge = -8.32667e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -6973,32 +6973,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001418\n+Vacc_SASA: Time elapsed: 0.011402\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.752300e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.268400e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.149000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.797000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.855900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.877300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.570531e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.514915e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.352196e-02\n Vprtstp: contraction number = 6.352196e-02\n Vprtstp: iteration = 2\n@@ -7012,32 +7012,32 @@\n Vprtstp: contraction number = 1.012293e-01\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.271886e-06\n Vprtstp: contraction number = 1.033361e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 6.595226e-07\n Vprtstp: contraction number = 1.051554e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.107415e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.246201e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 9.352800e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.024990e+00\n Vpmg_setPart:  lower corner = (-30.6595, -28.789, -27.497)\n Vpmg_setPart:  upper corner = (65.3405, 67.211, 68.503)\n Vpmg_setPart:  actual minima = (-30.6595, -28.789, -27.497)\n Vpmg_setPart:  actual maxima = (65.3405, 67.211, 68.503)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 9.389840581990E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.400000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 5.02661\n Vpbe_ctor2:  solute dimensions = 5.303 x 9.299 x 6.49\n Vpbe_ctor2:  solute charge = -8.32667e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -7083,30 +7083,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0518244 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001479\n+Vacc_SASA: Time elapsed: 0.010600\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.676700e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.699000e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.423000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.269000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.252600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.949500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.701301e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.622812e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.573900e-01\n Vprtstp: contraction number = 1.573900e-01\n Vprtstp: iteration = 2\n@@ -7123,32 +7123,32 @@\n Vprtstp: contraction number = 1.046499e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.765958e-06\n Vprtstp: contraction number = 1.060018e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.889858e-07\n Vprtstp: contraction number = 1.070160e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.306339e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.438724e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.646240e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.337470e-01\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.361370594878E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.200000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.500000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.0328757\n@@ -7169,32 +7169,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.511459\n+Vacc_SASA: Time elapsed: 0.504118\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.136927e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.720054e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.996000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.955000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.182000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.495100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.959191e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.872277e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.328224e-02\n Vprtstp: contraction number = 3.328224e-02\n Vprtstp: iteration = 2\n@@ -7211,32 +7211,32 @@\n Vprtstp: contraction number = 1.553323e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.764269e-06\n Vprtstp: contraction number = 1.696908e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.244306e-07\n Vprtstp: contraction number = 1.838895e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.157743e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.292169e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.684800e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.522470e-01\n Vpmg_setPart:  lower corner = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  upper corner = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  actual minima = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  actual maxima = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.622871644072E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.180000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.000000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.0328757\n@@ -7282,30 +7282,30 @@\n VPMG::extEnergy: extQfEnergy = 6899.11 kT\n VPMG::extEnergy: extDiEnergy = 3158.68 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.485021\n+Vacc_SASA: Time elapsed: 0.495172\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.979230e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.140140e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.238000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.827000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.916100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.983500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.146427e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.009994e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.025309e-01\n Vprtstp: contraction number = 1.025309e-01\n Vprtstp: iteration = 2\n@@ -7322,32 +7322,32 @@\n Vprtstp: contraction number = 1.507031e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 3.981847e-06\n Vprtstp: contraction number = 1.699776e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.281025e-07\n Vprtstp: contraction number = 1.828555e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.153304e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.268739e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.832920e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.518910e-01\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.075005771448E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.030000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -7368,32 +7368,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.487848\n+Vacc_SASA: Time elapsed: 0.492506\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.101754e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.716793e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.234000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.713000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.894000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.565500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.383208e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.259231e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.233304e-02\n Vprtstp: contraction number = 2.233304e-02\n Vprtstp: iteration = 2\n@@ -7407,30 +7407,30 @@\n Vprtstp: contraction number = 9.522390e-02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.574058e-06\n Vprtstp: contraction number = 9.845638e-02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.587415e-07\n Vprtstp: contraction number = 1.008486e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 9.818920e-01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.093403e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.906130e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.737410e-01\n Vpmg_setPart:  lower corner = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  upper corner = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  actual minima = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  actual maxima = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.004264667397E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.090000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -7478,30 +7478,30 @@\n VPMG::extEnergy: extQfEnergy = 9208.92 kT\n VPMG::extEnergy: extDiEnergy = 4238.63 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.485033\n+Vacc_SASA: Time elapsed: 0.494647\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.936440e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.075570e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.197000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.810000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.400000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.118400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.552887e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.388684e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.281343e-01\n Vprtstp: contraction number = 1.281343e-01\n Vprtstp: iteration = 2\n@@ -7518,34 +7518,34 @@\n Vprtstp: contraction number = 1.003059e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.185212e-06\n Vprtstp: contraction number = 1.017952e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.220913e-07\n Vprtstp: contraction number = 1.030122e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.178650e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.298677e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.970420e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.668850e-01\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.314075450214E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.200000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.050000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.672567e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.461153e+01\n"}, {"source1": "./usr/share/apbs/examples/actin-dimer/io.mc", "source2": "./usr/share/apbs/examples/actin-dimer/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:18:20 2025\n+# Creation Date and Time:  Sun Jan  7 09:32:58 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -262,217 +262,217 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.366249\n+Vacc_SASA: Time elapsed: 1.417126\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.648321e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.729851e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 9.475200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 8.854900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.036860e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.088520e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.785871e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.802982e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7775242.648804\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.247446e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.249427e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.252805e+05\n Vprtstp: contraction number = 5.252805e+05\n Vnewton: Attempting damping, relres = 0.062556\n Vnewton: Attempting damping, relres = 0.525334\n Vnewton: Damping accepted, relres = 0.062556\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.255619e-02\n Vprtstp: contraction number = 6.255619e-02\n Vnewton: Using errtol_s: 486389.547875\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.466870e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.370952e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.109788e+05\n Vprtstp: contraction number = 1.109788e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.292368e-02\n Vprtstp: contraction number = 2.065932e-01\n Vnewton: Using errtol_s: 100484.762247\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.461049e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.289632e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.281526e+04\n Vprtstp: contraction number = 3.281526e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.798952e-03\n Vprtstp: contraction number = 2.939527e-01\n Vnewton: Using errtol_s: 29537.770540\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.450611e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.243961e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.139405e+04\n Vprtstp: contraction number = 1.139405e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.318894e-03\n Vprtstp: contraction number = 3.471731e-01\n Vnewton: Using errtol_s: 10254.719067\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.137348e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.116739e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.292845e+03\n Vprtstp: contraction number = 4.292845e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.969084e-04\n Vprtstp: contraction number = 3.767615e-01\n Vnewton: Using errtol_s: 3863.583447\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.337270e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.308264e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.746643e+03\n Vprtstp: contraction number = 1.746643e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.021786e-04\n Vprtstp: contraction number = 4.068730e-01\n Vnewton: Using errtol_s: 1571.987642\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.537497e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.503156e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.833563e+02\n Vprtstp: contraction number = 7.833563e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 9.067555e-05\n Vprtstp: contraction number = 4.484923e-01\n Vnewton: Using errtol_s: 705.024393\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.730277e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.694874e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.880760e+02\n Vprtstp: contraction number = 3.880760e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.492075e-05\n Vprtstp: contraction number = 4.954009e-01\n Vnewton: Using errtol_s: 349.269694\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.920894e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.885659e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.071891e+02\n Vprtstp: contraction number = 2.071891e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.398262e-05\n Vprtstp: contraction number = 5.338875e-01\n Vnewton: Using errtol_s: 186.470725\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.113040e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.080138e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.168433e+02\n Vprtstp: contraction number = 1.168433e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.352487e-05\n Vprtstp: contraction number = 5.639446e-01\n Vnewton: Using errtol_s: 105.159166\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.308591e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.273393e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.826136e+01\n Vprtstp: contraction number = 6.826136e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 7.901399e-06\n Vprtstp: contraction number = 5.842124e-01\n Vnewton: Using errtol_s: 61.435293\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.490983e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.468478e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.091749e+01\n Vprtstp: contraction number = 4.091749e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 4.736285e-06\n Vprtstp: contraction number = 5.994236e-01\n Vnewton: Using errtol_s: 36.825768\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.683752e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.664286e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.493482e+01\n Vprtstp: contraction number = 2.493482e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 2.886257e-06\n Vprtstp: contraction number = 6.093926e-01\n Vnewton: Using errtol_s: 22.441349\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.877611e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.860862e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.538748e+01\n Vprtstp: contraction number = 1.538748e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 1.781132e-06\n Vprtstp: contraction number = 6.171079e-01\n Vnewton: Using errtol_s: 13.848733\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.071533e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.053413e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.579209e+00\n Vprtstp: contraction number = 9.579209e+00\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 1.108813e-06\n Vprtstp: contraction number = 6.225327e-01\n Vnewton: Using errtol_s: 8.621289\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.265702e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.246874e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.005674e+00\n Vprtstp: contraction number = 6.005674e+00\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 6.951690e-07\n Vprtstp: contraction number = 6.269489e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.152087e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.255263e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.130893e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.223722e+01\n Vpmg_setPart:  lower corner = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  upper corner = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -481,17 +481,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.412172567798E+00 kT\n Vpmg_energy:  qfEnergy = 1.232438411967E+05 kT\n Vpmg_energy:  dielEnergy = 6.161638379331E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.035600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.011800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.0735516\n@@ -537,193 +537,193 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.294338 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.356984\n+Vacc_SASA: Time elapsed: 1.354125\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.977393e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.971576e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 8.976600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 9.117900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.347250e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.389010e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.734672e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.715430e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 9262588.477712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.779397e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.760414e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.740096e+05\n Vprtstp: contraction number = 9.740096e+05\n Vnewton: Attempting damping, relres = 0.096135\n Vnewton: Attempting damping, relres = 0.545161\n Vnewton: Damping accepted, relres = 0.096135\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.613536e-02\n Vprtstp: contraction number = 9.613536e-02\n Vnewton: Using errtol_s: 890462.283513\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.992824e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.974532e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.907605e+05\n Vprtstp: contraction number = 1.907605e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.859794e-02\n Vprtstp: contraction number = 1.934558e-01\n Vnewton: Using errtol_s: 172265.062018\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.185643e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.170061e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.138633e+04\n Vprtstp: contraction number = 5.138633e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.994948e-03\n Vprtstp: contraction number = 2.685753e-01\n Vnewton: Using errtol_s: 46266.149079\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.377045e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.365845e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.656736e+04\n Vprtstp: contraction number = 1.656736e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.610090e-03\n Vprtstp: contraction number = 3.223437e-01\n Vnewton: Using errtol_s: 14913.601487\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.569818e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.561390e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.837272e+03\n Vprtstp: contraction number = 5.837272e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.672493e-04\n Vprtstp: contraction number = 3.523090e-01\n Vnewton: Using errtol_s: 5254.196377\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.763885e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.758280e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.147141e+03\n Vprtstp: contraction number = 2.147141e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.086390e-04\n Vprtstp: contraction number = 3.678083e-01\n Vnewton: Using errtol_s: 1932.536910\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.955077e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.954852e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.193498e+02\n Vprtstp: contraction number = 8.193498e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.961379e-05\n Vprtstp: contraction number = 3.815864e-01\n Vnewton: Using errtol_s: 737.429804\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.150971e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.148876e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352547e+02\n Vprtstp: contraction number = 3.352547e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.257526e-05\n Vprtstp: contraction number = 4.091660e-01\n Vnewton: Using errtol_s: 301.731240\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.349594e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.347701e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.500666e+02\n Vprtstp: contraction number = 1.500666e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.458127e-05\n Vprtstp: contraction number = 4.476179e-01\n Vnewton: Using errtol_s: 135.060298\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.550816e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.545560e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.280398e+01\n Vprtstp: contraction number = 7.280398e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.074013e-06\n Vprtstp: contraction number = 4.851438e-01\n Vnewton: Using errtol_s: 65.523671\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.751078e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.746804e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.740960e+01\n Vprtstp: contraction number = 3.740960e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.634908e-06\n Vprtstp: contraction number = 5.138397e-01\n Vnewton: Using errtol_s: 33.668661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.953871e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.949872e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.000118e+01\n Vprtstp: contraction number = 2.000118e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.943416e-06\n Vprtstp: contraction number = 5.346535e-01\n Vnewton: Using errtol_s: 18.001066\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.156594e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.142921e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.094514e+01\n Vprtstp: contraction number = 1.094514e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.063486e-06\n Vprtstp: contraction number = 5.472249e-01\n Vnewton: Using errtol_s: 9.850631\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.363654e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.341848e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.085292e+00\n Vprtstp: contraction number = 6.085292e+00\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 5.912779e-07\n Vprtstp: contraction number = 5.559810e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.804257e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.899913e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.793170e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.889685e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -732,15 +732,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.418972427545E+00 kT\n Vpmg_energy:  qfEnergy = 2.355397093328E+05 kT\n Vpmg_energy:  dielEnergy = 1.177642501639E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.792200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.750400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -763,217 +763,217 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.378901\n+Vacc_SASA: Time elapsed: 1.363463\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.677160e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.653555e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 9.495100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 9.081400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.182220e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.557560e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.822013e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.782091e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7837779.438687\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.869273e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.827203e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.264175e+05\n Vprtstp: contraction number = 5.264175e+05\n Vnewton: Attempting damping, relres = 0.062206\n Vnewton: Attempting damping, relres = 0.525499\n Vnewton: Damping accepted, relres = 0.062206\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.220619e-02\n Vprtstp: contraction number = 6.220619e-02\n Vnewton: Using errtol_s: 487558.369599\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.096657e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.039083e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.104882e+05\n Vprtstp: contraction number = 1.104882e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.277305e-02\n Vprtstp: contraction number = 2.053340e-01\n Vnewton: Using errtol_s: 100112.332342\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.304051e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.237391e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.234516e+04\n Vprtstp: contraction number = 3.234516e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.716136e-03\n Vprtstp: contraction number = 2.909357e-01\n Vnewton: Using errtol_s: 29126.250452\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.508681e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.437691e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.113222e+04\n Vprtstp: contraction number = 1.113222e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.278517e-03\n Vprtstp: contraction number = 3.440448e-01\n Vnewton: Using errtol_s: 10020.735856\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.710265e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.637367e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.146765e+03\n Vprtstp: contraction number = 4.146765e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.761620e-04\n Vprtstp: contraction number = 3.724330e-01\n Vnewton: Using errtol_s: 3732.052866\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.913046e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.832451e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.647764e+03\n Vprtstp: contraction number = 1.647764e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.891857e-04\n Vprtstp: contraction number = 3.973138e-01\n Vnewton: Using errtol_s: 1482.795933\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.120501e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.025519e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.190477e+02\n Vprtstp: contraction number = 7.190477e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.256252e-05\n Vprtstp: contraction number = 4.364099e-01\n Vnewton: Using errtol_s: 647.106851\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.331490e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.223541e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.514586e+02\n Vprtstp: contraction number = 3.514586e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.035656e-05\n Vprtstp: contraction number = 4.888000e-01\n Vnewton: Using errtol_s: 316.305821\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.541686e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.418857e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.878144e+02\n Vprtstp: contraction number = 1.878144e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.156625e-05\n Vprtstp: contraction number = 5.343927e-01\n Vnewton: Using errtol_s: 169.031531\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.749443e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.607798e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.065907e+02\n Vprtstp: contraction number = 1.065907e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.223961e-05\n Vprtstp: contraction number = 5.675353e-01\n Vnewton: Using errtol_s: 95.931363\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.955603e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.795903e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.270317e+01\n Vprtstp: contraction number = 6.270317e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 7.200099e-06\n Vprtstp: contraction number = 5.882621e-01\n Vnewton: Using errtol_s: 56.432788\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.168770e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.981614e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.774740e+01\n Vprtstp: contraction number = 3.774740e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 4.334473e-06\n Vprtstp: contraction number = 6.020019e-01\n Vnewton: Using errtol_s: 33.972645\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.382538e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.171219e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.304758e+01\n Vprtstp: contraction number = 2.304758e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 2.646517e-06\n Vprtstp: contraction number = 6.105742e-01\n Vnewton: Using errtol_s: 20.742819\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.589985e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.359423e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.421587e+01\n Vprtstp: contraction number = 1.421587e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 1.632386e-06\n Vprtstp: contraction number = 6.168053e-01\n Vnewton: Using errtol_s: 12.794282\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.798681e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.546074e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.829808e+00\n Vprtstp: contraction number = 8.829808e+00\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 1.013913e-06\n Vprtstp: contraction number = 6.211233e-01\n Vnewton: Using errtol_s: 7.946827\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.000698e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.734964e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.514712e+00\n Vprtstp: contraction number = 5.514712e+00\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 6.332457e-07\n Vprtstp: contraction number = 6.245562e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.360212e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.465166e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.138784e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.236657e+01\n Vpmg_setPart:  lower corner = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  upper corner = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -982,17 +982,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.438982867308E+00 kT\n Vpmg_energy:  qfEnergy = 1.232481159173E+05 kT\n Vpmg_energy:  dielEnergy = 6.161845360142E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.037100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.001500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.0735516\n@@ -1038,182 +1038,182 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.338388 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.378487\n+Vacc_SASA: Time elapsed: 1.414761\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.008680e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.453125e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 9.542900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 8.978000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.912120e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.188100e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.049586e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.028157e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 9316156.472817\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.054270e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.034082e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.759901e+05\n Vprtstp: contraction number = 9.759901e+05\n Vnewton: Attempting damping, relres = 0.095792\n Vnewton: Attempting damping, relres = 0.545068\n Vnewton: Damping accepted, relres = 0.095792\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.579182e-02\n Vprtstp: contraction number = 9.579182e-02\n Vnewton: Using errtol_s: 892411.563062\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.076290e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.055461e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.903231e+05\n Vprtstp: contraction number = 1.903231e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.845161e-02\n Vprtstp: contraction number = 1.926220e-01\n Vnewton: Using errtol_s: 171898.088650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.096340e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.075248e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.121980e+04\n Vprtstp: contraction number = 5.121980e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.949951e-03\n Vprtstp: contraction number = 2.682666e-01\n Vnewton: Using errtol_s: 46114.513884\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.116537e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.094186e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.657747e+04\n Vprtstp: contraction number = 1.657747e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.601844e-03\n Vprtstp: contraction number = 3.236081e-01\n Vnewton: Using errtol_s: 14923.031227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.136911e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.113397e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.880103e+03\n Vprtstp: contraction number = 5.880103e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.681354e-04\n Vprtstp: contraction number = 3.546758e-01\n Vnewton: Using errtol_s: 5292.838197\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.156935e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.132755e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.176489e+03\n Vprtstp: contraction number = 2.176489e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.102777e-04\n Vprtstp: contraction number = 3.701190e-01\n Vnewton: Using errtol_s: 1958.979878\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.177141e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.152244e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.247695e+02\n Vprtstp: contraction number = 8.247695e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.968018e-05\n Vprtstp: contraction number = 3.789284e-01\n Vnewton: Using errtol_s: 742.313034\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.197220e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.171775e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.261401e+02\n Vprtstp: contraction number = 3.261401e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.150750e-05\n Vprtstp: contraction number = 3.954245e-01\n Vnewton: Using errtol_s: 293.528762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.217092e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.191415e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.384546e+02\n Vprtstp: contraction number = 1.384546e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.337564e-05\n Vprtstp: contraction number = 4.245224e-01\n Vnewton: Using errtol_s: 124.609538\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.236795e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.210821e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.300596e+01\n Vprtstp: contraction number = 6.300596e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.086783e-06\n Vprtstp: contraction number = 4.550649e-01\n Vnewton: Using errtol_s: 56.705427\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.256796e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.230794e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.026431e+01\n Vprtstp: contraction number = 3.026431e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.923726e-06\n Vprtstp: contraction number = 4.803401e-01\n Vnewton: Using errtol_s: 27.237888\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.276475e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.251227e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.506906e+01\n Vprtstp: contraction number = 1.506906e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.455768e-06\n Vprtstp: contraction number = 4.979152e-01\n Vnewton: Using errtol_s: 13.562159\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.296446e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.271450e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.684345e+00\n Vprtstp: contraction number = 7.684345e+00\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 7.423567e-07\n Vprtstp: contraction number = 5.099418e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.638476e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.740545e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.604665e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.709525e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1222,17 +1222,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.434662074418E+00 kT\n Vpmg_energy:  qfEnergy = 2.352136568668E+05 kT\n Vpmg_energy:  dielEnergy = 1.176012292477E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.742300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.740000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.0735516\n@@ -1253,217 +1253,217 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.040453\n+Vacc_SASA: Time elapsed: 3.037059\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.510491e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.502764e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 9.051200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 9.336400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.635860e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.775830e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.359433e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.334716e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 15819726.247791\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.363992e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.339423e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.061014e+06\n Vprtstp: contraction number = 1.061014e+06\n Vnewton: Attempting damping, relres = 0.062452\n Vnewton: Attempting damping, relres = 0.525397\n Vnewton: Damping accepted, relres = 0.062452\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.245176e-02\n Vprtstp: contraction number = 6.245176e-02\n Vnewton: Using errtol_s: 987969.694273\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.385780e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.361419e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.221439e+05\n Vprtstp: contraction number = 2.221439e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.274712e-02\n Vprtstp: contraction number = 2.041114e-01\n Vnewton: Using errtol_s: 201655.898404\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.405209e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.382432e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.509302e+04\n Vprtstp: contraction number = 6.509302e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.704570e-03\n Vprtstp: contraction number = 2.906202e-01\n Vnewton: Using errtol_s: 58605.278995\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.424733e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.402677e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.250351e+04\n Vprtstp: contraction number = 2.250351e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.280353e-03\n Vprtstp: contraction number = 3.456144e-01\n Vnewton: Using errtol_s: 20254.828172\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.443716e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.423188e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.447408e+03\n Vprtstp: contraction number = 8.447408e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.805791e-04\n Vprtstp: contraction number = 3.753490e-01\n Vnewton: Using errtol_s: 7602.629655\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.463741e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.442999e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.399185e+03\n Vprtstp: contraction number = 3.399185e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.933739e-04\n Vprtstp: contraction number = 4.023769e-01\n Vnewton: Using errtol_s: 3059.122762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.483796e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.463099e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.505025e+03\n Vprtstp: contraction number = 1.505025e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.562081e-05\n Vprtstp: contraction number = 4.427733e-01\n Vnewton: Using errtol_s: 1354.497766\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.506470e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.483596e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.407337e+02\n Vprtstp: contraction number = 7.407337e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.214082e-05\n Vprtstp: contraction number = 4.921797e-01\n Vnewton: Using errtol_s: 666.656280\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.530621e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.503870e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955938e+02\n Vprtstp: contraction number = 3.955938e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.250569e-05\n Vprtstp: contraction number = 5.340591e-01\n Vnewton: Using errtol_s: 356.033867\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.554957e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.530809e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.238069e+02\n Vprtstp: contraction number = 2.238069e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.273259e-05\n Vprtstp: contraction number = 5.657500e-01\n Vnewton: Using errtol_s: 201.426156\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.580837e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.562458e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.312226e+02\n Vprtstp: contraction number = 1.312226e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 7.465385e-06\n Vprtstp: contraction number = 5.863208e-01\n Vnewton: Using errtol_s: 118.100345\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.606051e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.593673e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.886374e+01\n Vprtstp: contraction number = 7.886374e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 4.486638e-06\n Vprtstp: contraction number = 6.009922e-01\n Vnewton: Using errtol_s: 70.977384\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.625271e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.624971e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.812776e+01\n Vprtstp: contraction number = 4.812776e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 2.738037e-06\n Vprtstp: contraction number = 6.102647e-01\n Vnewton: Using errtol_s: 43.314994\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.644451e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.654122e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.971066e+01\n Vprtstp: contraction number = 2.971066e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 1.690269e-06\n Vprtstp: contraction number = 6.173289e-01\n Vnewton: Using errtol_s: 26.739596\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.663670e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.682477e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.848360e+01\n Vprtstp: contraction number = 1.848360e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 1.051550e-06\n Vprtstp: contraction number = 6.221201e-01\n Vnewton: Using errtol_s: 16.635240\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.682864e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.709684e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.157246e+01\n Vprtstp: contraction number = 1.157246e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 6.583687e-07\n Vprtstp: contraction number = 6.260933e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.396362e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.495018e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.998769e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.099142e+01\n Vpmg_setPart:  lower corner = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  upper corner = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1472,17 +1472,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.734614944651E+00 kT\n Vpmg_energy:  qfEnergy = 2.465748372430E+05 kT\n Vpmg_energy:  dielEnergy = 1.232753607231E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.903000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.876900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.0735516\n@@ -1528,182 +1528,182 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.649873 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.998609\n+Vacc_SASA: Time elapsed: 2.987283\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.951295e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.549093e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 8.999000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 8.793300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.312950e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.946030e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.749246e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.791345e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 18647566.992070\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.753730e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.800434e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.941752e+06\n Vprtstp: contraction number = 1.941752e+06\n Vnewton: Attempting damping, relres = 0.095497\n Vnewton: Attempting damping, relres = 0.544786\n Vnewton: Damping accepted, relres = 0.095497\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.549656e-02\n Vprtstp: contraction number = 9.549656e-02\n Vnewton: Using errtol_s: 1780778.449755\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.774317e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.835554e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.788571e+05\n Vprtstp: contraction number = 3.788571e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.837082e-02\n Vprtstp: contraction number = 1.923715e-01\n Vnewton: Using errtol_s: 342571.038812\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.793508e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.866952e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.019639e+05\n Vprtstp: contraction number = 1.019639e+05\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.923062e-03\n Vprtstp: contraction number = 2.679828e-01\n Vnewton: Using errtol_s: 91803.137006\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.812567e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.898267e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.295911e+04\n Vprtstp: contraction number = 3.295911e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.591047e-03\n Vprtstp: contraction number = 3.231823e-01\n Vnewton: Using errtol_s: 29669.150960\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.831769e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.926829e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.167703e+04\n Vprtstp: contraction number = 1.167703e+04\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.636468e-04\n Vprtstp: contraction number = 3.542616e-01\n Vnewton: Using errtol_s: 10510.641014\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.851452e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.955312e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.318326e+03\n Vprtstp: contraction number = 4.318326e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.084308e-04\n Vprtstp: contraction number = 3.697898e-01\n Vnewton: Using errtol_s: 3886.727604\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.870999e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.986898e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.645707e+03\n Vprtstp: contraction number = 1.645707e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.942966e-05\n Vprtstp: contraction number = 3.810841e-01\n Vnewton: Using errtol_s: 1481.169947\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.890616e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.016384e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.631576e+02\n Vprtstp: contraction number = 6.631576e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.200666e-05\n Vprtstp: contraction number = 4.029560e-01\n Vnewton: Using errtol_s: 596.846318\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.909847e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.046175e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.897130e+02\n Vprtstp: contraction number = 2.897130e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.398265e-05\n Vprtstp: contraction number = 4.368670e-01\n Vnewton: Using errtol_s: 260.742452\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.928885e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.077112e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.365123e+02\n Vprtstp: contraction number = 1.365123e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.588595e-06\n Vprtstp: contraction number = 4.711978e-01\n Vnewton: Using errtol_s: 122.861265\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.948209e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.106482e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.809649e+01\n Vprtstp: contraction number = 6.809649e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.286589e-06\n Vprtstp: contraction number = 4.988300e-01\n Vnewton: Using errtol_s: 61.286879\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.967735e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.137594e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.533208e+01\n Vprtstp: contraction number = 3.533208e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705256e-06\n Vprtstp: contraction number = 5.188530e-01\n Vnewton: Using errtol_s: 31.798881\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.987425e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.165802e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.878604e+01\n Vprtstp: contraction number = 1.878604e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.066833e-07\n Vprtstp: contraction number = 5.316991e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.548721e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.644286e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.972905e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.074988e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1712,23 +1712,23 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.745937546040E+00 kT\n Vpmg_energy:  qfEnergy = 4.708379041028E+05 kT\n Vpmg_energy:  dielEnergy = 2.354068218640E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.469500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.366400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.005395e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.189933e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:20:54 2025\n+# Creation Date and Time:  Sun Jan  7 09:35:35 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -1986,140 +1986,140 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.360564\n+Vacc_SASA: Time elapsed: 1.368632\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.300596e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.538007e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 9.357000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 8.521200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.834500e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.866140e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.412121e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.709929e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7775242.648804\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.869910e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.587845e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.519208e+05\n Vprtstp: contraction number = 4.519208e+05\n Vnewton: Attempting damping, relres = 0.054343\n Vnewton: Attempting damping, relres = 0.522411\n Vnewton: Damping accepted, relres = 0.054343\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.434337e-02\n Vprtstp: contraction number = 5.434337e-02\n Vnewton: Using errtol_s: 422532.874830\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.081702e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.020802e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.825836e+04\n Vprtstp: contraction number = 6.825836e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 8.031654e-03\n Vprtstp: contraction number = 1.477946e-01\n Vnewton: Using errtol_s: 62448.057923\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.079300e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.100000e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.274799e+04\n Vprtstp: contraction number = 1.274799e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.476725e-03\n Vprtstp: contraction number = 1.838631e-01\n Vnewton: Using errtol_s: 11481.894443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.007179e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.402269e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.642149e+03\n Vprtstp: contraction number = 2.642149e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.058466e-04\n Vprtstp: contraction number = 2.071114e-01\n Vnewton: Using errtol_s: 2378.031723\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.203572e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.707218e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.907005e+02\n Vprtstp: contraction number = 5.907005e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.837606e-05\n Vprtstp: contraction number = 2.235632e-01\n Vnewton: Using errtol_s: 531.640431\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.399412e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.012219e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.434663e+02\n Vprtstp: contraction number = 1.434663e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.660675e-05\n Vprtstp: contraction number = 2.428738e-01\n Vnewton: Using errtol_s: 129.121507\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.597634e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.329009e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.897369e+01\n Vprtstp: contraction number = 3.897369e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.511300e-06\n Vprtstp: contraction number = 2.716546e-01\n Vnewton: Using errtol_s: 35.076449\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.799404e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.631090e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.167165e+01\n Vprtstp: contraction number = 1.167165e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.351022e-06\n Vprtstp: contraction number = 2.994751e-01\n Vnewton: Using errtol_s: 10.504522\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.000234e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.932881e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.750775e+00\n Vprtstp: contraction number = 3.750775e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.341599e-07\n Vprtstp: contraction number = 3.213567e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.828777e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.929338e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.812713e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.913077e+01\n Vpmg_setPart:  lower corner = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  upper corner = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2128,15 +2128,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.649154177944E+00 kT\n Vpmg_energy:  qfEnergy = 1.233253101346E+05 kT\n Vpmg_energy:  dielEnergy = 6.165668863925E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.031200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.003180e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -2184,138 +2184,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.297837 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.353724\n+Vacc_SASA: Time elapsed: 1.413029\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.644793e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.081798e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 9.236800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 8.686100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.594310e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.776180e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.543214e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.603792e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 9261641.900268\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.588614e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.692373e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.279613e+05\n Vprtstp: contraction number = 8.279613e+05\n Vnewton: Attempting damping, relres = 0.082099\n Vnewton: Attempting damping, relres = 0.538543\n Vnewton: Damping accepted, relres = 0.082099\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.209891e-02\n Vprtstp: contraction number = 8.209891e-02\n Vnewton: Using errtol_s: 760370.715975\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.804925e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.033047e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.156529e+05\n Vprtstp: contraction number = 1.156529e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.133997e-02\n Vprtstp: contraction number = 1.381257e-01\n Vnewton: Using errtol_s: 105026.724448\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.006701e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.338110e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.966463e+04\n Vprtstp: contraction number = 1.966463e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.911861e-03\n Vprtstp: contraction number = 1.685949e-01\n Vnewton: Using errtol_s: 17706.967510\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.207474e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.627879e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.721579e+03\n Vprtstp: contraction number = 3.721579e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.617487e-04\n Vprtstp: contraction number = 1.892129e-01\n Vnewton: Using errtol_s: 3350.387034\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.411336e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.899574e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.320600e+02\n Vprtstp: contraction number = 7.320600e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.114465e-05\n Vprtstp: contraction number = 1.966687e-01\n Vnewton: Using errtol_s: 658.916270\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.616770e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.176669e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.450384e+02\n Vprtstp: contraction number = 1.450384e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.409447e-05\n Vprtstp: contraction number = 1.981101e-01\n Vnewton: Using errtol_s: 130.537961\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.825270e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.451782e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.437556e+01\n Vprtstp: contraction number = 3.437556e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.340452e-06\n Vprtstp: contraction number = 2.370044e-01\n Vnewton: Using errtol_s: 30.938074\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.036361e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.722677e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.059415e+01\n Vprtstp: contraction number = 1.059415e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.029507e-06\n Vprtstp: contraction number = 3.081938e-01\n Vnewton: Using errtol_s: 9.534923\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.256513e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.010784e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.916133e+00\n Vprtstp: contraction number = 3.916133e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.805503e-07\n Vprtstp: contraction number = 3.696433e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.886332e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.984490e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.656802e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.756435e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2324,15 +2324,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.591945419500E+00 kT\n Vpmg_energy:  qfEnergy = 2.356288022123E+05 kT\n Vpmg_energy:  dielEnergy = 1.178084778246E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.832800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.024700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -2355,140 +2355,140 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.377172\n+Vacc_SASA: Time elapsed: 1.377404\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.356212e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.612701e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 9.249400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 8.999900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.847680e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.062990e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.776239e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.635676e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7837779.438687\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.824576e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.729040e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.514612e+05\n Vprtstp: contraction number = 4.514612e+05\n Vnewton: Attempting damping, relres = 0.053797\n Vnewton: Attempting damping, relres = 0.522401\n Vnewton: Damping accepted, relres = 0.053797\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.379672e-02\n Vprtstp: contraction number = 5.379672e-02\n Vnewton: Using errtol_s: 421646.851825\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.047690e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.084992e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.805281e+04\n Vprtstp: contraction number = 6.805281e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 7.947357e-03\n Vprtstp: contraction number = 1.477294e-01\n Vnewton: Using errtol_s: 62289.628218\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.251125e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.395521e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.276985e+04\n Vprtstp: contraction number = 1.276985e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.467975e-03\n Vprtstp: contraction number = 1.847124e-01\n Vnewton: Using errtol_s: 11505.665992\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.453874e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.692128e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.685314e+03\n Vprtstp: contraction number = 2.685314e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.083318e-04\n Vprtstp: contraction number = 2.100388e-01\n Vnewton: Using errtol_s: 2416.636290\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.657743e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.999748e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.970818e+02\n Vprtstp: contraction number = 5.970818e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.855221e-05\n Vprtstp: contraction number = 2.223326e-01\n Vnewton: Using errtol_s: 537.297133\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.859591e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.308359e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.381270e+02\n Vprtstp: contraction number = 1.381270e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.586035e-05\n Vprtstp: contraction number = 2.313616e-01\n Vnewton: Using errtol_s: 124.309951\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.059794e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.596186e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.581259e+01\n Vprtstp: contraction number = 3.581259e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.112278e-06\n Vprtstp: contraction number = 2.592804e-01\n Vnewton: Using errtol_s: 32.231131\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.262522e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.899744e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.075720e+01\n Vprtstp: contraction number = 1.075720e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.235235e-06\n Vprtstp: contraction number = 3.003774e-01\n Vnewton: Using errtol_s: 9.681503\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.473353e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.176898e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.606387e+00\n Vprtstp: contraction number = 3.606387e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.141158e-07\n Vprtstp: contraction number = 3.352525e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.884372e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.985002e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.714365e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.817364e+01\n Vpmg_setPart:  lower corner = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  upper corner = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2497,15 +2497,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.659237014157E+00 kT\n Vpmg_energy:  qfEnergy = 1.233789041891E+05 kT\n Vpmg_energy:  dielEnergy = 6.168342765954E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.182500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.007300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -2553,138 +2553,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.338577 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.388484\n+Vacc_SASA: Time elapsed: 1.373746\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.787400e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.600221e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 9.929200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 8.859500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.952880e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.292210e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.062752e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.715032e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 9315222.001185\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.112113e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.759762e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.310439e+05\n Vprtstp: contraction number = 8.310439e+05\n Vnewton: Attempting damping, relres = 0.081942\n Vnewton: Attempting damping, relres = 0.538517\n Vnewton: Damping accepted, relres = 0.081942\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.194219e-02\n Vprtstp: contraction number = 8.194219e-02\n Vnewton: Using errtol_s: 763309.735899\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.349808e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.970501e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.164941e+05\n Vprtstp: contraction number = 1.164941e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.135719e-02\n Vprtstp: contraction number = 1.386000e-01\n Vnewton: Using errtol_s: 105794.756542\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.583390e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.017017e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.004035e+04\n Vprtstp: contraction number = 2.004035e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.937352e-03\n Vprtstp: contraction number = 1.705837e-01\n Vnewton: Using errtol_s: 18046.864412\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.803595e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.036132e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.874509e+03\n Vprtstp: contraction number = 3.874509e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.744478e-04\n Vprtstp: contraction number = 1.932781e-01\n Vnewton: Using errtol_s: 3488.064314\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.007097e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.056004e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.934449e+02\n Vprtstp: contraction number = 7.934449e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.666874e-05\n Vprtstp: contraction number = 2.047515e-01\n Vnewton: Using errtol_s: 714.186341\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.202444e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.075510e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.631165e+02\n Vprtstp: contraction number = 1.631165e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.576011e-05\n Vprtstp: contraction number = 2.055611e-01\n Vnewton: Using errtol_s: 146.808940\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.394277e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.102155e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.992341e+01\n Vprtstp: contraction number = 3.992341e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.857249e-06\n Vprtstp: contraction number = 2.447475e-01\n Vnewton: Using errtol_s: 35.931127\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.584513e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.129525e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.373524e+01\n Vprtstp: contraction number = 1.373524e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.327082e-06\n Vprtstp: contraction number = 3.440488e-01\n Vnewton: Using errtol_s: 12.362061\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.773229e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.158419e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.506580e+00\n Vprtstp: contraction number = 5.506580e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.320241e-07\n Vprtstp: contraction number = 4.008978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.869482e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.981971e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.088050e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.182500e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2693,17 +2693,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.613981699518E+00 kT\n Vpmg_energy:  qfEnergy = 2.353039534047E+05 kT\n Vpmg_energy:  dielEnergy = 1.176460315654E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.755300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.737400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.0735516\n@@ -2724,140 +2724,140 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.050624\n+Vacc_SASA: Time elapsed: 3.034799\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.134090e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.198971e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 9.122700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 9.246700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.301380e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.686550e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.450724e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.233239e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 15819726.247791\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.494997e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.237953e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.105286e+05\n Vprtstp: contraction number = 9.105286e+05\n Vnewton: Attempting damping, relres = 0.054151\n Vnewton: Attempting damping, relres = 0.522361\n Vnewton: Damping accepted, relres = 0.054151\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.415081e-02\n Vprtstp: contraction number = 5.415081e-02\n Vnewton: Using errtol_s: 856650.988867\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.698726e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.259258e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.365159e+05\n Vprtstp: contraction number = 1.365159e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 7.938600e-03\n Vprtstp: contraction number = 1.466017e-01\n Vnewton: Using errtol_s: 125586.474947\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.886096e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.278806e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.543138e+04\n Vprtstp: contraction number = 2.543138e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.449191e-03\n Vprtstp: contraction number = 1.825500e-01\n Vnewton: Using errtol_s: 22925.804865\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.007121e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.298358e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.291506e+03\n Vprtstp: contraction number = 5.291506e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.010412e-04\n Vprtstp: contraction number = 2.077305e-01\n Vnewton: Using errtol_s: 4762.388621\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.025057e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.316853e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.180651e+03\n Vprtstp: contraction number = 1.180651e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.716597e-05\n Vprtstp: contraction number = 2.231123e-01\n Vnewton: Using errtol_s: 1062.547289\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.043560e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.336262e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.813654e+02\n Vprtstp: contraction number = 2.813654e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.600723e-05\n Vprtstp: contraction number = 2.383235e-01\n Vnewton: Using errtol_s: 253.229951\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.061759e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.355325e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.533652e+01\n Vprtstp: contraction number = 7.533652e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.285970e-06\n Vprtstp: contraction number = 2.677522e-01\n Vnewton: Using errtol_s: 67.802871\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.080173e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.373914e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.308540e+01\n Vprtstp: contraction number = 2.308540e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.313362e-06\n Vprtstp: contraction number = 3.064328e-01\n Vnewton: Using errtol_s: 20.777024\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.098886e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.395619e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.670717e+00\n Vprtstp: contraction number = 7.670717e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.363948e-07\n Vprtstp: contraction number = 3.322731e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.692275e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.787105e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.838651e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.937690e+01\n Vpmg_setPart:  lower corner = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  upper corner = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2866,15 +2866,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.013375850535E+01 kT\n Vpmg_energy:  qfEnergy = 2.468101698845E+05 kT\n Vpmg_energy:  dielEnergy = 1.233922430579E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.879100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.514800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -2922,138 +2922,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.652629 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.989787\n+Vacc_SASA: Time elapsed: 2.994541\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.611393e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.038709e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 8.748700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 9.080900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.706690e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.947990e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.171401e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.478858e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 18644287.879827\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.176739e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.483388e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.651555e+06\n Vprtstp: contraction number = 1.651555e+06\n Vnewton: Attempting damping, relres = 0.081643\n Vnewton: Attempting damping, relres = 0.538237\n Vnewton: Damping accepted, relres = 0.081643\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164291e-02\n Vprtstp: contraction number = 8.164291e-02\n Vnewton: Using errtol_s: 1522173.863324\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.197763e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.504441e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.305601e+05\n Vprtstp: contraction number = 2.305601e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.125644e-02\n Vprtstp: contraction number = 1.378740e-01\n Vnewton: Using errtol_s: 209868.227405\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.219020e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.522934e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.940032e+04\n Vprtstp: contraction number = 3.940032e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.903339e-03\n Vprtstp: contraction number = 1.690890e-01\n Vnewton: Using errtol_s: 35486.402387\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.238644e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.542014e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.544305e+03\n Vprtstp: contraction number = 7.544305e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.642891e-04\n Vprtstp: contraction number = 1.913948e-01\n Vnewton: Using errtol_s: 6791.911566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.258986e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.560933e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.522155e+03\n Vprtstp: contraction number = 1.522155e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.348563e-05\n Vprtstp: contraction number = 2.017234e-01\n Vnewton: Using errtol_s: 1370.087193\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.279805e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.579263e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.106660e+02\n Vprtstp: contraction number = 3.106660e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.499708e-05\n Vprtstp: contraction number = 2.040818e-01\n Vnewton: Using errtol_s: 279.609899\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.300671e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.597552e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.690225e+01\n Vprtstp: contraction number = 7.690225e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.712245e-06\n Vprtstp: contraction number = 2.475312e-01\n Vnewton: Using errtol_s: 69.212171\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.321712e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.616395e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.600764e+01\n Vprtstp: contraction number = 2.600764e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.255497e-06\n Vprtstp: contraction number = 3.382042e-01\n Vnewton: Using errtol_s: 23.407850\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.342089e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.635652e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011646e+01\n Vprtstp: contraction number = 1.011646e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.883437e-07\n Vprtstp: contraction number = 3.889644e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.882631e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.981319e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.719972e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.821233e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -3062,23 +3062,23 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.005009553015E+01 kT\n Vpmg_energy:  qfEnergy = 4.710211065569E+05 kT\n Vpmg_energy:  dielEnergy = 2.354978106920E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.434800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.434700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.360922e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.652029e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:22:40 2025\n+# Creation Date and Time:  Sun Jan  7 09:36:56 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -3431,250 +3431,250 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.363639\n+Vacc_SASA: Time elapsed: 1.389689\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.579449e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.558387e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.070900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.968100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.290400e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.129540e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.951215e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.910992e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.163920e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.146861e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.136321e+05\n Vprtstp: contraction number = 2.136321e+05\n Vnewton: Attempting damping, relres = 0.047663\n Vnewton: Attempting damping, relres = 0.515490\n Vnewton: Damping accepted, relres = 0.047663\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.766304e-02\n Vprtstp: contraction number = 4.766304e-02\n Vnewton: Using errtol_s: 204994.485638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.008395e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.240318e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.587025e+04\n Vprtstp: contraction number = 4.587025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.727679e-03\n Vprtstp: contraction number = 2.040927e-01\n Vnewton: Using errtol_s: 41837.880528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.706732e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.194566e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.391016e+04\n Vprtstp: contraction number = 1.391016e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.912173e-03\n Vprtstp: contraction number = 2.993697e-01\n Vnewton: Using errtol_s: 12524.995351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.403033e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.103132e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.237707e+03\n Vprtstp: contraction number = 5.237707e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.096054e-03\n Vprtstp: contraction number = 3.763697e-01\n Vnewton: Using errtol_s: 4714.028550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.081630e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.082938e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.331453e+03\n Vprtstp: contraction number = 2.331453e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.878779e-04\n Vprtstp: contraction number = 4.451223e-01\n Vnewton: Using errtol_s: 2098.319320\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.815965e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.176642e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189035e+03\n Vprtstp: contraction number = 1.189035e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.488161e-04\n Vprtstp: contraction number = 5.099966e-01\n Vnewton: Using errtol_s: 1070.135650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.534722e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.367741e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.678182e+02\n Vprtstp: contraction number = 6.678182e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.397467e-04\n Vprtstp: contraction number = 5.616468e-01\n Vnewton: Using errtol_s: 601.038216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.238004e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.500319e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.994733e+02\n Vprtstp: contraction number = 3.994733e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.359319e-05\n Vprtstp: contraction number = 5.981764e-01\n Vnewton: Using errtol_s: 359.526862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.941866e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.052385e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.488647e+02\n Vprtstp: contraction number = 2.488647e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.207703e-05\n Vprtstp: contraction number = 6.229817e-01\n Vnewton: Using errtol_s: 223.978670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.667787e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.130020e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.588671e+02\n Vprtstp: contraction number = 1.588671e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.324425e-05\n Vprtstp: contraction number = 6.383669e-01\n Vnewton: Using errtol_s: 142.980568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.362618e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.204624e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.030284e+02\n Vprtstp: contraction number = 1.030284e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.155954e-05\n Vprtstp: contraction number = 6.485194e-01\n Vnewton: Using errtol_s: 92.725673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.008202e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.288925e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.760657e+01\n Vprtstp: contraction number = 6.760657e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.414722e-05\n Vprtstp: contraction number = 6.561932e-01\n Vnewton: Using errtol_s: 60.845953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.081641e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.369073e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.480217e+01\n Vprtstp: contraction number = 4.480217e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.375216e-06\n Vprtstp: contraction number = 6.626894e-01\n Vnewton: Using errtol_s: 40.321969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.153284e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.436954e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990735e+01\n Vprtstp: contraction number = 2.990735e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 6.258355e-06\n Vprtstp: contraction number = 6.675424e-01\n Vnewton: Using errtol_s: 26.916626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.223450e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.502568e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.008505e+01\n Vprtstp: contraction number = 2.008505e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 4.202958e-06\n Vprtstp: contraction number = 6.715755e-01\n Vnewton: Using errtol_s: 18.076547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.294818e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.571661e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356100e+01\n Vprtstp: contraction number = 1.356100e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 2.837748e-06\n Vprtstp: contraction number = 6.751787e-01\n Vnewton: Using errtol_s: 12.204901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.363118e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.644582e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.198733e+00\n Vprtstp: contraction number = 9.198733e+00\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 1.924909e-06\n Vprtstp: contraction number = 6.783227e-01\n Vnewton: Using errtol_s: 8.278861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.435252e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.717440e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.265697e+00\n Vprtstp: contraction number = 6.265697e+00\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.311147e-06\n Vprtstp: contraction number = 6.811478e-01\n Vnewton: Using errtol_s: 5.639128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.504717e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.789570e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.284635e+00\n Vprtstp: contraction number = 4.284635e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 8.965941e-07\n Vprtstp: contraction number = 6.838241e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.367587e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.393838e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.664903e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.689523e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -3683,17 +3683,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.479770161201E-01 kT\n Vpmg_energy:  qfEnergy = 1.169401599673E+03 kT\n Vpmg_energy:  dielEnergy = 6.300507194512E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.061000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.051000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -3739,171 +3739,171 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00574887 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.354365\n+Vacc_SASA: Time elapsed: 1.383504\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.668195e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.776944e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.190600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.478200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.173220e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.318530e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.755784e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.063464e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3431662.159805\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.776101e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.095241e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.373293e+05\n Vprtstp: contraction number = 3.373293e+05\n Vnewton: Attempting damping, relres = 0.089626\n Vnewton: Attempting damping, relres = 0.541581\n Vnewton: Damping accepted, relres = 0.089626\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.962597e-02\n Vprtstp: contraction number = 8.962597e-02\n Vnewton: Using errtol_s: 307566.035257\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.875301e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.248823e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.223173e+04\n Vprtstp: contraction number = 6.223173e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.639798e-02\n Vprtstp: contraction number = 1.829601e-01\n Vnewton: Using errtol_s: 56272.319668\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.962344e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.377658e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.604081e+04\n Vprtstp: contraction number = 1.604081e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.208259e-03\n Vprtstp: contraction number = 2.566328e-01\n Vnewton: Using errtol_s: 14441.323490\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.044888e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.516195e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.994316e+03\n Vprtstp: contraction number = 4.994316e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.309837e-03\n Vprtstp: contraction number = 3.112539e-01\n Vnewton: Using errtol_s: 4494.917566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.129794e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.645249e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.695194e+03\n Vprtstp: contraction number = 1.695194e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.445882e-04\n Vprtstp: contraction number = 3.394226e-01\n Vnewton: Using errtol_s: 1525.676669\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.213881e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.783439e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.988429e+02\n Vprtstp: contraction number = 5.988429e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.570548e-04\n Vprtstp: contraction number = 3.532589e-01\n Vnewton: Using errtol_s: 538.958849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.297449e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.918497e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.157694e+02\n Vprtstp: contraction number = 2.157694e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.658847e-05\n Vprtstp: contraction number = 3.603104e-01\n Vnewton: Using errtol_s: 194.192499\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.382365e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.061530e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.859364e+01\n Vprtstp: contraction number = 7.859364e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.061225e-05\n Vprtstp: contraction number = 3.642483e-01\n Vnewton: Using errtol_s: 70.734280\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.465810e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.210836e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.887021e+01\n Vprtstp: contraction number = 2.887021e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.571604e-06\n Vprtstp: contraction number = 3.673351e-01\n Vnewton: Using errtol_s: 25.983185\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.547712e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.358579e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.070116e+01\n Vprtstp: contraction number = 1.070116e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.806524e-06\n Vprtstp: contraction number = 3.706644e-01\n Vnewton: Using errtol_s: 9.631041\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.630701e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.513597e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.050515e+00\n Vprtstp: contraction number = 4.050515e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.062302e-06\n Vprtstp: contraction number = 3.785119e-01\n Vnewton: Using errtol_s: 3.645463\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.712383e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.673352e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.586893e+00\n Vprtstp: contraction number = 1.586893e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 4.161843e-07\n Vprtstp: contraction number = 3.917757e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.030168e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.055219e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.745749e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.774359e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -3912,15 +3912,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.504366495741E-01 kT\n Vpmg_energy:  qfEnergy = 1.061382616797E+04 kT\n Vpmg_energy:  dielEnergy = 5.339258776858E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.455100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.467400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -3943,272 +3943,272 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.417046\n+Vacc_SASA: Time elapsed: 1.392069\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.613753e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.693912e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.896400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.053700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.285140e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.402480e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.975858e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.007901e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.001010e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.037604e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.113974e+05\n Vprtstp: contraction number = 2.113974e+05\n Vnewton: Attempting damping, relres = 0.047573\n Vnewton: Attempting damping, relres = 0.515375\n Vnewton: Damping accepted, relres = 0.047573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.757263e-02\n Vprtstp: contraction number = 4.757263e-02\n Vnewton: Using errtol_s: 203448.048803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.084918e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.176014e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.589098e+04\n Vprtstp: contraction number = 4.589098e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.811582e-03\n Vprtstp: contraction number = 2.062443e-01\n Vnewton: Using errtol_s: 41959.996661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.155553e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.294740e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404662e+04\n Vprtstp: contraction number = 1.404662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.960291e-03\n Vprtstp: contraction number = 3.017139e-01\n Vnewton: Using errtol_s: 12659.913691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.224123e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.400630e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.279840e+03\n Vprtstp: contraction number = 5.279840e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111524e-03\n Vprtstp: contraction number = 3.754781e-01\n Vnewton: Using errtol_s: 4753.520446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.291284e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.520739e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.336921e+03\n Vprtstp: contraction number = 2.336921e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.918609e-04\n Vprtstp: contraction number = 4.425102e-01\n Vnewton: Using errtol_s: 2103.481419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.358221e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.646164e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194576e+03\n Vprtstp: contraction number = 1.194576e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.514070e-04\n Vprtstp: contraction number = 5.111344e-01\n Vnewton: Using errtol_s: 1075.161658\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.424744e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.774967e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.792983e+02\n Vprtstp: contraction number = 6.792983e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.429594e-04\n Vprtstp: contraction number = 5.686374e-01\n Vnewton: Using errtol_s: 611.377148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.492676e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.912151e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.154648e+02\n Vprtstp: contraction number = 4.154648e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.743449e-05\n Vprtstp: contraction number = 6.116036e-01\n Vnewton: Using errtol_s: 373.920435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.562936e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.039433e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660684e+02\n Vprtstp: contraction number = 2.660684e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.599388e-05\n Vprtstp: contraction number = 6.404095e-01\n Vnewton: Using errtol_s: 239.462182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.631182e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.167471e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755593e+02\n Vprtstp: contraction number = 1.755593e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.694626e-05\n Vprtstp: contraction number = 6.598268e-01\n Vnewton: Using errtol_s: 158.003576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.698701e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.288202e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183176e+02\n Vprtstp: contraction number = 1.183176e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.489979e-05\n Vprtstp: contraction number = 6.739462e-01\n Vnewton: Using errtol_s: 106.485913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.768911e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.409249e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.102710e+01\n Vprtstp: contraction number = 8.102710e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705205e-05\n Vprtstp: contraction number = 6.848271e-01\n Vnewton: Using errtol_s: 72.924443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.837790e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.524727e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.628393e+01\n Vprtstp: contraction number = 5.628393e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.184488e-05\n Vprtstp: contraction number = 6.946308e-01\n Vnewton: Using errtol_s: 50.655566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.908181e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.640403e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955755e+01\n Vprtstp: contraction number = 3.955755e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.324836e-06\n Vprtstp: contraction number = 7.028213e-01\n Vnewton: Using errtol_s: 35.601810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.975807e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.743705e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.808103e+01\n Vprtstp: contraction number = 2.808103e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.909617e-06\n Vprtstp: contraction number = 7.098779e-01\n Vnewton: Using errtol_s: 25.272937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.043263e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.836960e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.010039e+01\n Vprtstp: contraction number = 2.010039e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 4.230100e-06\n Vprtstp: contraction number = 7.157995e-01\n Vnewton: Using errtol_s: 18.090355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.111551e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.934833e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.449222e+01\n Vprtstp: contraction number = 1.449222e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 3.049867e-06\n Vprtstp: contraction number = 7.209918e-01\n Vnewton: Using errtol_s: 13.042997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.181209e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.034643e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051084e+01\n Vprtstp: contraction number = 1.051084e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 2.211992e-06\n Vprtstp: contraction number = 7.252749e-01\n Vnewton: Using errtol_s: 9.459758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.248474e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.150337e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.663626e+00\n Vprtstp: contraction number = 7.663626e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.612800e-06\n Vprtstp: contraction number = 7.291164e-01\n Vnewton: Using errtol_s: 6.897264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.317141e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.279849e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.612195e+00\n Vprtstp: contraction number = 5.612195e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 1.181079e-06\n Vprtstp: contraction number = 7.323158e-01\n Vnewton: Using errtol_s: 5.050976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.383861e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.415849e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.124624e+00\n Vprtstp: contraction number = 4.124624e+00\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 8.680215e-07\n Vprtstp: contraction number = 7.349396e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.464831e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.491503e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.502029e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.529430e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -4217,15 +4217,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.521116242377E-01 kT\n Vpmg_energy:  qfEnergy = 2.321247419853E+03 kT\n Vpmg_energy:  dielEnergy = 1.153524159473E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.091000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.614500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -4273,193 +4273,193 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0717623 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.375871\n+Vacc_SASA: Time elapsed: 1.379317\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.761312e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.866866e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.025300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.519700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.339750e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.217370e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.644456e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.725508e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3863048.260999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.666460e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.751266e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.079329e+05\n Vprtstp: contraction number = 4.079329e+05\n Vnewton: Attempting damping, relres = 0.096763\n Vnewton: Attempting damping, relres = 0.545251\n Vnewton: Damping accepted, relres = 0.096763\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.676296e-02\n Vprtstp: contraction number = 9.676296e-02\n Vnewton: Using errtol_s: 373799.984181\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.761682e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.865756e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.732785e+04\n Vprtstp: contraction number = 7.732785e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.807372e-02\n Vprtstp: contraction number = 1.867834e-01\n Vnewton: Using errtol_s: 69819.644697\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.843566e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.975430e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.985652e+04\n Vprtstp: contraction number = 1.985652e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.627077e-03\n Vprtstp: contraction number = 2.560113e-01\n Vnewton: Using errtol_s: 17874.621452\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.927348e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.115301e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.114622e+03\n Vprtstp: contraction number = 6.114622e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.424617e-03\n Vprtstp: contraction number = 3.078870e-01\n Vnewton: Using errtol_s: 5503.364448\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.012015e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.267210e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.092890e+03\n Vprtstp: contraction number = 2.092890e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.875987e-04\n Vprtstp: contraction number = 3.422665e-01\n Vnewton: Using errtol_s: 1883.617345\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.097857e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.427572e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.574998e+02\n Vprtstp: contraction number = 7.574998e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.764801e-04\n Vprtstp: contraction number = 3.619372e-01\n Vnewton: Using errtol_s: 681.751152\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.183852e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.573976e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.922283e+02\n Vprtstp: contraction number = 2.922283e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 6.808241e-05\n Vprtstp: contraction number = 3.857795e-01\n Vnewton: Using errtol_s: 263.005621\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.269557e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.708703e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.230857e+02\n Vprtstp: contraction number = 1.230857e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.867611e-05\n Vprtstp: contraction number = 4.211970e-01\n Vnewton: Using errtol_s: 110.777182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.356058e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.845457e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.644162e+01\n Vprtstp: contraction number = 5.644162e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.314958e-05\n Vprtstp: contraction number = 4.585554e-01\n Vnewton: Using errtol_s: 50.797474\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.444434e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.964105e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.814912e+01\n Vprtstp: contraction number = 2.814912e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.558089e-06\n Vprtstp: contraction number = 4.987298e-01\n Vnewton: Using errtol_s: 25.334216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.529495e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.124998e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.477957e+01\n Vprtstp: contraction number = 1.477957e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.443295e-06\n Vprtstp: contraction number = 5.250454e-01\n Vnewton: Using errtol_s: 13.301614\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.612133e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.276122e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.444333e+00\n Vprtstp: contraction number = 8.444333e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.967333e-06\n Vprtstp: contraction number = 5.713519e-01\n Vnewton: Using errtol_s: 7.599902\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.694432e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.435462e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.056221e+00\n Vprtstp: contraction number = 5.056221e+00\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.177982e-06\n Vprtstp: contraction number = 5.987712e-01\n Vnewton: Using errtol_s: 4.550602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.778584e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.584215e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.242153e+00\n Vprtstp: contraction number = 3.242153e+00\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.553462e-07\n Vprtstp: contraction number = 6.412203e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.205122e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.231553e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.958959e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.984926e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -4468,15 +4468,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.357803717027E-01 kT\n Vpmg_energy:  qfEnergy = 1.843358669820E+04 kT\n Vpmg_energy:  dielEnergy = 9.205606713262E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.540600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.537700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -4499,261 +4499,261 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.995452\n+Vacc_SASA: Time elapsed: 3.003035\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.257405e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.481966e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.351900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.049600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.310500e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.487130e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.203378e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.063796e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.228238e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.097239e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.298565e+05\n Vprtstp: contraction number = 4.298565e+05\n Vnewton: Attempting damping, relres = 0.048079\n Vnewton: Attempting damping, relres = 0.515481\n Vnewton: Damping accepted, relres = 0.048079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.807904e-02\n Vprtstp: contraction number = 4.807904e-02\n Vnewton: Using errtol_s: 418259.137179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.320779e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.271470e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.275297e+04\n Vprtstp: contraction number = 9.275297e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.791706e-03\n Vprtstp: contraction number = 2.036585e-01\n Vnewton: Using errtol_s: 85182.030508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.395352e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.406121e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.830324e+04\n Vprtstp: contraction number = 2.830324e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.931540e-03\n Vprtstp: contraction number = 2.993901e-01\n Vnewton: Using errtol_s: 25502.653903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.469458e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.518868e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066383e+04\n Vprtstp: contraction number = 1.066383e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.103407e-03\n Vprtstp: contraction number = 3.763916e-01\n Vnewton: Using errtol_s: 9598.985602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.546640e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.567642e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725476e+03\n Vprtstp: contraction number = 4.725476e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.889004e-04\n Vprtstp: contraction number = 4.430826e-01\n Vnewton: Using errtol_s: 4253.143226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.619783e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.619784e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402868e+03\n Vprtstp: contraction number = 2.402868e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.485940e-04\n Vprtstp: contraction number = 5.084757e-01\n Vnewton: Using errtol_s: 2162.620089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.694042e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.678905e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352802e+03\n Vprtstp: contraction number = 1.352802e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.399556e-04\n Vprtstp: contraction number = 5.629888e-01\n Vnewton: Using errtol_s: 1217.530795\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.767702e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.776101e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164880e+02\n Vprtstp: contraction number = 8.164880e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.447037e-05\n Vprtstp: contraction number = 6.035512e-01\n Vnewton: Using errtol_s: 734.842122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.841079e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.920124e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157033e+02\n Vprtstp: contraction number = 5.157033e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.335238e-05\n Vprtstp: contraction number = 6.316106e-01\n Vnewton: Using errtol_s: 464.134076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.913451e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.002716e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352095e+02\n Vprtstp: contraction number = 3.352095e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.467926e-05\n Vprtstp: contraction number = 6.500040e-01\n Vnewton: Using errtol_s: 301.688999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.985385e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.014600e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.222234e+02\n Vprtstp: contraction number = 2.222234e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.299022e-05\n Vprtstp: contraction number = 6.629387e-01\n Vnewton: Using errtol_s: 200.001301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.057381e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.024603e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.495221e+02\n Vprtstp: contraction number = 1.495221e+02\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.546887e-05\n Vprtstp: contraction number = 6.728456e-01\n Vnewton: Using errtol_s: 134.569993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.131087e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.036143e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018836e+02\n Vprtstp: contraction number = 1.018836e+02\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.054041e-05\n Vprtstp: contraction number = 6.813949e-01\n Vnewton: Using errtol_s: 91.695311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.203282e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.047865e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.012825e+01\n Vprtstp: contraction number = 7.012825e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.255144e-06\n Vprtstp: contraction number = 6.883171e-01\n Vnewton: Using errtol_s: 63.115450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.275869e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.058831e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.869976e+01\n Vprtstp: contraction number = 4.869976e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.038252e-06\n Vprtstp: contraction number = 6.944386e-01\n Vnewton: Using errtol_s: 43.829803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.350656e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.070444e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.408035e+01\n Vprtstp: contraction number = 3.408035e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 3.525795e-06\n Vprtstp: contraction number = 6.998052e-01\n Vnewton: Using errtol_s: 30.672326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.423323e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.081441e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401453e+01\n Vprtstp: contraction number = 2.401453e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 2.484432e-06\n Vprtstp: contraction number = 7.046444e-01\n Vnewton: Using errtol_s: 21.613084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.497279e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.091441e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.702723e+01\n Vprtstp: contraction number = 1.702723e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.761558e-06\n Vprtstp: contraction number = 7.090385e-01\n Vnewton: Using errtol_s: 15.324508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.570818e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.105074e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214065e+01\n Vprtstp: contraction number = 1.214065e+01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.256015e-06\n Vprtstp: contraction number = 7.130137e-01\n Vnewton: Using errtol_s: 10.926584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.643198e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.116223e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.699962e+00\n Vprtstp: contraction number = 8.699962e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 9.000575e-07\n Vprtstp: contraction number = 7.165978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.502409e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.528480e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.183327e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.211099e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -4762,15 +4762,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.970329890600E+00 kT\n Vpmg_energy:  qfEnergy = 3.499206035649E+03 kT\n Vpmg_energy:  dielEnergy = 1.787861710155E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.308000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.298000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -4818,182 +4818,182 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0806184 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.006398\n+Vacc_SASA: Time elapsed: 3.009847\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.413318e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.776122e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.996200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.863600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.996700e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.456800e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.071276e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.165405e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7257742.969900\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.087317e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.168289e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.332655e+05\n Vprtstp: contraction number = 7.332655e+05\n Vnewton: Attempting damping, relres = 0.092954\n Vnewton: Attempting damping, relres = 0.543087\n Vnewton: Damping accepted, relres = 0.092954\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.295377e-02\n Vprtstp: contraction number = 9.295377e-02\n Vnewton: Using errtol_s: 674634.557796\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.180831e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.176559e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.375383e+05\n Vprtstp: contraction number = 1.375383e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.716852e-02\n Vprtstp: contraction number = 1.846995e-01\n Vnewton: Using errtol_s: 124604.673279\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.263616e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.183870e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.550512e+04\n Vprtstp: contraction number = 3.550512e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.404594e-03\n Vprtstp: contraction number = 2.565507e-01\n Vnewton: Using errtol_s: 31967.413641\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.348603e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.198562e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.099641e+04\n Vprtstp: contraction number = 1.099641e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.363650e-03\n Vprtstp: contraction number = 3.095972e-01\n Vnewton: Using errtol_s: 9897.022727\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.432254e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.212804e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.730401e+03\n Vprtstp: contraction number = 3.730401e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.625937e-04\n Vprtstp: contraction number = 3.392320e-01\n Vnewton: Using errtol_s: 3357.386399\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.518797e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.228397e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.301607e+03\n Vprtstp: contraction number = 1.301607e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.614068e-04\n Vprtstp: contraction number = 3.489169e-01\n Vnewton: Using errtol_s: 1171.448936\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.599942e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.239105e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.645153e+02\n Vprtstp: contraction number = 4.645153e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.760250e-05\n Vprtstp: contraction number = 3.568778e-01\n Vnewton: Using errtol_s: 418.064161\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.684323e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.251058e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.772219e+02\n Vprtstp: contraction number = 1.772219e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.197650e-05\n Vprtstp: contraction number = 3.815199e-01\n Vnewton: Using errtol_s: 159.499808\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.765883e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.261738e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.471028e+01\n Vprtstp: contraction number = 7.471028e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 9.264488e-06\n Vprtstp: contraction number = 4.215634e-01\n Vnewton: Using errtol_s: 67.239276\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.849196e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.274137e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.443502e+01\n Vprtstp: contraction number = 3.443502e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 4.270137e-06\n Vprtstp: contraction number = 4.609145e-01\n Vnewton: Using errtol_s: 30.991559\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.934861e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.288943e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.720700e+01\n Vprtstp: contraction number = 1.720700e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.133763e-06\n Vprtstp: contraction number = 4.996942e-01\n Vnewton: Using errtol_s: 15.486302\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.017364e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.302914e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.259710e+00\n Vprtstp: contraction number = 9.259710e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.148258e-06\n Vprtstp: contraction number = 5.381377e-01\n Vnewton: Using errtol_s: 8.333763\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.103762e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.314957e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.358358e+00\n Vprtstp: contraction number = 5.358358e+00\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 6.644658e-07\n Vprtstp: contraction number = 5.786728e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.105657e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.128536e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.583039e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.611134e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -5002,27 +5002,27 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.140245135923E+00 kT\n Vpmg_energy:  qfEnergy = 2.905500135129E+04 kT\n Vpmg_energy:  dielEnergy = 1.454863366121E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.382100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.281300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.204434e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.326819e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:23:28 2025\n+# Creation Date and Time:  Sun Jan  7 09:37:35 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -5375,250 +5375,250 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.360211\n+Vacc_SASA: Time elapsed: 1.380275\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.539150e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.639015e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.032100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.026400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.162370e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.387940e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.922404e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.019891e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.115829e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.338870e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.136321e+05\n Vprtstp: contraction number = 2.136321e+05\n Vnewton: Attempting damping, relres = 0.047663\n Vnewton: Attempting damping, relres = 0.515490\n Vnewton: Damping accepted, relres = 0.047663\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.766304e-02\n Vprtstp: contraction number = 4.766304e-02\n Vnewton: Using errtol_s: 204994.485638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.974174e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.678807e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.587025e+04\n Vprtstp: contraction number = 4.587025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.727679e-03\n Vprtstp: contraction number = 2.040927e-01\n Vnewton: Using errtol_s: 41837.880528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.662209e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.518805e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.391016e+04\n Vprtstp: contraction number = 1.391016e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.912173e-03\n Vprtstp: contraction number = 2.993697e-01\n Vnewton: Using errtol_s: 12524.995351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.390848e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.585183e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.237707e+03\n Vprtstp: contraction number = 5.237707e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.096054e-03\n Vprtstp: contraction number = 3.763697e-01\n Vnewton: Using errtol_s: 4714.028550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.117343e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.431653e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.331453e+03\n Vprtstp: contraction number = 2.331453e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.878779e-04\n Vprtstp: contraction number = 4.451223e-01\n Vnewton: Using errtol_s: 2098.319320\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.797808e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.744229e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189035e+03\n Vprtstp: contraction number = 1.189035e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.488161e-04\n Vprtstp: contraction number = 5.099966e-01\n Vnewton: Using errtol_s: 1070.135650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.506615e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.851721e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.678182e+02\n Vprtstp: contraction number = 6.678182e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.397467e-04\n Vprtstp: contraction number = 5.616468e-01\n Vnewton: Using errtol_s: 601.038216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.242900e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.011211e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.994733e+02\n Vprtstp: contraction number = 3.994733e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.359319e-05\n Vprtstp: contraction number = 5.981764e-01\n Vnewton: Using errtol_s: 359.526862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.976062e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.132411e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.488647e+02\n Vprtstp: contraction number = 2.488647e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.207703e-05\n Vprtstp: contraction number = 6.229817e-01\n Vnewton: Using errtol_s: 223.978670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.678423e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.251249e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.588671e+02\n Vprtstp: contraction number = 1.588671e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.324425e-05\n Vprtstp: contraction number = 6.383669e-01\n Vnewton: Using errtol_s: 142.980568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.370503e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.393046e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.030284e+02\n Vprtstp: contraction number = 1.030284e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.155954e-05\n Vprtstp: contraction number = 6.485194e-01\n Vnewton: Using errtol_s: 92.725673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.006139e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.530543e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.760657e+01\n Vprtstp: contraction number = 6.760657e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.414722e-05\n Vprtstp: contraction number = 6.561932e-01\n Vnewton: Using errtol_s: 60.845953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.076410e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.622057e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.480217e+01\n Vprtstp: contraction number = 4.480217e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.375216e-06\n Vprtstp: contraction number = 6.626894e-01\n Vnewton: Using errtol_s: 40.321969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.145208e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.708146e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990735e+01\n Vprtstp: contraction number = 2.990735e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 6.258355e-06\n Vprtstp: contraction number = 6.675424e-01\n Vnewton: Using errtol_s: 26.916626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.215089e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.755657e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.008505e+01\n Vprtstp: contraction number = 2.008505e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 4.202958e-06\n Vprtstp: contraction number = 6.715755e-01\n Vnewton: Using errtol_s: 18.076547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.283362e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.799177e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356100e+01\n Vprtstp: contraction number = 1.356100e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 2.837748e-06\n Vprtstp: contraction number = 6.751787e-01\n Vnewton: Using errtol_s: 12.204901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.351455e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.843620e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.198733e+00\n Vprtstp: contraction number = 9.198733e+00\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 1.924909e-06\n Vprtstp: contraction number = 6.783227e-01\n Vnewton: Using errtol_s: 8.278861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.422135e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.889423e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.265697e+00\n Vprtstp: contraction number = 6.265697e+00\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.311147e-06\n Vprtstp: contraction number = 6.811478e-01\n Vnewton: Using errtol_s: 5.639128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.490012e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.937200e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.284635e+00\n Vprtstp: contraction number = 4.284635e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 8.965941e-07\n Vprtstp: contraction number = 6.838241e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.357259e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.382095e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.771096e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.798481e+01\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -5627,17 +5627,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.939690296929E-01 kT\n Vpmg_energy:  qfEnergy = 9.376673747482E+03 kT\n Vpmg_energy:  dielEnergy = 4.692177592704E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.510000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.976000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -5683,171 +5683,171 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0275394 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.375078\n+Vacc_SASA: Time elapsed: 1.365809\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.853062e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.061586e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.533700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.119500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.307210e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.981250e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.762858e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.204470e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 6495765.822087\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.788150e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.220133e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.362765e+05\n Vprtstp: contraction number = 6.362765e+05\n Vnewton: Attempting damping, relres = 0.088746\n Vnewton: Attempting damping, relres = 0.541895\n Vnewton: Damping accepted, relres = 0.088746\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.874646e-02\n Vprtstp: contraction number = 8.874646e-02\n Vnewton: Using errtol_s: 576476.204773\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.892067e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.313589e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.170231e+05\n Vprtstp: contraction number = 1.170231e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.623146e-02\n Vprtstp: contraction number = 1.828970e-01\n Vnewton: Using errtol_s: 105435.741217\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.977542e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.392847e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.955662e+04\n Vprtstp: contraction number = 2.955662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.095304e-03\n Vprtstp: contraction number = 2.523066e-01\n Vnewton: Using errtol_s: 26602.134295\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.065746e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.495616e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.995691e+03\n Vprtstp: contraction number = 8.995691e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.246378e-03\n Vprtstp: contraction number = 3.043434e-01\n Vnewton: Using errtol_s: 8096.182717\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.156951e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.599278e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.013650e+03\n Vprtstp: contraction number = 3.013650e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.175484e-04\n Vprtstp: contraction number = 3.350093e-01\n Vnewton: Using errtol_s: 2712.296685\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.254038e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.673756e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.048604e+03\n Vprtstp: contraction number = 1.048604e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.452864e-04\n Vprtstp: contraction number = 3.479510e-01\n Vnewton: Using errtol_s: 943.746446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.349136e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.791038e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.603662e+02\n Vprtstp: contraction number = 3.603662e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.992953e-05\n Vprtstp: contraction number = 3.436628e-01\n Vnewton: Using errtol_s: 324.330531\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.442999e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.861219e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.297355e+02\n Vprtstp: contraction number = 1.297355e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.797512e-05\n Vprtstp: contraction number = 3.600099e-01\n Vnewton: Using errtol_s: 116.762190\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.535099e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.007612e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.314764e+01\n Vprtstp: contraction number = 5.314764e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.363712e-06\n Vprtstp: contraction number = 4.096613e-01\n Vnewton: Using errtol_s: 47.832946\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.628761e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.124511e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.432172e+01\n Vprtstp: contraction number = 2.432172e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.369821e-06\n Vprtstp: contraction number = 4.576253e-01\n Vnewton: Using errtol_s: 21.889567\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.721211e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.244906e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.198142e+01\n Vprtstp: contraction number = 1.198142e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.660048e-06\n Vprtstp: contraction number = 4.926220e-01\n Vnewton: Using errtol_s: 10.783282\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.814981e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.399343e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.178209e+00\n Vprtstp: contraction number = 6.178209e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 8.560021e-07\n Vprtstp: contraction number = 5.156491e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.136198e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.162963e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.326533e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.350577e+01\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -5856,15 +5856,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.071195296219E-01 kT\n Vpmg_energy:  qfEnergy = 7.513083652575E+04 kT\n Vpmg_energy:  dielEnergy = 3.773034407889E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.450500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.335200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -5887,272 +5887,272 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.396654\n+Vacc_SASA: Time elapsed: 1.411234\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.637258e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.705134e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.139600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.073600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.540960e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.340300e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.095292e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.731504e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.126447e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.759458e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.113974e+05\n Vprtstp: contraction number = 2.113974e+05\n Vnewton: Attempting damping, relres = 0.047573\n Vnewton: Attempting damping, relres = 0.515375\n Vnewton: Damping accepted, relres = 0.047573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.757263e-02\n Vprtstp: contraction number = 4.757263e-02\n Vnewton: Using errtol_s: 203448.048803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.238937e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.873057e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.589098e+04\n Vprtstp: contraction number = 4.589098e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.811582e-03\n Vprtstp: contraction number = 2.062443e-01\n Vnewton: Using errtol_s: 41959.996661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.334228e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.969327e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404662e+04\n Vprtstp: contraction number = 1.404662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.960291e-03\n Vprtstp: contraction number = 3.017139e-01\n Vnewton: Using errtol_s: 12659.913691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.426686e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.093833e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.279840e+03\n Vprtstp: contraction number = 5.279840e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111524e-03\n Vprtstp: contraction number = 3.754781e-01\n Vnewton: Using errtol_s: 4753.520446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.510320e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.209202e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.336921e+03\n Vprtstp: contraction number = 2.336921e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.918609e-04\n Vprtstp: contraction number = 4.425102e-01\n Vnewton: Using errtol_s: 2103.481419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.596563e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.330151e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194576e+03\n Vprtstp: contraction number = 1.194576e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.514070e-04\n Vprtstp: contraction number = 5.111344e-01\n Vnewton: Using errtol_s: 1075.161658\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.677158e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.456489e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.792983e+02\n Vprtstp: contraction number = 6.792983e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.429594e-04\n Vprtstp: contraction number = 5.686374e-01\n Vnewton: Using errtol_s: 611.377148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.759367e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.587504e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.154648e+02\n Vprtstp: contraction number = 4.154648e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.743449e-05\n Vprtstp: contraction number = 6.116036e-01\n Vnewton: Using errtol_s: 373.920435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.841576e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.714162e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660684e+02\n Vprtstp: contraction number = 2.660684e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.599388e-05\n Vprtstp: contraction number = 6.404095e-01\n Vnewton: Using errtol_s: 239.462182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.923156e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.845314e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755593e+02\n Vprtstp: contraction number = 1.755593e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.694626e-05\n Vprtstp: contraction number = 6.598268e-01\n Vnewton: Using errtol_s: 158.003576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.007512e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.955966e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183176e+02\n Vprtstp: contraction number = 1.183176e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.489979e-05\n Vprtstp: contraction number = 6.739462e-01\n Vnewton: Using errtol_s: 106.485913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.086293e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.034322e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.102710e+01\n Vprtstp: contraction number = 8.102710e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705205e-05\n Vprtstp: contraction number = 6.848271e-01\n Vnewton: Using errtol_s: 72.924443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.167963e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.102614e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.628393e+01\n Vprtstp: contraction number = 5.628393e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.184488e-05\n Vprtstp: contraction number = 6.946308e-01\n Vnewton: Using errtol_s: 50.655566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.249807e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.206886e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955755e+01\n Vprtstp: contraction number = 3.955755e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.324836e-06\n Vprtstp: contraction number = 7.028213e-01\n Vnewton: Using errtol_s: 35.601810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.325615e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.324825e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.808103e+01\n Vprtstp: contraction number = 2.808103e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.909617e-06\n Vprtstp: contraction number = 7.098779e-01\n Vnewton: Using errtol_s: 25.272937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.404419e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.420498e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.010039e+01\n Vprtstp: contraction number = 2.010039e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 4.230100e-06\n Vprtstp: contraction number = 7.157995e-01\n Vnewton: Using errtol_s: 18.090355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.483548e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.530622e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.449222e+01\n Vprtstp: contraction number = 1.449222e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 3.049867e-06\n Vprtstp: contraction number = 7.209918e-01\n Vnewton: Using errtol_s: 13.042997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.565586e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.612785e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051084e+01\n Vprtstp: contraction number = 1.051084e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 2.211992e-06\n Vprtstp: contraction number = 7.252749e-01\n Vnewton: Using errtol_s: 9.459758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.647449e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.733184e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.663626e+00\n Vprtstp: contraction number = 7.663626e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.612800e-06\n Vprtstp: contraction number = 7.291164e-01\n Vnewton: Using errtol_s: 6.897264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.725759e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.815229e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.612195e+00\n Vprtstp: contraction number = 5.612195e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 1.181079e-06\n Vprtstp: contraction number = 7.323158e-01\n Vnewton: Using errtol_s: 5.050976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.805465e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.952822e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.124624e+00\n Vprtstp: contraction number = 4.124624e+00\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 8.680215e-07\n Vprtstp: contraction number = 7.349396e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.775798e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.806431e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.328837e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.355863e+01\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -6161,17 +6161,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.529259077785E-03 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 3.922111986755E-02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.051000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.494900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -6217,149 +6217,149 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00111303 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.377058\n+Vacc_SASA: Time elapsed: 1.436490\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.606683e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.721727e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.960500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.055800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.300000e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.199630e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.059136e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.261256e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 659220.576503\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.082838e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.289452e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.405229e+04\n Vprtstp: contraction number = 7.405229e+04\n Vnewton: Attempting damping, relres = 0.101194\n Vnewton: Attempting damping, relres = 0.547249\n Vnewton: Damping accepted, relres = 0.101194\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011936e-01\n Vprtstp: contraction number = 1.011936e-01\n Vnewton: Using errtol_s: 66708.882844\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.179163e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.430789e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.227539e+04\n Vprtstp: contraction number = 1.227539e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.676045e-02\n Vprtstp: contraction number = 1.656277e-01\n Vnewton: Using errtol_s: 11048.836228\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.275708e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.555937e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.508807e+03\n Vprtstp: contraction number = 2.508807e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.425225e-03\n Vprtstp: contraction number = 2.043635e-01\n Vnewton: Using errtol_s: 2257.978588\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.362796e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.642869e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.967621e+02\n Vprtstp: contraction number = 5.967621e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 8.147347e-04\n Vprtstp: contraction number = 2.378632e-01\n Vnewton: Using errtol_s: 537.089910\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.439879e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.757506e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.589401e+02\n Vprtstp: contraction number = 1.589401e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 2.169933e-04\n Vprtstp: contraction number = 2.663361e-01\n Vnewton: Using errtol_s: 143.046443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.511851e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.846900e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.567685e+01\n Vprtstp: contraction number = 4.567685e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 6.236027e-05\n Vprtstp: contraction number = 2.873834e-01\n Vnewton: Using errtol_s: 41.109175\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.592746e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.932651e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.380678e+01\n Vprtstp: contraction number = 1.380678e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.884969e-05\n Vprtstp: contraction number = 3.022708e-01\n Vnewton: Using errtol_s: 12.426102\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.671592e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.057000e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.334509e+00\n Vprtstp: contraction number = 4.334509e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.917683e-06\n Vprtstp: contraction number = 3.139406e-01\n Vnewton: Using errtol_s: 3.901058\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.748880e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.144406e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.401869e+00\n Vprtstp: contraction number = 1.401869e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.913900e-06\n Vprtstp: contraction number = 3.234205e-01\n Vnewton: Using errtol_s: 1.261682\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.827581e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.220425e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.640279e-01\n Vprtstp: contraction number = 4.640279e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.335135e-07\n Vprtstp: contraction number = 3.310066e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.369226e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.631126e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.054560e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.080475e+01\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -6368,17 +6368,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.627786122684E-03 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 3.231910516623E-02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.456800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.473900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -6399,261 +6399,261 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.999878\n+Vacc_SASA: Time elapsed: 2.999591\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.382318e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.473971e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.968900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.919700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.142840e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.398360e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.261503e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.694095e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.282885e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.730367e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.298565e+05\n Vprtstp: contraction number = 4.298565e+05\n Vnewton: Attempting damping, relres = 0.048079\n Vnewton: Attempting damping, relres = 0.515481\n Vnewton: Damping accepted, relres = 0.048079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.807904e-02\n Vprtstp: contraction number = 4.807904e-02\n Vnewton: Using errtol_s: 418259.137179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.385989e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.886074e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.275297e+04\n Vprtstp: contraction number = 9.275297e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.791706e-03\n Vprtstp: contraction number = 2.036585e-01\n Vnewton: Using errtol_s: 85182.030508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.464184e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.020736e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.830324e+04\n Vprtstp: contraction number = 2.830324e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.931540e-03\n Vprtstp: contraction number = 2.993901e-01\n Vnewton: Using errtol_s: 25502.653903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.545654e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.162262e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066383e+04\n Vprtstp: contraction number = 1.066383e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.103407e-03\n Vprtstp: contraction number = 3.763916e-01\n Vnewton: Using errtol_s: 9598.985602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.621698e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.299590e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725476e+03\n Vprtstp: contraction number = 4.725476e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.889004e-04\n Vprtstp: contraction number = 4.430826e-01\n Vnewton: Using errtol_s: 4253.143226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.703500e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.381565e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402868e+03\n Vprtstp: contraction number = 2.402868e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.485940e-04\n Vprtstp: contraction number = 5.084757e-01\n Vnewton: Using errtol_s: 2162.620089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.788596e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.505862e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352802e+03\n Vprtstp: contraction number = 1.352802e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.399556e-04\n Vprtstp: contraction number = 5.629888e-01\n Vnewton: Using errtol_s: 1217.530795\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.875902e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.575946e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164880e+02\n Vprtstp: contraction number = 8.164880e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.447037e-05\n Vprtstp: contraction number = 6.035512e-01\n Vnewton: Using errtol_s: 734.842122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.959901e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.650489e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157033e+02\n Vprtstp: contraction number = 5.157033e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.335238e-05\n Vprtstp: contraction number = 6.316106e-01\n Vnewton: Using errtol_s: 464.134076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.046395e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.751171e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352095e+02\n Vprtstp: contraction number = 3.352095e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.467926e-05\n Vprtstp: contraction number = 6.500040e-01\n Vnewton: Using errtol_s: 301.688999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.131740e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.887405e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.222234e+02\n Vprtstp: contraction number = 2.222234e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.299022e-05\n Vprtstp: contraction number = 6.629387e-01\n Vnewton: Using errtol_s: 200.001301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.217692e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.023637e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.495221e+02\n Vprtstp: contraction number = 1.495221e+02\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.546887e-05\n Vprtstp: contraction number = 6.728456e-01\n Vnewton: Using errtol_s: 134.569993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.304772e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.128848e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018836e+02\n Vprtstp: contraction number = 1.018836e+02\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.054041e-05\n Vprtstp: contraction number = 6.813949e-01\n Vnewton: Using errtol_s: 91.695311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.387921e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.251868e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.012825e+01\n Vprtstp: contraction number = 7.012825e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.255144e-06\n Vprtstp: contraction number = 6.883171e-01\n Vnewton: Using errtol_s: 63.115450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.469791e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.383317e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.869976e+01\n Vprtstp: contraction number = 4.869976e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.038252e-06\n Vprtstp: contraction number = 6.944386e-01\n Vnewton: Using errtol_s: 43.829803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.556827e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.484657e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.408035e+01\n Vprtstp: contraction number = 3.408035e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 3.525795e-06\n Vprtstp: contraction number = 6.998052e-01\n Vnewton: Using errtol_s: 30.672326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.643758e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.567874e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401453e+01\n Vprtstp: contraction number = 2.401453e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 2.484432e-06\n Vprtstp: contraction number = 7.046444e-01\n Vnewton: Using errtol_s: 21.613084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.728647e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.650766e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.702723e+01\n Vprtstp: contraction number = 1.702723e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.761558e-06\n Vprtstp: contraction number = 7.090385e-01\n Vnewton: Using errtol_s: 15.324508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.807212e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.791389e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214065e+01\n Vprtstp: contraction number = 1.214065e+01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.256015e-06\n Vprtstp: contraction number = 7.130137e-01\n Vnewton: Using errtol_s: 10.926584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.892528e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.921470e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.699962e+00\n Vprtstp: contraction number = 8.699962e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 9.000575e-07\n Vprtstp: contraction number = 7.165978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.701714e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.725655e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.351116e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.377522e+01\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -6662,15 +6662,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.345658970657E-01 kT\n Vpmg_energy:  qfEnergy = 9.376279132276E+03 kT\n Vpmg_energy:  dielEnergy = 4.692311982408E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.149000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.544700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -6718,171 +6718,171 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0322419 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.014749\n+Vacc_SASA: Time elapsed: 3.062214\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.575312e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.785392e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.972700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.020800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.324980e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.053500e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.348347e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.044965e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7084866.598925\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.372814e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.047601e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.984768e+05\n Vprtstp: contraction number = 6.984768e+05\n Vnewton: Attempting damping, relres = 0.089369\n Vnewton: Attempting damping, relres = 0.542089\n Vnewton: Damping accepted, relres = 0.089369\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.936880e-02\n Vprtstp: contraction number = 8.936880e-02\n Vnewton: Using errtol_s: 633166.041219\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.481143e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.061596e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.273163e+05\n Vprtstp: contraction number = 1.273163e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.619364e-02\n Vprtstp: contraction number = 1.812001e-01\n Vnewton: Using errtol_s: 114729.758442\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.567330e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.076127e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.151737e+04\n Vprtstp: contraction number = 3.151737e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.003932e-03\n Vprtstp: contraction number = 2.472534e-01\n Vnewton: Using errtol_s: 28367.322157\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.652313e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.089155e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.393741e+03\n Vprtstp: contraction number = 9.393741e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.193311e-03\n Vprtstp: contraction number = 2.980349e-01\n Vnewton: Using errtol_s: 8454.451884\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.740017e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.105867e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.092776e+03\n Vprtstp: contraction number = 3.092776e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.928814e-04\n Vprtstp: contraction number = 3.292363e-01\n Vnewton: Using errtol_s: 2783.512220\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.829414e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.116333e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.061371e+03\n Vprtstp: contraction number = 1.061371e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.348278e-04\n Vprtstp: contraction number = 3.431770e-01\n Vnewton: Using errtol_s: 955.237298\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.919131e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.131779e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.607964e+02\n Vprtstp: contraction number = 3.607964e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.583260e-05\n Vprtstp: contraction number = 3.399342e-01\n Vnewton: Using errtol_s: 324.717847\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.010241e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.141362e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.293597e+02\n Vprtstp: contraction number = 1.293597e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.643277e-05\n Vprtstp: contraction number = 3.585389e-01\n Vnewton: Using errtol_s: 116.423976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.103338e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.154722e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.299042e+01\n Vprtstp: contraction number = 5.299042e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 6.731454e-06\n Vprtstp: contraction number = 4.096360e-01\n Vnewton: Using errtol_s: 47.691450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.192527e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.170008e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.428459e+01\n Vprtstp: contraction number = 2.428459e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.084907e-06\n Vprtstp: contraction number = 4.582824e-01\n Vnewton: Using errtol_s: 21.856153\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.273559e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.185075e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.197548e+01\n Vprtstp: contraction number = 1.197548e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.521262e-06\n Vprtstp: contraction number = 4.931307e-01\n Vnewton: Using errtol_s: 10.777941\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.364150e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.195346e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.181341e+00\n Vprtstp: contraction number = 6.181341e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.852242e-07\n Vprtstp: contraction number = 5.161662e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.092373e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.118754e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.618777e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.641910e+01\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -6891,27 +6891,27 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.664866970310E-01 kT\n Vpmg_energy:  qfEnergy = 7.513063949705E+04 kT\n Vpmg_energy:  dielEnergy = 3.773048802351E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.661000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.013200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.467936e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.209720e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:24:11 2025\n+# Creation Date and Time:  Sun Jan  7 09:38:08 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -7264,250 +7264,250 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.414547\n+Vacc_SASA: Time elapsed: 1.377239\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.612129e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.645547e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.348600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.011300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.209750e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.346010e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.980696e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.032011e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.242270e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.369764e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.136321e+05\n Vprtstp: contraction number = 2.136321e+05\n Vnewton: Attempting damping, relres = 0.047663\n Vnewton: Attempting damping, relres = 0.515490\n Vnewton: Damping accepted, relres = 0.047663\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.766304e-02\n Vprtstp: contraction number = 4.766304e-02\n Vnewton: Using errtol_s: 204994.485638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.236256e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.731765e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.587025e+04\n Vprtstp: contraction number = 4.587025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.727679e-03\n Vprtstp: contraction number = 2.040927e-01\n Vnewton: Using errtol_s: 41837.880528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.043060e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.837773e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.391016e+04\n Vprtstp: contraction number = 1.391016e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.912173e-03\n Vprtstp: contraction number = 2.993697e-01\n Vnewton: Using errtol_s: 12524.995351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.907953e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.146225e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.237707e+03\n Vprtstp: contraction number = 5.237707e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.096054e-03\n Vprtstp: contraction number = 3.763697e-01\n Vnewton: Using errtol_s: 4714.028550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.699622e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.520471e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.331453e+03\n Vprtstp: contraction number = 2.331453e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.878779e-04\n Vprtstp: contraction number = 4.451223e-01\n Vnewton: Using errtol_s: 2098.319320\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.520983e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.748881e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189035e+03\n Vprtstp: contraction number = 1.189035e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.488161e-04\n Vprtstp: contraction number = 5.099966e-01\n Vnewton: Using errtol_s: 1070.135650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.351663e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.788876e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.678182e+02\n Vprtstp: contraction number = 6.678182e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.397467e-04\n Vprtstp: contraction number = 5.616468e-01\n Vnewton: Using errtol_s: 601.038216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.150352e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.078669e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.994733e+02\n Vprtstp: contraction number = 3.994733e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.359319e-05\n Vprtstp: contraction number = 5.981764e-01\n Vnewton: Using errtol_s: 359.526862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.945661e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.188019e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.488647e+02\n Vprtstp: contraction number = 2.488647e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.207703e-05\n Vprtstp: contraction number = 6.229817e-01\n Vnewton: Using errtol_s: 223.978670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.801021e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.316057e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.588671e+02\n Vprtstp: contraction number = 1.588671e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.324425e-05\n Vprtstp: contraction number = 6.383669e-01\n Vnewton: Using errtol_s: 142.980568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.062266e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.440694e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.030284e+02\n Vprtstp: contraction number = 1.030284e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.155954e-05\n Vprtstp: contraction number = 6.485194e-01\n Vnewton: Using errtol_s: 92.725673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.138254e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.536316e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.760657e+01\n Vprtstp: contraction number = 6.760657e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.414722e-05\n Vprtstp: contraction number = 6.561932e-01\n Vnewton: Using errtol_s: 60.845953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.215655e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.657352e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.480217e+01\n Vprtstp: contraction number = 4.480217e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.375216e-06\n Vprtstp: contraction number = 6.626894e-01\n Vnewton: Using errtol_s: 40.321969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.294848e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.794373e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990735e+01\n Vprtstp: contraction number = 2.990735e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 6.258355e-06\n Vprtstp: contraction number = 6.675424e-01\n Vnewton: Using errtol_s: 26.916626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.374880e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.912442e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.008505e+01\n Vprtstp: contraction number = 2.008505e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 4.202958e-06\n Vprtstp: contraction number = 6.715755e-01\n Vnewton: Using errtol_s: 18.076547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.447965e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.023050e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356100e+01\n Vprtstp: contraction number = 1.356100e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 2.837748e-06\n Vprtstp: contraction number = 6.751787e-01\n Vnewton: Using errtol_s: 12.204901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.520342e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.156604e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.198733e+00\n Vprtstp: contraction number = 9.198733e+00\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 1.924909e-06\n Vprtstp: contraction number = 6.783227e-01\n Vnewton: Using errtol_s: 8.278861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.599242e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.285452e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.265697e+00\n Vprtstp: contraction number = 6.265697e+00\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.311147e-06\n Vprtstp: contraction number = 6.811478e-01\n Vnewton: Using errtol_s: 5.639128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.680406e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.401788e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.284635e+00\n Vprtstp: contraction number = 4.284635e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 8.965941e-07\n Vprtstp: contraction number = 6.838241e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.546777e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.572714e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.313715e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.341638e+01\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -7516,15 +7516,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.966602122039E-02 kT\n Vpmg_energy:  qfEnergy = 3.975619983960E+01 kT\n Vpmg_energy:  dielEnergy = 4.589187237063E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.762000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.067000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -7572,160 +7572,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00234933 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.352261\n+Vacc_SASA: Time elapsed: 1.360561\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.667767e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.761429e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.005500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.071100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.293410e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.586100e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.939225e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.724319e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2418328.609890\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.966318e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.759519e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.297991e+05\n Vprtstp: contraction number = 2.297991e+05\n Vnewton: Attempting damping, relres = 0.085636\n Vnewton: Attempting damping, relres = 0.540011\n Vnewton: Damping accepted, relres = 0.085636\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.563556e-02\n Vprtstp: contraction number = 8.563556e-02\n Vnewton: Using errtol_s: 207094.936691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.086612e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.945322e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.943259e+04\n Vprtstp: contraction number = 3.943259e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.467770e-02\n Vprtstp: contraction number = 1.713972e-01\n Vnewton: Using errtol_s: 35495.493076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.175515e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.048597e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.192651e+03\n Vprtstp: contraction number = 9.192651e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.421180e-03\n Vprtstp: contraction number = 2.330870e-01\n Vnewton: Using errtol_s: 8273.537556\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.269562e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.215319e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.625902e+03\n Vprtstp: contraction number = 2.625902e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 9.772537e-04\n Vprtstp: contraction number = 2.856481e-01\n Vnewton: Using errtol_s: 2363.320499\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.355663e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.287913e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.336695e+02\n Vprtstp: contraction number = 8.336695e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.102569e-04\n Vprtstp: contraction number = 3.174784e-01\n Vnewton: Using errtol_s: 750.303246\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.444821e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.449425e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.790113e+02\n Vprtstp: contraction number = 2.790113e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.038363e-04\n Vprtstp: contraction number = 3.346783e-01\n Vnewton: Using errtol_s: 251.110249\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.537326e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.528746e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.595120e+01\n Vprtstp: contraction number = 9.595120e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.570900e-05\n Vprtstp: contraction number = 3.438971e-01\n Vnewton: Using errtol_s: 86.356086\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.634445e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.610271e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.363636e+01\n Vprtstp: contraction number = 3.363636e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.251804e-05\n Vprtstp: contraction number = 3.505570e-01\n Vnewton: Using errtol_s: 30.272729\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.730452e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.762712e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.212621e+01\n Vprtstp: contraction number = 1.212621e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.512865e-06\n Vprtstp: contraction number = 3.605089e-01\n Vnewton: Using errtol_s: 10.913589\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.820219e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.905383e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.547757e+00\n Vprtstp: contraction number = 4.547757e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.692484e-06\n Vprtstp: contraction number = 3.750353e-01\n Vnewton: Using errtol_s: 4.092981\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.903856e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.029883e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.787566e+00\n Vprtstp: contraction number = 1.787566e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.652567e-07\n Vprtstp: contraction number = 3.930654e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.043748e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.069821e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.432538e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.462603e+01\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -7734,17 +7734,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.201138998655E-02 kT\n Vpmg_energy:  qfEnergy = 4.154611536454E+02 kT\n Vpmg_energy:  dielEnergy = 2.802895931375E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.484800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.947200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -7765,272 +7765,272 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.393657\n+Vacc_SASA: Time elapsed: 1.405944\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.613831e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.692804e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.903100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.975400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.313050e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.270160e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.172306e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.356897e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.200395e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.383220e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.113974e+05\n Vprtstp: contraction number = 2.113974e+05\n Vnewton: Attempting damping, relres = 0.047573\n Vnewton: Attempting damping, relres = 0.515375\n Vnewton: Damping accepted, relres = 0.047573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.757263e-02\n Vprtstp: contraction number = 4.757263e-02\n Vnewton: Using errtol_s: 203448.048803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.311611e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.521300e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.589098e+04\n Vprtstp: contraction number = 4.589098e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.811582e-03\n Vprtstp: contraction number = 2.062443e-01\n Vnewton: Using errtol_s: 41959.996661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.392577e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.614864e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404662e+04\n Vprtstp: contraction number = 1.404662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.960291e-03\n Vprtstp: contraction number = 3.017139e-01\n Vnewton: Using errtol_s: 12659.913691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.471920e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.747073e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.279840e+03\n Vprtstp: contraction number = 5.279840e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111524e-03\n Vprtstp: contraction number = 3.754781e-01\n Vnewton: Using errtol_s: 4753.520446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.549007e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.860916e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.336921e+03\n Vprtstp: contraction number = 2.336921e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.918609e-04\n Vprtstp: contraction number = 4.425102e-01\n Vnewton: Using errtol_s: 2103.481419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.626946e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.929759e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194576e+03\n Vprtstp: contraction number = 1.194576e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.514070e-04\n Vprtstp: contraction number = 5.111344e-01\n Vnewton: Using errtol_s: 1075.161658\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.711052e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.998705e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.792983e+02\n Vprtstp: contraction number = 6.792983e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.429594e-04\n Vprtstp: contraction number = 5.686374e-01\n Vnewton: Using errtol_s: 611.377148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.787722e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.064824e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.154648e+02\n Vprtstp: contraction number = 4.154648e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.743449e-05\n Vprtstp: contraction number = 6.116036e-01\n Vnewton: Using errtol_s: 373.920435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.866482e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.144118e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660684e+02\n Vprtstp: contraction number = 2.660684e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.599388e-05\n Vprtstp: contraction number = 6.404095e-01\n Vnewton: Using errtol_s: 239.462182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.944428e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.266342e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755593e+02\n Vprtstp: contraction number = 1.755593e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.694626e-05\n Vprtstp: contraction number = 6.598268e-01\n Vnewton: Using errtol_s: 158.003576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.020871e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.375173e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183176e+02\n Vprtstp: contraction number = 1.183176e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.489979e-05\n Vprtstp: contraction number = 6.739462e-01\n Vnewton: Using errtol_s: 106.485913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.098749e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.501331e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.102710e+01\n Vprtstp: contraction number = 8.102710e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705205e-05\n Vprtstp: contraction number = 6.848271e-01\n Vnewton: Using errtol_s: 72.924443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.179028e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.618472e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.628393e+01\n Vprtstp: contraction number = 5.628393e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.184488e-05\n Vprtstp: contraction number = 6.946308e-01\n Vnewton: Using errtol_s: 50.655566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.265477e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.701240e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955755e+01\n Vprtstp: contraction number = 3.955755e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.324836e-06\n Vprtstp: contraction number = 7.028213e-01\n Vnewton: Using errtol_s: 35.601810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.357643e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.754459e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.808103e+01\n Vprtstp: contraction number = 2.808103e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.909617e-06\n Vprtstp: contraction number = 7.098779e-01\n Vnewton: Using errtol_s: 25.272937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.443001e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.824145e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.010039e+01\n Vprtstp: contraction number = 2.010039e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 4.230100e-06\n Vprtstp: contraction number = 7.157995e-01\n Vnewton: Using errtol_s: 18.090355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.533891e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.875545e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.449222e+01\n Vprtstp: contraction number = 1.449222e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 3.049867e-06\n Vprtstp: contraction number = 7.209918e-01\n Vnewton: Using errtol_s: 13.042997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.620772e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.921722e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051084e+01\n Vprtstp: contraction number = 1.051084e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 2.211992e-06\n Vprtstp: contraction number = 7.252749e-01\n Vnewton: Using errtol_s: 9.459758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.703450e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.967307e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.663626e+00\n Vprtstp: contraction number = 7.663626e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.612800e-06\n Vprtstp: contraction number = 7.291164e-01\n Vnewton: Using errtol_s: 6.897264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.782909e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.019567e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.612195e+00\n Vprtstp: contraction number = 5.612195e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 1.181079e-06\n Vprtstp: contraction number = 7.323158e-01\n Vnewton: Using errtol_s: 5.050976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.866601e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.073871e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.124624e+00\n Vprtstp: contraction number = 4.124624e+00\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 8.680215e-07\n Vprtstp: contraction number = 7.349396e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.768035e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.794111e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.759068e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.785838e+01\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8039,17 +8039,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.651047489982E-01 kT\n Vpmg_energy:  qfEnergy = 3.716292902858E+03 kT\n Vpmg_energy:  dielEnergy = 1.798539842617E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.842000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.626100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -8095,160 +8095,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00429089 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.388072\n+Vacc_SASA: Time elapsed: 1.389059\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.812041e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.951025e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.177300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.710400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.570370e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.181720e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.152434e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.340530e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3456404.072365\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.178167e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.372040e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.424168e+05\n Vprtstp: contraction number = 3.424168e+05\n Vnewton: Attempting damping, relres = 0.089811\n Vnewton: Attempting damping, relres = 0.542258\n Vnewton: Damping accepted, relres = 0.089811\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.981102e-02\n Vprtstp: contraction number = 8.981102e-02\n Vnewton: Using errtol_s: 310423.190924\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.302796e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.437299e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.148381e+04\n Vprtstp: contraction number = 6.148381e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.602901e-02\n Vprtstp: contraction number = 1.784748e-01\n Vnewton: Using errtol_s: 55402.729239\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.400177e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.482580e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.483491e+04\n Vprtstp: contraction number = 1.483491e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.863008e-03\n Vprtstp: contraction number = 2.410011e-01\n Vnewton: Using errtol_s: 13352.116026\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.491254e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.527489e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.268024e+03\n Vprtstp: contraction number = 4.268024e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111340e-03\n Vprtstp: contraction number = 2.876878e-01\n Vnewton: Using errtol_s: 3841.240882\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.585942e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.572009e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.355750e+03\n Vprtstp: contraction number = 1.355750e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.530190e-04\n Vprtstp: contraction number = 3.176516e-01\n Vnewton: Using errtol_s: 1220.176206\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.668352e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.616265e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.554936e+02\n Vprtstp: contraction number = 4.554936e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.186043e-04\n Vprtstp: contraction number = 3.359715e-01\n Vnewton: Using errtol_s: 409.944430\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.758050e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.660276e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.577730e+02\n Vprtstp: contraction number = 1.577730e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.108191e-05\n Vprtstp: contraction number = 3.463779e-01\n Vnewton: Using errtol_s: 141.995679\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.844038e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.705089e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.547816e+01\n Vprtstp: contraction number = 5.547816e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.444575e-05\n Vprtstp: contraction number = 3.516328e-01\n Vnewton: Using errtol_s: 49.930345\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.940127e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.751473e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.964653e+01\n Vprtstp: contraction number = 1.964653e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.115686e-06\n Vprtstp: contraction number = 3.541309e-01\n Vnewton: Using errtol_s: 17.681880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.033867e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.795444e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.015901e+00\n Vprtstp: contraction number = 7.015901e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.826844e-06\n Vprtstp: contraction number = 3.571063e-01\n Vnewton: Using errtol_s: 6.314311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.123249e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.863117e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.553268e+00\n Vprtstp: contraction number = 2.553268e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.648357e-07\n Vprtstp: contraction number = 3.639258e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.049059e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.078230e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.228357e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.493557e+00\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8257,15 +8257,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.579314308709E-01 kT\n Vpmg_energy:  qfEnergy = 2.986093532858E+04 kT\n Vpmg_energy:  dielEnergy = 1.486705407480E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.399600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.304200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -8288,261 +8288,261 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.007718\n+Vacc_SASA: Time elapsed: 3.005086\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.406329e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.490835e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.699200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.955000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.691600e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.874070e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.574264e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.337940e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.604855e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.353156e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.298565e+05\n Vprtstp: contraction number = 4.298565e+05\n Vnewton: Attempting damping, relres = 0.048079\n Vnewton: Attempting damping, relres = 0.515481\n Vnewton: Damping accepted, relres = 0.048079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.807904e-02\n Vprtstp: contraction number = 4.807904e-02\n Vnewton: Using errtol_s: 418259.137179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.714923e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.414110e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.275297e+04\n Vprtstp: contraction number = 9.275297e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.791706e-03\n Vprtstp: contraction number = 2.036585e-01\n Vnewton: Using errtol_s: 85182.030508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.799888e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.457883e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.830324e+04\n Vprtstp: contraction number = 2.830324e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.931540e-03\n Vprtstp: contraction number = 2.993901e-01\n Vnewton: Using errtol_s: 25502.653903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.884324e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.502400e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066383e+04\n Vprtstp: contraction number = 1.066383e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.103407e-03\n Vprtstp: contraction number = 3.763916e-01\n Vnewton: Using errtol_s: 9598.985602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.961612e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.548790e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725476e+03\n Vprtstp: contraction number = 4.725476e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.889004e-04\n Vprtstp: contraction number = 4.430826e-01\n Vnewton: Using errtol_s: 4253.143226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.039760e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.590853e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402868e+03\n Vprtstp: contraction number = 2.402868e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.485940e-04\n Vprtstp: contraction number = 5.084757e-01\n Vnewton: Using errtol_s: 2162.620089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.117532e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.638120e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352802e+03\n Vprtstp: contraction number = 1.352802e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.399556e-04\n Vprtstp: contraction number = 5.629888e-01\n Vnewton: Using errtol_s: 1217.530795\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.197231e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.683274e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164880e+02\n Vprtstp: contraction number = 8.164880e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.447037e-05\n Vprtstp: contraction number = 6.035512e-01\n Vnewton: Using errtol_s: 734.842122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.279090e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.725018e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157033e+02\n Vprtstp: contraction number = 5.157033e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.335238e-05\n Vprtstp: contraction number = 6.316106e-01\n Vnewton: Using errtol_s: 464.134076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.364029e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.778268e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352095e+02\n Vprtstp: contraction number = 3.352095e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.467926e-05\n Vprtstp: contraction number = 6.500040e-01\n Vnewton: Using errtol_s: 301.688999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.440111e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.830134e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.222234e+02\n Vprtstp: contraction number = 2.222234e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.299022e-05\n Vprtstp: contraction number = 6.629387e-01\n Vnewton: Using errtol_s: 200.001301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.515659e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.878217e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.495221e+02\n Vprtstp: contraction number = 1.495221e+02\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.546887e-05\n Vprtstp: contraction number = 6.728456e-01\n Vnewton: Using errtol_s: 134.569993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.607264e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.921990e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018836e+02\n Vprtstp: contraction number = 1.018836e+02\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.054041e-05\n Vprtstp: contraction number = 6.813949e-01\n Vnewton: Using errtol_s: 91.695311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.698175e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.966196e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.012825e+01\n Vprtstp: contraction number = 7.012825e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.255144e-06\n Vprtstp: contraction number = 6.883171e-01\n Vnewton: Using errtol_s: 63.115450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.786322e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.010645e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.869976e+01\n Vprtstp: contraction number = 4.869976e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.038252e-06\n Vprtstp: contraction number = 6.944386e-01\n Vnewton: Using errtol_s: 43.829803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.875833e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.055616e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.408035e+01\n Vprtstp: contraction number = 3.408035e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 3.525795e-06\n Vprtstp: contraction number = 6.998052e-01\n Vnewton: Using errtol_s: 30.672326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.964990e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.099944e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401453e+01\n Vprtstp: contraction number = 2.401453e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 2.484432e-06\n Vprtstp: contraction number = 7.046444e-01\n Vnewton: Using errtol_s: 21.613084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.049412e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.144865e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.702723e+01\n Vprtstp: contraction number = 1.702723e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.761558e-06\n Vprtstp: contraction number = 7.090385e-01\n Vnewton: Using errtol_s: 15.324508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.132004e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.190759e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214065e+01\n Vprtstp: contraction number = 1.214065e+01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.256015e-06\n Vprtstp: contraction number = 7.130137e-01\n Vnewton: Using errtol_s: 10.926584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.215276e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.232875e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.699962e+00\n Vprtstp: contraction number = 8.699962e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 9.000575e-07\n Vprtstp: contraction number = 7.165978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.714522e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.744865e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.308243e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.520113e+00\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8551,15 +8551,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.659936219773E-01 kT\n Vpmg_energy:  qfEnergy = 3.771591154168E+03 kT\n Vpmg_energy:  dielEnergy = 1.850889250612E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.946000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.919000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -8607,160 +8607,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0122306 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.010573\n+Vacc_SASA: Time elapsed: 3.006832\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.547674e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.744799e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.063700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.964100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.339820e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.009960e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.671777e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.668350e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 5774426.010351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.696479e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.685434e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.536200e+05\n Vprtstp: contraction number = 5.536200e+05\n Vnewton: Attempting damping, relres = 0.086816\n Vnewton: Attempting damping, relres = 0.540697\n Vnewton: Damping accepted, relres = 0.086816\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.681646e-02\n Vprtstp: contraction number = 8.681646e-02\n Vnewton: Using errtol_s: 501315.229123\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.811541e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.741263e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.813919e+04\n Vprtstp: contraction number = 9.813919e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.530865e-02\n Vprtstp: contraction number = 1.763335e-01\n Vnewton: Using errtol_s: 88398.668796\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.905551e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.783886e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.359807e+04\n Vprtstp: contraction number = 2.359807e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.678183e-03\n Vprtstp: contraction number = 2.402683e-01\n Vnewton: Using errtol_s: 21239.395305\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.992706e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.830798e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.835940e+03\n Vprtstp: contraction number = 6.835940e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.065460e-03\n Vprtstp: contraction number = 2.896703e-01\n Vnewton: Using errtol_s: 6152.421286\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.090701e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.874704e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.186690e+03\n Vprtstp: contraction number = 2.186690e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.408183e-04\n Vprtstp: contraction number = 3.198790e-01\n Vnewton: Using errtol_s: 1968.030266\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.182737e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.940258e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.369221e+02\n Vprtstp: contraction number = 7.369221e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.148566e-04\n Vprtstp: contraction number = 3.370025e-01\n Vnewton: Using errtol_s: 663.231119\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.279776e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.095406e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.557331e+02\n Vprtstp: contraction number = 2.557331e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.985850e-05\n Vprtstp: contraction number = 3.470283e-01\n Vnewton: Using errtol_s: 230.159953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.378105e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.210168e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.020719e+01\n Vprtstp: contraction number = 9.020719e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.405966e-05\n Vprtstp: contraction number = 3.527394e-01\n Vnewton: Using errtol_s: 81.186485\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.466342e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.347190e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.225420e+01\n Vprtstp: contraction number = 3.225420e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.027128e-06\n Vprtstp: contraction number = 3.575568e-01\n Vnewton: Using errtol_s: 29.028780\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.555061e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.482049e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.171930e+01\n Vprtstp: contraction number = 1.171930e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.826566e-06\n Vprtstp: contraction number = 3.633419e-01\n Vnewton: Using errtol_s: 10.547373\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.646329e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.626401e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.353564e+00\n Vprtstp: contraction number = 4.353564e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.785449e-07\n Vprtstp: contraction number = 3.714865e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.061095e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.087562e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.080877e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.104795e+01\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8769,27 +8769,27 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 3.126180200466E-01 kT\n Vpmg_energy:  qfEnergy = 3.029835397910E+04 kT\n Vpmg_energy:  dielEnergy = 1.515709858498E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.538600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.842500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.761284e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.779734e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:24:56 2025\n+# Creation Date and Time:  Sun Jan  7 09:38:39 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -9142,250 +9142,250 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.414888\n+Vacc_SASA: Time elapsed: 1.369760\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.654479e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.651535e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.040800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.083000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.495790e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.479390e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.044837e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.104783e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.341964e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.441375e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.136321e+05\n Vprtstp: contraction number = 2.136321e+05\n Vnewton: Attempting damping, relres = 0.047663\n Vnewton: Attempting damping, relres = 0.515490\n Vnewton: Damping accepted, relres = 0.047663\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.766304e-02\n Vprtstp: contraction number = 4.766304e-02\n Vnewton: Using errtol_s: 204994.485638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.351835e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.647515e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.587025e+04\n Vprtstp: contraction number = 4.587025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.727679e-03\n Vprtstp: contraction number = 2.040927e-01\n Vnewton: Using errtol_s: 41837.880528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.235173e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.626142e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.391016e+04\n Vprtstp: contraction number = 1.391016e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.912173e-03\n Vprtstp: contraction number = 2.993697e-01\n Vnewton: Using errtol_s: 12524.995351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.036294e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.802855e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.237707e+03\n Vprtstp: contraction number = 5.237707e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.096054e-03\n Vprtstp: contraction number = 3.763697e-01\n Vnewton: Using errtol_s: 4714.028550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.840729e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.013922e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.331453e+03\n Vprtstp: contraction number = 2.331453e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.878779e-04\n Vprtstp: contraction number = 4.451223e-01\n Vnewton: Using errtol_s: 2098.319320\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.638071e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.083147e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189035e+03\n Vprtstp: contraction number = 1.189035e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.488161e-04\n Vprtstp: contraction number = 5.099966e-01\n Vnewton: Using errtol_s: 1070.135650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.453916e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.164762e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.678182e+02\n Vprtstp: contraction number = 6.678182e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.397467e-04\n Vprtstp: contraction number = 5.616468e-01\n Vnewton: Using errtol_s: 601.038216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.252791e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.055169e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.994733e+02\n Vprtstp: contraction number = 3.994733e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.359319e-05\n Vprtstp: contraction number = 5.981764e-01\n Vnewton: Using errtol_s: 359.526862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.105688e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.191209e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.488647e+02\n Vprtstp: contraction number = 2.488647e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.207703e-05\n Vprtstp: contraction number = 6.229817e-01\n Vnewton: Using errtol_s: 223.978670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.985404e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.316688e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.588671e+02\n Vprtstp: contraction number = 1.588671e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.324425e-05\n Vprtstp: contraction number = 6.383669e-01\n Vnewton: Using errtol_s: 142.980568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.083562e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.443423e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.030284e+02\n Vprtstp: contraction number = 1.030284e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.155954e-05\n Vprtstp: contraction number = 6.485194e-01\n Vnewton: Using errtol_s: 92.725673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.171469e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.586474e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.760657e+01\n Vprtstp: contraction number = 6.760657e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.414722e-05\n Vprtstp: contraction number = 6.561932e-01\n Vnewton: Using errtol_s: 60.845953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.257839e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.704951e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.480217e+01\n Vprtstp: contraction number = 4.480217e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.375216e-06\n Vprtstp: contraction number = 6.626894e-01\n Vnewton: Using errtol_s: 40.321969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.340681e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.828011e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990735e+01\n Vprtstp: contraction number = 2.990735e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 6.258355e-06\n Vprtstp: contraction number = 6.675424e-01\n Vnewton: Using errtol_s: 26.916626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.420941e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.932980e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.008505e+01\n Vprtstp: contraction number = 2.008505e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 4.202958e-06\n Vprtstp: contraction number = 6.715755e-01\n Vnewton: Using errtol_s: 18.076547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.504890e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.056183e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356100e+01\n Vprtstp: contraction number = 1.356100e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 2.837748e-06\n Vprtstp: contraction number = 6.751787e-01\n Vnewton: Using errtol_s: 12.204901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.591897e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.204406e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.198733e+00\n Vprtstp: contraction number = 9.198733e+00\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 1.924909e-06\n Vprtstp: contraction number = 6.783227e-01\n Vnewton: Using errtol_s: 8.278861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.673932e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.334862e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.265697e+00\n Vprtstp: contraction number = 6.265697e+00\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.311147e-06\n Vprtstp: contraction number = 6.811478e-01\n Vnewton: Using errtol_s: 5.639128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.751496e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.471105e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.284635e+00\n Vprtstp: contraction number = 4.284635e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 8.965941e-07\n Vprtstp: contraction number = 6.838241e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.618422e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.646737e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.369221e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.397655e+01\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -9394,15 +9394,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.475399192616E+00 kT\n Vpmg_energy:  qfEnergy = 1.444578731292E+04 kT\n Vpmg_energy:  dielEnergy = 7.168962891577E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.028800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.444500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -9450,171 +9450,171 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.244357 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.350853\n+Vacc_SASA: Time elapsed: 1.378639\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.902476e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.090206e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.670400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.020900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.245110e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.494130e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.041332e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.820168e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7151537.194828\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.067063e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.856633e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.220296e+05\n Vprtstp: contraction number = 7.220296e+05\n Vnewton: Attempting damping, relres = 0.092215\n Vnewton: Attempting damping, relres = 0.543248\n Vnewton: Damping accepted, relres = 0.092215\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.221458e-02\n Vprtstp: contraction number = 9.221458e-02\n Vnewton: Using errtol_s: 659475.973035\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.177865e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.030871e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.360213e+05\n Vprtstp: contraction number = 1.360213e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.716437e-02\n Vprtstp: contraction number = 1.861351e-01\n Vnewton: Using errtol_s: 122751.620274\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.265349e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.152966e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.560242e+04\n Vprtstp: contraction number = 3.560242e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.482910e-03\n Vprtstp: contraction number = 2.611753e-01\n Vnewton: Using errtol_s: 32059.695083\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.354545e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.320129e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.131656e+04\n Vprtstp: contraction number = 1.131656e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.424570e-03\n Vprtstp: contraction number = 3.177779e-01\n Vnewton: Using errtol_s: 10187.862459\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.441388e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.483455e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.913208e+03\n Vprtstp: contraction number = 3.913208e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.925362e-04\n Vprtstp: contraction number = 3.457439e-01\n Vnewton: Using errtol_s: 3522.390814\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.524311e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.596435e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.383064e+03\n Vprtstp: contraction number = 1.383064e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.740621e-04\n Vprtstp: contraction number = 3.533996e-01\n Vnewton: Using errtol_s: 1244.811552\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.619596e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.755349e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.895564e+02\n Vprtstp: contraction number = 4.895564e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 6.160970e-05\n Vprtstp: contraction number = 3.539524e-01\n Vnewton: Using errtol_s: 440.604077\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.715131e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.869821e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.817812e+02\n Vprtstp: contraction number = 1.817812e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.287666e-05\n Vprtstp: contraction number = 3.713159e-01\n Vnewton: Using errtol_s: 163.603290\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.798581e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.033196e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.297744e+01\n Vprtstp: contraction number = 7.297744e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 9.184003e-06\n Vprtstp: contraction number = 4.014573e-01\n Vnewton: Using errtol_s: 65.679739\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.885635e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.175380e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.147662e+01\n Vprtstp: contraction number = 3.147662e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.961242e-06\n Vprtstp: contraction number = 4.313197e-01\n Vnewton: Using errtol_s: 28.328967\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.970015e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.304939e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.429069e+01\n Vprtstp: contraction number = 1.429069e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.798442e-06\n Vprtstp: contraction number = 4.540096e-01\n Vnewton: Using errtol_s: 12.861624\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.056619e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.459680e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.773546e+00\n Vprtstp: contraction number = 6.773546e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 8.524311e-07\n Vprtstp: contraction number = 4.739831e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.090455e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.116834e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.782132e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.810864e+01\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -9623,17 +9623,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.623170000406E+00 kT\n Vpmg_energy:  qfEnergy = 1.125246141954E+05 kT\n Vpmg_energy:  dielEnergy = 5.603584772163E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.379900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.744100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -9654,272 +9654,272 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.394252\n+Vacc_SASA: Time elapsed: 1.396008\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.653733e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.702354e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.077300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.006200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.401520e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.561680e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.327288e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.803909e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.354785e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.839207e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.113974e+05\n Vprtstp: contraction number = 2.113974e+05\n Vnewton: Attempting damping, relres = 0.047573\n Vnewton: Attempting damping, relres = 0.515375\n Vnewton: Damping accepted, relres = 0.047573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.757263e-02\n Vprtstp: contraction number = 4.757263e-02\n Vnewton: Using errtol_s: 203448.048803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.446395e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.997186e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.589098e+04\n Vprtstp: contraction number = 4.589098e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.811582e-03\n Vprtstp: contraction number = 2.062443e-01\n Vnewton: Using errtol_s: 41959.996661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.529374e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.130648e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404662e+04\n Vprtstp: contraction number = 1.404662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.960291e-03\n Vprtstp: contraction number = 3.017139e-01\n Vnewton: Using errtol_s: 12659.913691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.618761e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.238074e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.279840e+03\n Vprtstp: contraction number = 5.279840e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111524e-03\n Vprtstp: contraction number = 3.754781e-01\n Vnewton: Using errtol_s: 4753.520446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.706214e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.368429e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.336921e+03\n Vprtstp: contraction number = 2.336921e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.918609e-04\n Vprtstp: contraction number = 4.425102e-01\n Vnewton: Using errtol_s: 2103.481419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.780299e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.497971e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194576e+03\n Vprtstp: contraction number = 1.194576e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.514070e-04\n Vprtstp: contraction number = 5.111344e-01\n Vnewton: Using errtol_s: 1075.161658\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.864632e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.626646e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.792983e+02\n Vprtstp: contraction number = 6.792983e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.429594e-04\n Vprtstp: contraction number = 5.686374e-01\n Vnewton: Using errtol_s: 611.377148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.953881e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.746200e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.154648e+02\n Vprtstp: contraction number = 4.154648e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.743449e-05\n Vprtstp: contraction number = 6.116036e-01\n Vnewton: Using errtol_s: 373.920435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.039271e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.869010e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660684e+02\n Vprtstp: contraction number = 2.660684e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.599388e-05\n Vprtstp: contraction number = 6.404095e-01\n Vnewton: Using errtol_s: 239.462182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.125526e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.994534e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755593e+02\n Vprtstp: contraction number = 1.755593e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.694626e-05\n Vprtstp: contraction number = 6.598268e-01\n Vnewton: Using errtol_s: 158.003576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.207137e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.102537e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183176e+02\n Vprtstp: contraction number = 1.183176e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.489979e-05\n Vprtstp: contraction number = 6.739462e-01\n Vnewton: Using errtol_s: 106.485913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.291762e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.226761e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.102710e+01\n Vprtstp: contraction number = 8.102710e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705205e-05\n Vprtstp: contraction number = 6.848271e-01\n Vnewton: Using errtol_s: 72.924443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.370430e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.280504e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.628393e+01\n Vprtstp: contraction number = 5.628393e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.184488e-05\n Vprtstp: contraction number = 6.946308e-01\n Vnewton: Using errtol_s: 50.655566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.450606e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.322760e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955755e+01\n Vprtstp: contraction number = 3.955755e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.324836e-06\n Vprtstp: contraction number = 7.028213e-01\n Vnewton: Using errtol_s: 35.601810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.528169e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.367603e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.808103e+01\n Vprtstp: contraction number = 2.808103e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.909617e-06\n Vprtstp: contraction number = 7.098779e-01\n Vnewton: Using errtol_s: 25.272937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.600421e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.413441e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.010039e+01\n Vprtstp: contraction number = 2.010039e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 4.230100e-06\n Vprtstp: contraction number = 7.157995e-01\n Vnewton: Using errtol_s: 18.090355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.675433e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.454515e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.449222e+01\n Vprtstp: contraction number = 1.449222e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 3.049867e-06\n Vprtstp: contraction number = 7.209918e-01\n Vnewton: Using errtol_s: 13.042997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.757710e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.500287e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051084e+01\n Vprtstp: contraction number = 1.051084e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 2.211992e-06\n Vprtstp: contraction number = 7.252749e-01\n Vnewton: Using errtol_s: 9.459758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.837591e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.545894e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.663626e+00\n Vprtstp: contraction number = 7.663626e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.612800e-06\n Vprtstp: contraction number = 7.291164e-01\n Vnewton: Using errtol_s: 6.897264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.911759e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.585820e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.612195e+00\n Vprtstp: contraction number = 5.612195e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 1.181079e-06\n Vprtstp: contraction number = 7.323158e-01\n Vnewton: Using errtol_s: 5.050976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.986871e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.632036e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.124624e+00\n Vprtstp: contraction number = 4.124624e+00\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 8.680215e-07\n Vprtstp: contraction number = 7.349396e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.727165e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.755504e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.869889e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.899021e+01\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -9928,15 +9928,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.730884767842E-02 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 2.814808503921E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.996000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.880000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -9984,160 +9984,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.000691975 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.376592\n+Vacc_SASA: Time elapsed: 1.376846\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.623453e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.686842e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.408600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.887300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.332370e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.877710e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.246940e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.866089e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 951047.684475\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.274160e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.883194e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.162547e+05\n Vprtstp: contraction number = 1.162547e+05\n Vnewton: Attempting damping, relres = 0.112161\n Vnewton: Attempting damping, relres = 0.552182\n Vnewton: Damping accepted, relres = 0.112161\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.121606e-01\n Vprtstp: contraction number = 1.121606e-01\n Vnewton: Using errtol_s: 106670.078940\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.373683e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.936312e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.126153e+04\n Vprtstp: contraction number = 2.126153e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.016407e-02\n Vprtstp: contraction number = 1.797785e-01\n Vnewton: Using errtol_s: 19176.991465\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.445036e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.980690e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.910429e+03\n Vprtstp: contraction number = 4.910429e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.647657e-03\n Vprtstp: contraction number = 2.304920e-01\n Vnewton: Using errtol_s: 4420.143642\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.514365e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.040124e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.327403e+03\n Vprtstp: contraction number = 1.327403e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.256188e-03\n Vprtstp: contraction number = 2.702841e-01\n Vnewton: Using errtol_s: 1194.694354\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.584766e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.086369e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.951603e+02\n Vprtstp: contraction number = 3.951603e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.739525e-04\n Vprtstp: contraction number = 2.976884e-01\n Vnewton: Using errtol_s: 355.646671\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.657959e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.127637e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.251397e+02\n Vprtstp: contraction number = 1.251397e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.184231e-04\n Vprtstp: contraction number = 3.166794e-01\n Vnewton: Using errtol_s: 112.625980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.729455e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.173273e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.114263e+01\n Vprtstp: contraction number = 4.114263e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.893431e-05\n Vprtstp: contraction number = 3.287731e-01\n Vnewton: Using errtol_s: 37.028389\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.805244e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.214700e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.383573e+01\n Vprtstp: contraction number = 1.383573e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.309310e-05\n Vprtstp: contraction number = 3.362869e-01\n Vnewton: Using errtol_s: 12.452161\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.878322e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.256944e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725230e+00\n Vprtstp: contraction number = 4.725230e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.471602e-06\n Vprtstp: contraction number = 3.415236e-01\n Vnewton: Using errtol_s: 4.252707\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.948304e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.302697e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.633794e+00\n Vprtstp: contraction number = 1.633794e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.546100e-06\n Vprtstp: contraction number = 3.457598e-01\n Vnewton: Using errtol_s: 1.470415\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.021246e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.347601e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.703633e-01\n Vprtstp: contraction number = 5.703633e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.397489e-07\n Vprtstp: contraction number = 3.491035e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.332191e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.615890e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.153698e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.377985e+00\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -10146,17 +10146,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.677193160789E-02 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 2.890717240309E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.439200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.431900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -10177,261 +10177,261 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.008624\n+Vacc_SASA: Time elapsed: 3.006804\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.384888e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.483409e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.934200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.880500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.287990e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.799740e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.445807e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.751968e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.470731e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.768134e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.298565e+05\n Vprtstp: contraction number = 4.298565e+05\n Vnewton: Attempting damping, relres = 0.048079\n Vnewton: Attempting damping, relres = 0.515481\n Vnewton: Damping accepted, relres = 0.048079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.807904e-02\n Vprtstp: contraction number = 4.807904e-02\n Vnewton: Using errtol_s: 418259.137179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.573603e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.820713e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.275297e+04\n Vprtstp: contraction number = 9.275297e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.791706e-03\n Vprtstp: contraction number = 2.036585e-01\n Vnewton: Using errtol_s: 85182.030508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.658692e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.864032e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.830324e+04\n Vprtstp: contraction number = 2.830324e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.931540e-03\n Vprtstp: contraction number = 2.993901e-01\n Vnewton: Using errtol_s: 25502.653903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.739185e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.912371e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066383e+04\n Vprtstp: contraction number = 1.066383e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.103407e-03\n Vprtstp: contraction number = 3.763916e-01\n Vnewton: Using errtol_s: 9598.985602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.828013e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.955163e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725476e+03\n Vprtstp: contraction number = 4.725476e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.889004e-04\n Vprtstp: contraction number = 4.430826e-01\n Vnewton: Using errtol_s: 4253.143226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.917362e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.997697e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402868e+03\n Vprtstp: contraction number = 2.402868e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.485940e-04\n Vprtstp: contraction number = 5.084757e-01\n Vnewton: Using errtol_s: 2162.620089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.999048e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.050921e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352802e+03\n Vprtstp: contraction number = 1.352802e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.399556e-04\n Vprtstp: contraction number = 5.629888e-01\n Vnewton: Using errtol_s: 1217.530795\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.076323e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.093961e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164880e+02\n Vprtstp: contraction number = 8.164880e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.447037e-05\n Vprtstp: contraction number = 6.035512e-01\n Vnewton: Using errtol_s: 734.842122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.159714e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.136957e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157033e+02\n Vprtstp: contraction number = 5.157033e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.335238e-05\n Vprtstp: contraction number = 6.316106e-01\n Vnewton: Using errtol_s: 464.134076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.239895e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.180445e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352095e+02\n Vprtstp: contraction number = 3.352095e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.467926e-05\n Vprtstp: contraction number = 6.500040e-01\n Vnewton: Using errtol_s: 301.688999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.316981e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.227758e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.222234e+02\n Vprtstp: contraction number = 2.222234e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.299022e-05\n Vprtstp: contraction number = 6.629387e-01\n Vnewton: Using errtol_s: 200.001301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.397263e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.271083e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.495221e+02\n Vprtstp: contraction number = 1.495221e+02\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.546887e-05\n Vprtstp: contraction number = 6.728456e-01\n Vnewton: Using errtol_s: 134.569993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.486580e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.314702e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018836e+02\n Vprtstp: contraction number = 1.018836e+02\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.054041e-05\n Vprtstp: contraction number = 6.813949e-01\n Vnewton: Using errtol_s: 91.695311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.566155e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.357886e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.012825e+01\n Vprtstp: contraction number = 7.012825e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.255144e-06\n Vprtstp: contraction number = 6.883171e-01\n Vnewton: Using errtol_s: 63.115450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.646185e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.405679e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.869976e+01\n Vprtstp: contraction number = 4.869976e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.038252e-06\n Vprtstp: contraction number = 6.944386e-01\n Vnewton: Using errtol_s: 43.829803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.727465e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.448794e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.408035e+01\n Vprtstp: contraction number = 3.408035e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 3.525795e-06\n Vprtstp: contraction number = 6.998052e-01\n Vnewton: Using errtol_s: 30.672326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.814668e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.491589e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401453e+01\n Vprtstp: contraction number = 2.401453e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 2.484432e-06\n Vprtstp: contraction number = 7.046444e-01\n Vnewton: Using errtol_s: 21.613084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.899180e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.538691e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.702723e+01\n Vprtstp: contraction number = 1.702723e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.761558e-06\n Vprtstp: contraction number = 7.090385e-01\n Vnewton: Using errtol_s: 15.324508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.979087e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.582243e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214065e+01\n Vprtstp: contraction number = 1.214065e+01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.256015e-06\n Vprtstp: contraction number = 7.130137e-01\n Vnewton: Using errtol_s: 10.926584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.057110e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.624306e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.699962e+00\n Vprtstp: contraction number = 8.699962e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 9.000575e-07\n Vprtstp: contraction number = 7.165978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.677561e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.702898e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.096587e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.300084e+00\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -10440,15 +10440,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.633470349209E+00 kT\n Vpmg_energy:  qfEnergy = 1.444874244202E+04 kT\n Vpmg_energy:  dielEnergy = 7.168739971796E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.140000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.901000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -10496,171 +10496,171 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.23862 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.008145\n+Vacc_SASA: Time elapsed: 3.007611\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.652158e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.789835e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.586700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.884700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.269070e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.876730e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.516965e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.064260e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8022421.271471\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.543558e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.081549e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.182694e+05\n Vprtstp: contraction number = 8.182694e+05\n Vnewton: Attempting damping, relres = 0.093297\n Vnewton: Attempting damping, relres = 0.543649\n Vnewton: Damping accepted, relres = 0.093297\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.329693e-02\n Vprtstp: contraction number = 9.329693e-02\n Vnewton: Using errtol_s: 748467.258105\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.655724e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.134292e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.535104e+05\n Vprtstp: contraction number = 1.535104e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.727080e-02\n Vprtstp: contraction number = 1.851165e-01\n Vnewton: Using errtol_s: 138553.663149\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.746696e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.177839e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.960039e+04\n Vprtstp: contraction number = 3.960039e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.444863e-03\n Vprtstp: contraction number = 2.573628e-01\n Vnewton: Using errtol_s: 35658.564568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.836149e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.221577e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.238461e+04\n Vprtstp: contraction number = 1.238461e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.389740e-03\n Vprtstp: contraction number = 3.126620e-01\n Vnewton: Using errtol_s: 11149.079578\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.923275e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.269912e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.220923e+03\n Vprtstp: contraction number = 4.220923e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.735885e-04\n Vprtstp: contraction number = 3.407749e-01\n Vnewton: Using errtol_s: 3799.326730\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.004272e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.313689e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.473378e+03\n Vprtstp: contraction number = 1.473378e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.652984e-04\n Vprtstp: contraction number = 3.490339e-01\n Vnewton: Using errtol_s: 1326.093695\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.082728e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.360670e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.152403e+02\n Vprtstp: contraction number = 5.152403e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.780294e-05\n Vprtstp: contraction number = 3.496884e-01\n Vnewton: Using errtol_s: 463.719535\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.168844e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.408570e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.890344e+02\n Vprtstp: contraction number = 1.890344e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.120696e-05\n Vprtstp: contraction number = 3.668838e-01\n Vnewton: Using errtol_s: 170.131203\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.252112e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.452958e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.514797e+01\n Vprtstp: contraction number = 7.514797e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 8.430525e-06\n Vprtstp: contraction number = 3.975357e-01\n Vnewton: Using errtol_s: 67.633227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.342914e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.497836e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.220080e+01\n Vprtstp: contraction number = 3.220080e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.612467e-06\n Vprtstp: contraction number = 4.284985e-01\n Vnewton: Using errtol_s: 28.980733\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.432608e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.543283e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.453992e+01\n Vprtstp: contraction number = 1.453992e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.631169e-06\n Vprtstp: contraction number = 4.515389e-01\n Vnewton: Using errtol_s: 13.085928\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.515094e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.584449e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.875948e+00\n Vprtstp: contraction number = 6.875948e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.713824e-07\n Vprtstp: contraction number = 4.729015e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.075297e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.102078e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.585498e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.810128e+00\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -10669,27 +10669,27 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.853787896122E+00 kT\n Vpmg_energy:  qfEnergy = 1.125276033199E+05 kT\n Vpmg_energy:  dielEnergy = 5.603543842121E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.285500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.266200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.620058e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.649032e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:25:38 2025\n+# Creation Date and Time:  Sun Jan  7 09:39:09 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -11042,250 +11042,250 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.410264\n+Vacc_SASA: Time elapsed: 1.378957\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.659593e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.652124e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.971500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.024500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.306340e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.860180e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.027056e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.046170e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.292159e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.209094e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.136321e+05\n Vprtstp: contraction number = 2.136321e+05\n Vnewton: Attempting damping, relres = 0.047663\n Vnewton: Attempting damping, relres = 0.515490\n Vnewton: Damping accepted, relres = 0.047663\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.766304e-02\n Vprtstp: contraction number = 4.766304e-02\n Vnewton: Using errtol_s: 204994.485638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.387721e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.745894e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.587025e+04\n Vprtstp: contraction number = 4.587025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.727679e-03\n Vprtstp: contraction number = 2.040927e-01\n Vnewton: Using errtol_s: 41837.880528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.223143e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.199810e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.391016e+04\n Vprtstp: contraction number = 1.391016e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.912173e-03\n Vprtstp: contraction number = 2.993697e-01\n Vnewton: Using errtol_s: 12524.995351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.007558e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.656149e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.237707e+03\n Vprtstp: contraction number = 5.237707e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.096054e-03\n Vprtstp: contraction number = 3.763697e-01\n Vnewton: Using errtol_s: 4714.028550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.771935e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.141510e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.331453e+03\n Vprtstp: contraction number = 2.331453e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.878779e-04\n Vprtstp: contraction number = 4.451223e-01\n Vnewton: Using errtol_s: 2098.319320\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.513728e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.560709e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189035e+03\n Vprtstp: contraction number = 1.189035e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.488161e-04\n Vprtstp: contraction number = 5.099966e-01\n Vnewton: Using errtol_s: 1070.135650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.275688e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.017270e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.678182e+02\n Vprtstp: contraction number = 6.678182e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.397467e-04\n Vprtstp: contraction number = 5.616468e-01\n Vnewton: Using errtol_s: 601.038216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.996122e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.476176e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.994733e+02\n Vprtstp: contraction number = 3.994733e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.359319e-05\n Vprtstp: contraction number = 5.981764e-01\n Vnewton: Using errtol_s: 359.526862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.730817e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.942936e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.488647e+02\n Vprtstp: contraction number = 2.488647e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.207703e-05\n Vprtstp: contraction number = 6.229817e-01\n Vnewton: Using errtol_s: 223.978670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.554056e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.368957e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.588671e+02\n Vprtstp: contraction number = 1.588671e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.324425e-05\n Vprtstp: contraction number = 6.383669e-01\n Vnewton: Using errtol_s: 142.980568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.032198e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.843290e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.030284e+02\n Vprtstp: contraction number = 1.030284e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.155954e-05\n Vprtstp: contraction number = 6.485194e-01\n Vnewton: Using errtol_s: 92.725673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.111067e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.347336e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.760657e+01\n Vprtstp: contraction number = 6.760657e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.414722e-05\n Vprtstp: contraction number = 6.561932e-01\n Vnewton: Using errtol_s: 60.845953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.188858e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.808535e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.480217e+01\n Vprtstp: contraction number = 4.480217e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.375216e-06\n Vprtstp: contraction number = 6.626894e-01\n Vnewton: Using errtol_s: 40.321969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.267947e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.258360e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990735e+01\n Vprtstp: contraction number = 2.990735e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 6.258355e-06\n Vprtstp: contraction number = 6.675424e-01\n Vnewton: Using errtol_s: 26.916626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.349749e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.716930e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.008505e+01\n Vprtstp: contraction number = 2.008505e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 4.202958e-06\n Vprtstp: contraction number = 6.715755e-01\n Vnewton: Using errtol_s: 18.076547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.431263e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.168359e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356100e+01\n Vprtstp: contraction number = 1.356100e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 2.837748e-06\n Vprtstp: contraction number = 6.751787e-01\n Vnewton: Using errtol_s: 12.204901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.520698e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.586078e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.198733e+00\n Vprtstp: contraction number = 9.198733e+00\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 1.924909e-06\n Vprtstp: contraction number = 6.783227e-01\n Vnewton: Using errtol_s: 8.278861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.600794e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.004823e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.265697e+00\n Vprtstp: contraction number = 6.265697e+00\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.311147e-06\n Vprtstp: contraction number = 6.811478e-01\n Vnewton: Using errtol_s: 5.639128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.677077e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.050097e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.284635e+00\n Vprtstp: contraction number = 4.284635e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 8.965941e-07\n Vprtstp: contraction number = 6.838241e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.539673e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.565759e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.813176e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.036090e+00\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -11294,15 +11294,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.108926489514E-02 kT\n Vpmg_energy:  qfEnergy = 2.835800313442E+02 kT\n Vpmg_energy:  dielEnergy = 1.215330905259E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.138000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.920000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -11350,160 +11350,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00194731 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.353875\n+Vacc_SASA: Time elapsed: 1.354942\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.659943e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.709474e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.242400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.943200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.384000e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.842290e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.937189e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.280167e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1613641.621006\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.965352e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.294268e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.672701e+05\n Vprtstp: contraction number = 1.672701e+05\n Vnewton: Attempting damping, relres = 0.093643\n Vnewton: Attempting damping, relres = 0.544180\n Vnewton: Damping accepted, relres = 0.093643\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.364296e-02\n Vprtstp: contraction number = 9.364296e-02\n Vnewton: Using errtol_s: 151106.180064\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.077033e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.349460e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.923422e+04\n Vprtstp: contraction number = 2.923422e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.630658e-02\n Vprtstp: contraction number = 1.741357e-01\n Vnewton: Using errtol_s: 26312.974291\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.165623e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.396274e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.609437e+03\n Vprtstp: contraction number = 6.609437e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.686501e-03\n Vprtstp: contraction number = 2.260744e-01\n Vnewton: Using errtol_s: 5948.690797\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.255993e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.442239e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.798444e+03\n Vprtstp: contraction number = 1.798444e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.003087e-03\n Vprtstp: contraction number = 2.720974e-01\n Vnewton: Using errtol_s: 1618.623129\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.343027e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.487583e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.516770e+02\n Vprtstp: contraction number = 5.516770e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.076965e-04\n Vprtstp: contraction number = 3.067495e-01\n Vnewton: Using errtol_s: 496.511822\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.426744e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.533501e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.808462e+02\n Vprtstp: contraction number = 1.808462e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.008662e-04\n Vprtstp: contraction number = 3.278106e-01\n Vnewton: Using errtol_s: 162.761828\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.515692e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.577298e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.118139e+01\n Vprtstp: contraction number = 6.118139e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.412361e-05\n Vprtstp: contraction number = 3.383059e-01\n Vnewton: Using errtol_s: 55.063279\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.607810e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.622670e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.100954e+01\n Vprtstp: contraction number = 2.100954e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.171796e-05\n Vprtstp: contraction number = 3.433974e-01\n Vnewton: Using errtol_s: 18.908586\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.692463e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.671755e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.287024e+00\n Vprtstp: contraction number = 7.287024e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.064299e-06\n Vprtstp: contraction number = 3.468436e-01\n Vnewton: Using errtol_s: 6.558322\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.779495e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.716083e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.550680e+00\n Vprtstp: contraction number = 2.550680e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.422628e-06\n Vprtstp: contraction number = 3.500304e-01\n Vnewton: Using errtol_s: 2.295612\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.870614e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.762222e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.008406e-01\n Vprtstp: contraction number = 9.008406e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.024390e-07\n Vprtstp: contraction number = 3.531767e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.012466e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.039970e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.171461e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.392116e+00\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -11512,15 +11512,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.604786476037E-02 kT\n Vpmg_energy:  qfEnergy = 2.451766100693E+03 kT\n Vpmg_energy:  dielEnergy = 1.154345981477E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.501900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.481200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -11543,272 +11543,272 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.413526\n+Vacc_SASA: Time elapsed: 1.407171\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.647155e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.687248e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.915600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.868400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.283090e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.813210e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.142214e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.988497e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.168399e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.004971e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.113974e+05\n Vprtstp: contraction number = 2.113974e+05\n Vnewton: Attempting damping, relres = 0.047573\n Vnewton: Attempting damping, relres = 0.515375\n Vnewton: Damping accepted, relres = 0.047573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.757263e-02\n Vprtstp: contraction number = 4.757263e-02\n Vnewton: Using errtol_s: 203448.048803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.255782e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.056545e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.589098e+04\n Vprtstp: contraction number = 4.589098e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.811582e-03\n Vprtstp: contraction number = 2.062443e-01\n Vnewton: Using errtol_s: 41959.996661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.323674e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.102684e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404662e+04\n Vprtstp: contraction number = 1.404662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.960291e-03\n Vprtstp: contraction number = 3.017139e-01\n Vnewton: Using errtol_s: 12659.913691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.389726e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.144562e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.279840e+03\n Vprtstp: contraction number = 5.279840e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111524e-03\n Vprtstp: contraction number = 3.754781e-01\n Vnewton: Using errtol_s: 4753.520446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.455974e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.187443e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.336921e+03\n Vprtstp: contraction number = 2.336921e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.918609e-04\n Vprtstp: contraction number = 4.425102e-01\n Vnewton: Using errtol_s: 2103.481419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.521494e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.231169e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194576e+03\n Vprtstp: contraction number = 1.194576e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.514070e-04\n Vprtstp: contraction number = 5.111344e-01\n Vnewton: Using errtol_s: 1075.161658\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.587940e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.308010e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.792983e+02\n Vprtstp: contraction number = 6.792983e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.429594e-04\n Vprtstp: contraction number = 5.686374e-01\n Vnewton: Using errtol_s: 611.377148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.655334e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.351957e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.154648e+02\n Vprtstp: contraction number = 4.154648e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.743449e-05\n Vprtstp: contraction number = 6.116036e-01\n Vnewton: Using errtol_s: 373.920435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.729002e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.397404e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660684e+02\n Vprtstp: contraction number = 2.660684e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.599388e-05\n Vprtstp: contraction number = 6.404095e-01\n Vnewton: Using errtol_s: 239.462182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.800820e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.439601e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755593e+02\n Vprtstp: contraction number = 1.755593e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.694626e-05\n Vprtstp: contraction number = 6.598268e-01\n Vnewton: Using errtol_s: 158.003576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.868957e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.483083e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183176e+02\n Vprtstp: contraction number = 1.183176e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.489979e-05\n Vprtstp: contraction number = 6.739462e-01\n Vnewton: Using errtol_s: 106.485913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.939692e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.526744e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.102710e+01\n Vprtstp: contraction number = 8.102710e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705205e-05\n Vprtstp: contraction number = 6.848271e-01\n Vnewton: Using errtol_s: 72.924443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.014724e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.572515e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.628393e+01\n Vprtstp: contraction number = 5.628393e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.184488e-05\n Vprtstp: contraction number = 6.946308e-01\n Vnewton: Using errtol_s: 50.655566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.085739e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.614576e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955755e+01\n Vprtstp: contraction number = 3.955755e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.324836e-06\n Vprtstp: contraction number = 7.028213e-01\n Vnewton: Using errtol_s: 35.601810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.157855e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.660838e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.808103e+01\n Vprtstp: contraction number = 2.808103e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.909617e-06\n Vprtstp: contraction number = 7.098779e-01\n Vnewton: Using errtol_s: 25.272937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.233161e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.714735e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.010039e+01\n Vprtstp: contraction number = 2.010039e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 4.230100e-06\n Vprtstp: contraction number = 7.157995e-01\n Vnewton: Using errtol_s: 18.090355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.308201e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.765583e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.449222e+01\n Vprtstp: contraction number = 1.449222e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 3.049867e-06\n Vprtstp: contraction number = 7.209918e-01\n Vnewton: Using errtol_s: 13.042997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.382991e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.814971e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051084e+01\n Vprtstp: contraction number = 1.051084e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 2.211992e-06\n Vprtstp: contraction number = 7.252749e-01\n Vnewton: Using errtol_s: 9.459758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.459991e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.860741e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.663626e+00\n Vprtstp: contraction number = 7.663626e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.612800e-06\n Vprtstp: contraction number = 7.291164e-01\n Vnewton: Using errtol_s: 6.897264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.533420e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.902021e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.612195e+00\n Vprtstp: contraction number = 5.612195e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 1.181079e-06\n Vprtstp: contraction number = 7.323158e-01\n Vnewton: Using errtol_s: 5.050976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.601513e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.947660e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.124624e+00\n Vprtstp: contraction number = 4.124624e+00\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 8.680215e-07\n Vprtstp: contraction number = 7.349396e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.517958e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.543896e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.952995e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.015876e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -11817,17 +11817,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.931678298316E+00 kT\n Vpmg_energy:  qfEnergy = 1.306896751937E+04 kT\n Vpmg_energy:  dielEnergy = 6.531231404824E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.649000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.969000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -11873,193 +11873,193 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.20964 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.403245\n+Vacc_SASA: Time elapsed: 1.384511\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.901908e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.098630e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.936300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.538100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.254530e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.959100e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.877284e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.218825e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 6738070.309592\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.900994e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.236442e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.878637e+05\n Vprtstp: contraction number = 6.878637e+05\n Vnewton: Attempting damping, relres = 0.093216\n Vnewton: Attempting damping, relres = 0.543864\n Vnewton: Damping accepted, relres = 0.093216\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.321581e-02\n Vprtstp: contraction number = 9.321581e-02\n Vnewton: Using errtol_s: 628094.651911\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.015266e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.291404e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.296036e+05\n Vprtstp: contraction number = 1.296036e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.735879e-02\n Vprtstp: contraction number = 1.862215e-01\n Vnewton: Using errtol_s: 116964.740632\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.105756e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.332646e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.402622e+04\n Vprtstp: contraction number = 3.402622e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.547490e-03\n Vprtstp: contraction number = 2.619705e-01\n Vnewton: Using errtol_s: 30641.306038\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.199593e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.378725e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.090470e+04\n Vprtstp: contraction number = 1.090470e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.456938e-03\n Vprtstp: contraction number = 3.203829e-01\n Vnewton: Using errtol_s: 9816.950613\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.288083e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.423877e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.894978e+03\n Vprtstp: contraction number = 3.894978e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.203198e-04\n Vprtstp: contraction number = 3.571324e-01\n Vnewton: Using errtol_s: 3505.951173\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.379148e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.470893e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.485775e+03\n Vprtstp: contraction number = 1.485775e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.984627e-04\n Vprtstp: contraction number = 3.814246e-01\n Vnewton: Using errtol_s: 1337.255961\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.464246e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.512373e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.014858e+02\n Vprtstp: contraction number = 6.014858e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.034105e-05\n Vprtstp: contraction number = 4.048168e-01\n Vnewton: Using errtol_s: 541.343626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.549956e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.596196e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.638957e+02\n Vprtstp: contraction number = 2.638957e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.524853e-05\n Vprtstp: contraction number = 4.387363e-01\n Vnewton: Using errtol_s: 237.507104\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.638424e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.640958e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.262556e+02\n Vprtstp: contraction number = 1.262556e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.686391e-05\n Vprtstp: contraction number = 4.784287e-01\n Vnewton: Using errtol_s: 113.630225\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.724491e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.686357e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.580661e+01\n Vprtstp: contraction number = 6.580661e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.789758e-06\n Vprtstp: contraction number = 5.212170e-01\n Vnewton: Using errtol_s: 59.226009\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.808681e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.731347e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.615710e+01\n Vprtstp: contraction number = 3.615710e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.829486e-06\n Vprtstp: contraction number = 5.494446e-01\n Vnewton: Using errtol_s: 32.541413\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.890060e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.777786e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.063008e+01\n Vprtstp: contraction number = 2.063008e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 2.755549e-06\n Vprtstp: contraction number = 5.705677e-01\n Vnewton: Using errtol_s: 18.567080\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.972154e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.822561e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.211023e+01\n Vprtstp: contraction number = 1.211023e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.617557e-06\n Vprtstp: contraction number = 5.870182e-01\n Vnewton: Using errtol_s: 10.899214\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.053177e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.864209e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.261707e+00\n Vprtstp: contraction number = 7.261707e+00\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 9.699420e-07\n Vprtstp: contraction number = 5.996338e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.247322e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.272882e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.840445e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.079830e+00\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -12068,15 +12068,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.020343911890E+00 kT\n Vpmg_energy:  qfEnergy = 1.026826573171E+05 kT\n Vpmg_energy:  dielEnergy = 5.129339805665E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.661300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.283600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -12099,261 +12099,261 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.003024\n+Vacc_SASA: Time elapsed: 3.029403\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.369042e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.486748e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.905600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.999900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.249450e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.961250e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.488614e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.275351e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.510372e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.292056e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.298565e+05\n Vprtstp: contraction number = 4.298565e+05\n Vnewton: Attempting damping, relres = 0.048079\n Vnewton: Attempting damping, relres = 0.515481\n Vnewton: Damping accepted, relres = 0.048079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.807904e-02\n Vprtstp: contraction number = 4.807904e-02\n Vnewton: Using errtol_s: 418259.137179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.610346e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.346095e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.275297e+04\n Vprtstp: contraction number = 9.275297e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.791706e-03\n Vprtstp: contraction number = 2.036585e-01\n Vnewton: Using errtol_s: 85182.030508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.695178e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.389831e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.830324e+04\n Vprtstp: contraction number = 2.830324e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.931540e-03\n Vprtstp: contraction number = 2.993901e-01\n Vnewton: Using errtol_s: 25502.653903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.778832e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.436750e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066383e+04\n Vprtstp: contraction number = 1.066383e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.103407e-03\n Vprtstp: contraction number = 3.763916e-01\n Vnewton: Using errtol_s: 9598.985602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.864102e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.480502e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725476e+03\n Vprtstp: contraction number = 4.725476e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.889004e-04\n Vprtstp: contraction number = 4.430826e-01\n Vnewton: Using errtol_s: 4253.143226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.946982e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.525034e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402868e+03\n Vprtstp: contraction number = 2.402868e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.485940e-04\n Vprtstp: contraction number = 5.084757e-01\n Vnewton: Using errtol_s: 2162.620089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.029809e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.573828e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352802e+03\n Vprtstp: contraction number = 1.352802e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.399556e-04\n Vprtstp: contraction number = 5.629888e-01\n Vnewton: Using errtol_s: 1217.530795\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.112124e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.618408e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164880e+02\n Vprtstp: contraction number = 8.164880e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.447037e-05\n Vprtstp: contraction number = 6.035512e-01\n Vnewton: Using errtol_s: 734.842122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.193990e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.665845e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157033e+02\n Vprtstp: contraction number = 5.157033e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.335238e-05\n Vprtstp: contraction number = 6.316106e-01\n Vnewton: Using errtol_s: 464.134076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.271463e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.713633e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352095e+02\n Vprtstp: contraction number = 3.352095e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.467926e-05\n Vprtstp: contraction number = 6.500040e-01\n Vnewton: Using errtol_s: 301.688999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.358485e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.758525e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.222234e+02\n Vprtstp: contraction number = 2.222234e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.299022e-05\n Vprtstp: contraction number = 6.629387e-01\n Vnewton: Using errtol_s: 200.001301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.444913e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.803632e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.495221e+02\n Vprtstp: contraction number = 1.495221e+02\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.546887e-05\n Vprtstp: contraction number = 6.728456e-01\n Vnewton: Using errtol_s: 134.569993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.527309e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.848593e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018836e+02\n Vprtstp: contraction number = 1.018836e+02\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.054041e-05\n Vprtstp: contraction number = 6.813949e-01\n Vnewton: Using errtol_s: 91.695311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.606288e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.892734e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.012825e+01\n Vprtstp: contraction number = 7.012825e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.255144e-06\n Vprtstp: contraction number = 6.883171e-01\n Vnewton: Using errtol_s: 63.115450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.688030e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.940259e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.869976e+01\n Vprtstp: contraction number = 4.869976e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.038252e-06\n Vprtstp: contraction number = 6.944386e-01\n Vnewton: Using errtol_s: 43.829803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.765457e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.984114e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.408035e+01\n Vprtstp: contraction number = 3.408035e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 3.525795e-06\n Vprtstp: contraction number = 6.998052e-01\n Vnewton: Using errtol_s: 30.672326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.843585e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.030806e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401453e+01\n Vprtstp: contraction number = 2.401453e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 2.484432e-06\n Vprtstp: contraction number = 7.046444e-01\n Vnewton: Using errtol_s: 21.613084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.924188e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.075458e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.702723e+01\n Vprtstp: contraction number = 1.702723e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.761558e-06\n Vprtstp: contraction number = 7.090385e-01\n Vnewton: Using errtol_s: 15.324508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.000591e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.120944e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214065e+01\n Vprtstp: contraction number = 1.214065e+01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.256015e-06\n Vprtstp: contraction number = 7.130137e-01\n Vnewton: Using errtol_s: 10.926584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.078404e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.169412e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.699962e+00\n Vprtstp: contraction number = 8.699962e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 9.000575e-07\n Vprtstp: contraction number = 7.165978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.657863e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.682784e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.294834e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.516008e+00\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -12362,15 +12362,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.165566732606E+00 kT\n Vpmg_energy:  qfEnergy = 1.340422491969E+04 kT\n Vpmg_energy:  dielEnergy = 6.679021613149E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.489000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.114000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -12418,193 +12418,193 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.210204 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.007402\n+Vacc_SASA: Time elapsed: 3.012776\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.657274e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.877177e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.986200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.045100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.414980e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.073260e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.541185e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.618677e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8285587.408912\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.571950e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.636516e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.439767e+05\n Vprtstp: contraction number = 8.439767e+05\n Vnewton: Attempting damping, relres = 0.093056\n Vnewton: Attempting damping, relres = 0.543707\n Vnewton: Damping accepted, relres = 0.093056\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.305605e-02\n Vprtstp: contraction number = 9.305605e-02\n Vnewton: Using errtol_s: 771024.060477\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.687008e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.690457e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.575262e+05\n Vprtstp: contraction number = 1.575262e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.715846e-02\n Vprtstp: contraction number = 1.843885e-01\n Vnewton: Using errtol_s: 142167.953902\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.785697e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.736042e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.047316e+04\n Vprtstp: contraction number = 4.047316e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.398299e-03\n Vprtstp: contraction number = 2.563341e-01\n Vnewton: Using errtol_s: 36442.493025\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.874570e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.840570e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.265955e+04\n Vprtstp: contraction number = 1.265955e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.375423e-03\n Vprtstp: contraction number = 3.127169e-01\n Vnewton: Using errtol_s: 11396.183497\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.958257e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.886860e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.418878e+03\n Vprtstp: contraction number = 4.418878e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.800426e-04\n Vprtstp: contraction number = 3.490147e-01\n Vnewton: Using errtol_s: 3977.435333\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.048048e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.933631e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.644482e+03\n Vprtstp: contraction number = 1.644482e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.786343e-04\n Vprtstp: contraction number = 3.721217e-01\n Vnewton: Using errtol_s: 1480.089823\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.132294e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.978974e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.478261e+02\n Vprtstp: contraction number = 6.478261e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.036914e-05\n Vprtstp: contraction number = 3.939286e-01\n Vnewton: Using errtol_s: 583.049663\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.217600e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.024218e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.772344e+02\n Vprtstp: contraction number = 2.772344e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.011396e-05\n Vprtstp: contraction number = 4.279428e-01\n Vnewton: Using errtol_s: 249.511882\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.309095e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.065654e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.301479e+02\n Vprtstp: contraction number = 1.301479e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.413700e-05\n Vprtstp: contraction number = 4.694500e-01\n Vnewton: Using errtol_s: 117.133345\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.393738e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.111329e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.695205e+01\n Vprtstp: contraction number = 6.695205e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.272497e-06\n Vprtstp: contraction number = 5.144300e-01\n Vnewton: Using errtol_s: 60.256908\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.473964e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.156759e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.650946e+01\n Vprtstp: contraction number = 3.650946e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.965746e-06\n Vprtstp: contraction number = 5.453073e-01\n Vnewton: Using errtol_s: 32.858531\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.559207e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.199805e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.073747e+01\n Vprtstp: contraction number = 2.073747e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 2.252553e-06\n Vprtstp: contraction number = 5.680025e-01\n Vnewton: Using errtol_s: 18.663727\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.644935e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.296974e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.213300e+01\n Vprtstp: contraction number = 1.213300e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.317915e-06\n Vprtstp: contraction number = 5.850760e-01\n Vnewton: Using errtol_s: 10.919699\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.732462e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.344418e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.261261e+00\n Vprtstp: contraction number = 7.261261e+00\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.887354e-07\n Vprtstp: contraction number = 5.984722e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.270862e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.298318e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.629073e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.877763e+00\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -12613,27 +12613,27 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.327562716911E+00 kT\n Vpmg_energy:  qfEnergy = 1.051514241768E+05 kT\n Vpmg_energy:  dielEnergy = 5.245601820017E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.288500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.284900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.838756e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 6.409088e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:26:21 2025\n+# Creation Date and Time:  Sun Jan  7 09:39:35 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -12986,250 +12986,250 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.361494\n+Vacc_SASA: Time elapsed: 1.378781\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.584076e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.651059e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.185000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.007900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.001040e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.899130e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.975980e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.043330e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.122889e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.232936e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.136321e+05\n Vprtstp: contraction number = 2.136321e+05\n Vnewton: Attempting damping, relres = 0.047663\n Vnewton: Attempting damping, relres = 0.515490\n Vnewton: Damping accepted, relres = 0.047663\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.766304e-02\n Vprtstp: contraction number = 4.766304e-02\n Vnewton: Using errtol_s: 204994.485638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.876520e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.790230e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.587025e+04\n Vprtstp: contraction number = 4.587025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.727679e-03\n Vprtstp: contraction number = 2.040927e-01\n Vnewton: Using errtol_s: 41837.880528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.590787e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.230849e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.391016e+04\n Vprtstp: contraction number = 1.391016e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.912173e-03\n Vprtstp: contraction number = 2.993697e-01\n Vnewton: Using errtol_s: 12524.995351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.290030e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.702957e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.237707e+03\n Vprtstp: contraction number = 5.237707e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.096054e-03\n Vprtstp: contraction number = 3.763697e-01\n Vnewton: Using errtol_s: 4714.028550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.941440e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.177289e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.331453e+03\n Vprtstp: contraction number = 2.331453e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.878779e-04\n Vprtstp: contraction number = 4.451223e-01\n Vnewton: Using errtol_s: 2098.319320\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.634875e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.615132e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189035e+03\n Vprtstp: contraction number = 1.189035e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.488161e-04\n Vprtstp: contraction number = 5.099966e-01\n Vnewton: Using errtol_s: 1070.135650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.394325e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.055884e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.678182e+02\n Vprtstp: contraction number = 6.678182e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.397467e-04\n Vprtstp: contraction number = 5.616468e-01\n Vnewton: Using errtol_s: 601.038216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.128995e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.701718e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.994733e+02\n Vprtstp: contraction number = 3.994733e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.359319e-05\n Vprtstp: contraction number = 5.981764e-01\n Vnewton: Using errtol_s: 359.526862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.857569e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.169386e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.488647e+02\n Vprtstp: contraction number = 2.488647e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.207703e-05\n Vprtstp: contraction number = 6.229817e-01\n Vnewton: Using errtol_s: 223.978670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.648448e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.652231e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.588671e+02\n Vprtstp: contraction number = 1.588671e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.324425e-05\n Vprtstp: contraction number = 6.383669e-01\n Vnewton: Using errtol_s: 142.980568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.447767e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.102669e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.030284e+02\n Vprtstp: contraction number = 1.030284e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.155954e-05\n Vprtstp: contraction number = 6.485194e-01\n Vnewton: Using errtol_s: 92.725673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.021385e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.553293e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.760657e+01\n Vprtstp: contraction number = 6.760657e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.414722e-05\n Vprtstp: contraction number = 6.561932e-01\n Vnewton: Using errtol_s: 60.845953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.096247e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.003216e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.480217e+01\n Vprtstp: contraction number = 4.480217e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.375216e-06\n Vprtstp: contraction number = 6.626894e-01\n Vnewton: Using errtol_s: 40.321969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.176967e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.449310e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990735e+01\n Vprtstp: contraction number = 2.990735e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 6.258355e-06\n Vprtstp: contraction number = 6.675424e-01\n Vnewton: Using errtol_s: 26.916626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.261586e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.898112e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.008505e+01\n Vprtstp: contraction number = 2.008505e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 4.202958e-06\n Vprtstp: contraction number = 6.715755e-01\n Vnewton: Using errtol_s: 18.076547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.339925e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.453026e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356100e+01\n Vprtstp: contraction number = 1.356100e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 2.837748e-06\n Vprtstp: contraction number = 6.751787e-01\n Vnewton: Using errtol_s: 12.204901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.418242e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.018563e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.198733e+00\n Vprtstp: contraction number = 9.198733e+00\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 1.924909e-06\n Vprtstp: contraction number = 6.783227e-01\n Vnewton: Using errtol_s: 8.278861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.494326e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.065639e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.265697e+00\n Vprtstp: contraction number = 6.265697e+00\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.311147e-06\n Vprtstp: contraction number = 6.811478e-01\n Vnewton: Using errtol_s: 5.639128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.569388e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.111792e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.284635e+00\n Vprtstp: contraction number = 4.284635e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 8.965941e-07\n Vprtstp: contraction number = 6.838241e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.433421e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.456774e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.438133e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.665524e+00\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -13238,17 +13238,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.135373636445E-01 kT\n Vpmg_energy:  qfEnergy = 1.691003222948E+03 kT\n Vpmg_energy:  dielEnergy = 8.436188542984E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.029000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.126000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -13294,160 +13294,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00316557 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.353803\n+Vacc_SASA: Time elapsed: 1.364076\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.608920e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.853728e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.127000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.116600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.920810e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.972780e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.815691e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.358358e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2672785.067134\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.830723e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.374826e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.848718e+05\n Vprtstp: contraction number = 2.848718e+05\n Vnewton: Attempting damping, relres = 0.096187\n Vnewton: Attempting damping, relres = 0.545650\n Vnewton: Damping accepted, relres = 0.096187\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.618699e-02\n Vprtstp: contraction number = 9.618699e-02\n Vnewton: Using errtol_s: 257087.160547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.926384e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.463491e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.201088e+04\n Vprtstp: contraction number = 5.201088e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.751490e-02\n Vprtstp: contraction number = 1.820922e-01\n Vnewton: Using errtol_s: 46813.558642\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.020700e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.512916e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.230808e+04\n Vprtstp: contraction number = 1.230808e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.144590e-03\n Vprtstp: contraction number = 2.366322e-01\n Vnewton: Using errtol_s: 11077.597147\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.118444e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.563010e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.460119e+03\n Vprtstp: contraction number = 3.460119e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.165151e-03\n Vprtstp: contraction number = 2.811258e-01\n Vnewton: Using errtol_s: 3114.198540\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.211042e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.608522e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.085640e+03\n Vprtstp: contraction number = 1.085640e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.655733e-04\n Vprtstp: contraction number = 3.137561e-01\n Vnewton: Using errtol_s: 977.098856\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.298113e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.655139e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.609545e+02\n Vprtstp: contraction number = 3.609545e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.215452e-04\n Vprtstp: contraction number = 3.324784e-01\n Vnewton: Using errtol_s: 324.864231\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.384886e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.705132e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.235133e+02\n Vprtstp: contraction number = 1.235133e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.159074e-05\n Vprtstp: contraction number = 3.421833e-01\n Vnewton: Using errtol_s: 111.163117\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.469703e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.750450e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.301270e+01\n Vprtstp: contraction number = 4.301270e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.448364e-05\n Vprtstp: contraction number = 3.482419e-01\n Vnewton: Using errtol_s: 38.711660\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.555094e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.796625e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.517421e+01\n Vprtstp: contraction number = 1.517421e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.109589e-06\n Vprtstp: contraction number = 3.527835e-01\n Vnewton: Using errtol_s: 13.656834\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.648184e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.846433e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.423218e+00\n Vprtstp: contraction number = 5.423218e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.826149e-06\n Vprtstp: contraction number = 3.573964e-01\n Vnewton: Using errtol_s: 4.880904\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.742302e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.899834e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.968727e+00\n Vprtstp: contraction number = 1.968727e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.629250e-07\n Vprtstp: contraction number = 3.630180e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.991673e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.021710e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.837578e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.073483e+00\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -13456,17 +13456,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.949229903470E-01 kT\n Vpmg_energy:  qfEnergy = 1.339241623976E+04 kT\n Vpmg_energy:  dielEnergy = 6.685521328541E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.754700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.535900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -13487,272 +13487,272 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.399940\n+Vacc_SASA: Time elapsed: 1.413267\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.659564e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.701558e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.203800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.013000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.277240e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.976060e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.009364e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.137809e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.034930e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.155165e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.113974e+05\n Vprtstp: contraction number = 2.113974e+05\n Vnewton: Attempting damping, relres = 0.047573\n Vnewton: Attempting damping, relres = 0.515375\n Vnewton: Damping accepted, relres = 0.047573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.757263e-02\n Vprtstp: contraction number = 4.757263e-02\n Vnewton: Using errtol_s: 203448.048803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.136973e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.211325e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.589098e+04\n Vprtstp: contraction number = 4.589098e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.811582e-03\n Vprtstp: contraction number = 2.062443e-01\n Vnewton: Using errtol_s: 41959.996661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.224567e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.254306e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404662e+04\n Vprtstp: contraction number = 1.404662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.960291e-03\n Vprtstp: contraction number = 3.017139e-01\n Vnewton: Using errtol_s: 12659.913691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.307137e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.303739e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.279840e+03\n Vprtstp: contraction number = 5.279840e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111524e-03\n Vprtstp: contraction number = 3.754781e-01\n Vnewton: Using errtol_s: 4753.520446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.384795e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.352504e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.336921e+03\n Vprtstp: contraction number = 2.336921e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.918609e-04\n Vprtstp: contraction number = 4.425102e-01\n Vnewton: Using errtol_s: 2103.481419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.460494e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.401681e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194576e+03\n Vprtstp: contraction number = 1.194576e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.514070e-04\n Vprtstp: contraction number = 5.111344e-01\n Vnewton: Using errtol_s: 1075.161658\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.531560e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.447819e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.792983e+02\n Vprtstp: contraction number = 6.792983e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.429594e-04\n Vprtstp: contraction number = 5.686374e-01\n Vnewton: Using errtol_s: 611.377148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.604502e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.492314e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.154648e+02\n Vprtstp: contraction number = 4.154648e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.743449e-05\n Vprtstp: contraction number = 6.116036e-01\n Vnewton: Using errtol_s: 373.920435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.677873e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.536685e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660684e+02\n Vprtstp: contraction number = 2.660684e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.599388e-05\n Vprtstp: contraction number = 6.404095e-01\n Vnewton: Using errtol_s: 239.462182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.752380e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.581714e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755593e+02\n Vprtstp: contraction number = 1.755593e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.694626e-05\n Vprtstp: contraction number = 6.598268e-01\n Vnewton: Using errtol_s: 158.003576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.823905e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.626072e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183176e+02\n Vprtstp: contraction number = 1.183176e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.489979e-05\n Vprtstp: contraction number = 6.739462e-01\n Vnewton: Using errtol_s: 106.485913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.896637e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.673645e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.102710e+01\n Vprtstp: contraction number = 8.102710e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705205e-05\n Vprtstp: contraction number = 6.848271e-01\n Vnewton: Using errtol_s: 72.924443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.970891e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.718694e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.628393e+01\n Vprtstp: contraction number = 5.628393e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.184488e-05\n Vprtstp: contraction number = 6.946308e-01\n Vnewton: Using errtol_s: 50.655566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.047654e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.761938e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955755e+01\n Vprtstp: contraction number = 3.955755e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.324836e-06\n Vprtstp: contraction number = 7.028213e-01\n Vnewton: Using errtol_s: 35.601810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.124889e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.807388e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.808103e+01\n Vprtstp: contraction number = 2.808103e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.909617e-06\n Vprtstp: contraction number = 7.098779e-01\n Vnewton: Using errtol_s: 25.272937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.206176e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.852720e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.010039e+01\n Vprtstp: contraction number = 2.010039e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 4.230100e-06\n Vprtstp: contraction number = 7.157995e-01\n Vnewton: Using errtol_s: 18.090355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.283230e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.898063e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.449222e+01\n Vprtstp: contraction number = 1.449222e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 3.049867e-06\n Vprtstp: contraction number = 7.209918e-01\n Vnewton: Using errtol_s: 13.042997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.360931e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.942884e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051084e+01\n Vprtstp: contraction number = 1.051084e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 2.211992e-06\n Vprtstp: contraction number = 7.252749e-01\n Vnewton: Using errtol_s: 9.459758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.437018e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.988131e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.663626e+00\n Vprtstp: contraction number = 7.663626e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.612800e-06\n Vprtstp: contraction number = 7.291164e-01\n Vnewton: Using errtol_s: 6.897264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.518451e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.033757e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.612195e+00\n Vprtstp: contraction number = 5.612195e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 1.181079e-06\n Vprtstp: contraction number = 7.323158e-01\n Vnewton: Using errtol_s: 5.050976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.595885e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.077816e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.124624e+00\n Vprtstp: contraction number = 4.124624e+00\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 8.680215e-07\n Vprtstp: contraction number = 7.349396e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.656656e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.682940e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.763785e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.999645e+00\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -13761,17 +13761,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.295996694909E-02 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 1.633599871123E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.300000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.035000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -13817,149 +13817,149 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00294201 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.383950\n+Vacc_SASA: Time elapsed: 1.379126\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.567266e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.691670e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.051900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.117000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.018010e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.996680e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.847353e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.308270e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1184087.054280\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.862975e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.324966e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.354114e+05\n Vprtstp: contraction number = 1.354114e+05\n Vnewton: Attempting damping, relres = 0.103158\n Vnewton: Attempting damping, relres = 0.548288\n Vnewton: Damping accepted, relres = 0.103158\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.031582e-01\n Vprtstp: contraction number = 1.031582e-01\n Vnewton: Using errtol_s: 122148.348169\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.935805e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.382607e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.326538e+04\n Vprtstp: contraction number = 2.326538e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.769124e-02\n Vprtstp: contraction number = 1.714961e-01\n Vnewton: Using errtol_s: 20947.970777\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.003578e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.426552e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.939304e+03\n Vprtstp: contraction number = 4.939304e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.754561e-03\n Vprtstp: contraction number = 2.122271e-01\n Vnewton: Using errtol_s: 4445.727289\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.071854e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.469797e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.225369e+03\n Vprtstp: contraction number = 1.225369e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 9.313919e-04\n Vprtstp: contraction number = 2.480695e-01\n Vnewton: Using errtol_s: 1102.849143\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.138088e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.518236e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.425596e+02\n Vprtstp: contraction number = 3.425596e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 2.603732e-04\n Vprtstp: contraction number = 2.795528e-01\n Vnewton: Using errtol_s: 308.304585\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.207715e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.562734e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.033702e+02\n Vprtstp: contraction number = 1.033702e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 7.856958e-05\n Vprtstp: contraction number = 3.017575e-01\n Vnewton: Using errtol_s: 93.033224\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.282731e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.605147e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.261191e+01\n Vprtstp: contraction number = 3.261191e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.478764e-05\n Vprtstp: contraction number = 3.154865e-01\n Vnewton: Using errtol_s: 29.350728\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.355437e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.662745e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.060426e+01\n Vprtstp: contraction number = 1.060426e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.060077e-06\n Vprtstp: contraction number = 3.251651e-01\n Vnewton: Using errtol_s: 9.543833\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.433771e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.707800e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.527652e+00\n Vprtstp: contraction number = 3.527652e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.681295e-06\n Vprtstp: contraction number = 3.326637e-01\n Vnewton: Using errtol_s: 3.174887\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.508610e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.753071e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.192253e+00\n Vprtstp: contraction number = 1.192253e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 9.062069e-07\n Vprtstp: contraction number = 3.379736e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.172551e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.405796e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.836008e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.072841e+00\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -13968,17 +13968,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.599874663970E-02 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 1.358739023374E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.458900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.440800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -13999,261 +13999,261 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.001629\n+Vacc_SASA: Time elapsed: 3.005274\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.324068e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.495160e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.023100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.008200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.426540e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.958830e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.925884e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.165346e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.946051e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.182654e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.298565e+05\n Vprtstp: contraction number = 4.298565e+05\n Vnewton: Attempting damping, relres = 0.048079\n Vnewton: Attempting damping, relres = 0.515481\n Vnewton: Damping accepted, relres = 0.048079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.807904e-02\n Vprtstp: contraction number = 4.807904e-02\n Vnewton: Using errtol_s: 418259.137179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.031225e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.236306e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.275297e+04\n Vprtstp: contraction number = 9.275297e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.791706e-03\n Vprtstp: contraction number = 2.036585e-01\n Vnewton: Using errtol_s: 85182.030508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.103414e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.283692e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.830324e+04\n Vprtstp: contraction number = 2.830324e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.931540e-03\n Vprtstp: contraction number = 2.993901e-01\n Vnewton: Using errtol_s: 25502.653903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.181096e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.328790e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066383e+04\n Vprtstp: contraction number = 1.066383e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.103407e-03\n Vprtstp: contraction number = 3.763916e-01\n Vnewton: Using errtol_s: 9598.985602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.257885e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.373826e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725476e+03\n Vprtstp: contraction number = 4.725476e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.889004e-04\n Vprtstp: contraction number = 4.430826e-01\n Vnewton: Using errtol_s: 4253.143226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.333417e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.423121e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402868e+03\n Vprtstp: contraction number = 2.402868e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.485940e-04\n Vprtstp: contraction number = 5.084757e-01\n Vnewton: Using errtol_s: 2162.620089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.409544e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.541541e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352802e+03\n Vprtstp: contraction number = 1.352802e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.399556e-04\n Vprtstp: contraction number = 5.629888e-01\n Vnewton: Using errtol_s: 1217.530795\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.485586e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.589436e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164880e+02\n Vprtstp: contraction number = 8.164880e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.447037e-05\n Vprtstp: contraction number = 6.035512e-01\n Vnewton: Using errtol_s: 734.842122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.559574e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.634784e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157033e+02\n Vprtstp: contraction number = 5.157033e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.335238e-05\n Vprtstp: contraction number = 6.316106e-01\n Vnewton: Using errtol_s: 464.134076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.635118e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.678948e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352095e+02\n Vprtstp: contraction number = 3.352095e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.467926e-05\n Vprtstp: contraction number = 6.500040e-01\n Vnewton: Using errtol_s: 301.688999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.709624e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.723354e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.222234e+02\n Vprtstp: contraction number = 2.222234e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.299022e-05\n Vprtstp: contraction number = 6.629387e-01\n Vnewton: Using errtol_s: 200.001301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.791597e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.768403e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.495221e+02\n Vprtstp: contraction number = 1.495221e+02\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.546887e-05\n Vprtstp: contraction number = 6.728456e-01\n Vnewton: Using errtol_s: 134.569993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.875495e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.812566e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018836e+02\n Vprtstp: contraction number = 1.018836e+02\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.054041e-05\n Vprtstp: contraction number = 6.813949e-01\n Vnewton: Using errtol_s: 91.695311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.951167e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.862488e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.012825e+01\n Vprtstp: contraction number = 7.012825e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.255144e-06\n Vprtstp: contraction number = 6.883171e-01\n Vnewton: Using errtol_s: 63.115450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.024033e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.928666e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.869976e+01\n Vprtstp: contraction number = 4.869976e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.038252e-06\n Vprtstp: contraction number = 6.944386e-01\n Vnewton: Using errtol_s: 43.829803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.098139e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.976645e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.408035e+01\n Vprtstp: contraction number = 3.408035e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 3.525795e-06\n Vprtstp: contraction number = 6.998052e-01\n Vnewton: Using errtol_s: 30.672326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.169449e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.022179e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401453e+01\n Vprtstp: contraction number = 2.401453e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 2.484432e-06\n Vprtstp: contraction number = 7.046444e-01\n Vnewton: Using errtol_s: 21.613084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.244041e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.067286e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.702723e+01\n Vprtstp: contraction number = 1.702723e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.761558e-06\n Vprtstp: contraction number = 7.090385e-01\n Vnewton: Using errtol_s: 15.324508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.318552e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.114286e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214065e+01\n Vprtstp: contraction number = 1.214065e+01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.256015e-06\n Vprtstp: contraction number = 7.130137e-01\n Vnewton: Using errtol_s: 10.926584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.391360e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.157371e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.699962e+00\n Vprtstp: contraction number = 8.699962e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 9.000575e-07\n Vprtstp: contraction number = 7.165978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.530822e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.557688e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.029996e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.052104e+01\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -14262,15 +14262,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.987808702613E-01 kT\n Vpmg_energy:  qfEnergy = 1.699917781088E+03 kT\n Vpmg_energy:  dielEnergy = 8.464002723965E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.168000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.315000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -14318,160 +14318,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0124265 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.007742\n+Vacc_SASA: Time elapsed: 3.008957\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.463687e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.628415e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.042400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.916200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.387080e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.919260e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.831351e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.582256e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3745818.555400\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.856513e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.601080e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.036148e+05\n Vprtstp: contraction number = 4.036148e+05\n Vnewton: Attempting damping, relres = 0.097470\n Vnewton: Attempting damping, relres = 0.545903\n Vnewton: Damping accepted, relres = 0.097470\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.746961e-02\n Vprtstp: contraction number = 9.746961e-02\n Vnewton: Using errtol_s: 365103.476411\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.967513e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.656102e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.291408e+04\n Vprtstp: contraction number = 7.291408e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.752435e-02\n Vprtstp: contraction number = 1.797929e-01\n Vnewton: Using errtol_s: 65643.018240\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.052996e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.701171e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.675888e+04\n Vprtstp: contraction number = 1.675888e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.026892e-03\n Vprtstp: contraction number = 2.297884e-01\n Vnewton: Using errtol_s: 15084.007144\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.136367e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.745371e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.533188e+03\n Vprtstp: contraction number = 4.533188e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.089215e-03\n Vprtstp: contraction number = 2.704853e-01\n Vnewton: Using errtol_s: 4080.002297\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.220983e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.789736e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.369611e+03\n Vprtstp: contraction number = 1.369611e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.290808e-04\n Vprtstp: contraction number = 3.021265e-01\n Vnewton: Using errtol_s: 1232.676861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.306621e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.833581e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.398009e+02\n Vprtstp: contraction number = 4.398009e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.056716e-04\n Vprtstp: contraction number = 3.211115e-01\n Vnewton: Using errtol_s: 395.826722\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.391262e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.880859e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.460593e+02\n Vprtstp: contraction number = 1.460593e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.509370e-05\n Vprtstp: contraction number = 3.321014e-01\n Vnewton: Using errtol_s: 131.454614\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.472340e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.924145e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.960244e+01\n Vprtstp: contraction number = 4.960244e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.191794e-05\n Vprtstp: contraction number = 3.396035e-01\n Vnewton: Using errtol_s: 44.642449\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.558844e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.968686e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.713194e+01\n Vprtstp: contraction number = 1.713194e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.116267e-06\n Vprtstp: contraction number = 3.453841e-01\n Vnewton: Using errtol_s: 15.418791\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.639461e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.012493e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.017264e+00\n Vprtstp: contraction number = 6.017264e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.445758e-06\n Vprtstp: contraction number = 3.512303e-01\n Vnewton: Using errtol_s: 5.415546\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.722483e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.059464e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.154066e+00\n Vprtstp: contraction number = 2.154066e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.175534e-07\n Vprtstp: contraction number = 3.579807e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.631533e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.902263e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.138399e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.366416e+00\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -14480,27 +14480,27 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 3.618650308113E-01 kT\n Vpmg_energy:  qfEnergy = 1.339466431031E+04 kT\n Vpmg_energy:  dielEnergy = 6.686807479145E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.420200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.418200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.821425e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 6.123376e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:27:06 2025\n+# Creation Date and Time:  Sun Jan  7 09:40:00 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -14853,250 +14853,250 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.366556\n+Vacc_SASA: Time elapsed: 1.369865\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.530527e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.652423e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.008400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.013600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.027370e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.913000e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.876854e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.050218e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.051644e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.225754e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.136321e+05\n Vprtstp: contraction number = 2.136321e+05\n Vnewton: Attempting damping, relres = 0.047663\n Vnewton: Attempting damping, relres = 0.515490\n Vnewton: Damping accepted, relres = 0.047663\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.766304e-02\n Vprtstp: contraction number = 4.766304e-02\n Vnewton: Using errtol_s: 204994.485638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.862663e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.788467e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.587025e+04\n Vprtstp: contraction number = 4.587025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.727679e-03\n Vprtstp: contraction number = 2.040927e-01\n Vnewton: Using errtol_s: 41837.880528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.550993e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.245457e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.391016e+04\n Vprtstp: contraction number = 1.391016e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.912173e-03\n Vprtstp: contraction number = 2.993697e-01\n Vnewton: Using errtol_s: 12524.995351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.233323e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.696515e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.237707e+03\n Vprtstp: contraction number = 5.237707e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.096054e-03\n Vprtstp: contraction number = 3.763697e-01\n Vnewton: Using errtol_s: 4714.028550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.922800e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.144257e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.331453e+03\n Vprtstp: contraction number = 2.331453e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.878779e-04\n Vprtstp: contraction number = 4.451223e-01\n Vnewton: Using errtol_s: 2098.319320\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.608243e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.608162e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189035e+03\n Vprtstp: contraction number = 1.189035e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.488161e-04\n Vprtstp: contraction number = 5.099966e-01\n Vnewton: Using errtol_s: 1070.135650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.285513e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.068532e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.678182e+02\n Vprtstp: contraction number = 6.678182e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.397467e-04\n Vprtstp: contraction number = 5.616468e-01\n Vnewton: Using errtol_s: 601.038216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.968098e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.530229e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.994733e+02\n Vprtstp: contraction number = 3.994733e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.359319e-05\n Vprtstp: contraction number = 5.981764e-01\n Vnewton: Using errtol_s: 359.526862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.691809e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.991338e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.488647e+02\n Vprtstp: contraction number = 2.488647e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.207703e-05\n Vprtstp: contraction number = 6.229817e-01\n Vnewton: Using errtol_s: 223.978670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.373496e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.440058e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.588671e+02\n Vprtstp: contraction number = 1.588671e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.324425e-05\n Vprtstp: contraction number = 6.383669e-01\n Vnewton: Using errtol_s: 142.980568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.067496e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.896755e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.030284e+02\n Vprtstp: contraction number = 1.030284e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.155954e-05\n Vprtstp: contraction number = 6.485194e-01\n Vnewton: Using errtol_s: 92.725673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.764370e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.345856e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.760657e+01\n Vprtstp: contraction number = 6.760657e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.414722e-05\n Vprtstp: contraction number = 6.561932e-01\n Vnewton: Using errtol_s: 60.845953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.047721e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.821257e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.480217e+01\n Vprtstp: contraction number = 4.480217e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.375216e-06\n Vprtstp: contraction number = 6.626894e-01\n Vnewton: Using errtol_s: 40.321969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.119055e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.273923e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990735e+01\n Vprtstp: contraction number = 2.990735e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 6.258355e-06\n Vprtstp: contraction number = 6.675424e-01\n Vnewton: Using errtol_s: 26.916626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.191592e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.751762e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.008505e+01\n Vprtstp: contraction number = 2.008505e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 4.202958e-06\n Vprtstp: contraction number = 6.715755e-01\n Vnewton: Using errtol_s: 18.076547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.267038e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.220304e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356100e+01\n Vprtstp: contraction number = 1.356100e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 2.837748e-06\n Vprtstp: contraction number = 6.751787e-01\n Vnewton: Using errtol_s: 12.204901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.353593e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.653677e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.198733e+00\n Vprtstp: contraction number = 9.198733e+00\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 1.924909e-06\n Vprtstp: contraction number = 6.783227e-01\n Vnewton: Using errtol_s: 8.278861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.440865e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.013955e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.265697e+00\n Vprtstp: contraction number = 6.265697e+00\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.311147e-06\n Vprtstp: contraction number = 6.811478e-01\n Vnewton: Using errtol_s: 5.639128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.531333e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.058715e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.284635e+00\n Vprtstp: contraction number = 4.284635e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 8.965941e-07\n Vprtstp: contraction number = 6.838241e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.415461e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.438656e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.903059e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.131868e+00\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -15105,15 +15105,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.410514495807E-03 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 1.129100557647E+00 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.950000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.067000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -15161,160 +15161,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.000190853 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.356509\n+Vacc_SASA: Time elapsed: 1.357878\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.566233e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.672209e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.176800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.092700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.389490e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.975820e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.789962e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.287387e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1032634.725607\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.811637e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.306492e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.090058e+05\n Vprtstp: contraction number = 1.090058e+05\n Vnewton: Attempting damping, relres = 0.095383\n Vnewton: Attempting damping, relres = 0.544753\n Vnewton: Damping accepted, relres = 0.095383\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.538325e-02\n Vprtstp: contraction number = 9.538325e-02\n Vnewton: Using errtol_s: 98496.056858\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.904681e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.358782e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.829312e+04\n Vprtstp: contraction number = 1.829312e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.595089e-02\n Vprtstp: contraction number = 1.672295e-01\n Vnewton: Using errtol_s: 16471.442714\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.984367e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.406621e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.867524e+03\n Vprtstp: contraction number = 3.867524e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.370960e-03\n Vprtstp: contraction number = 2.113337e-01\n Vnewton: Using errtol_s: 3480.970171\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.063581e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.450773e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.812010e+02\n Vprtstp: contraction number = 9.812010e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 8.551815e-04\n Vprtstp: contraction number = 2.536908e-01\n Vnewton: Using errtol_s: 883.090100\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.141488e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.499276e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.836594e+02\n Vprtstp: contraction number = 2.836594e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 2.472259e-04\n Vprtstp: contraction number = 2.890917e-01\n Vnewton: Using errtol_s: 255.294034\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.219320e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.542960e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.927772e+01\n Vprtstp: contraction number = 8.927772e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 7.781068e-05\n Vprtstp: contraction number = 3.147352e-01\n Vnewton: Using errtol_s: 80.350015\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.298717e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.589931e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.937189e+01\n Vprtstp: contraction number = 2.937189e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.559929e-05\n Vprtstp: contraction number = 3.289945e-01\n Vnewton: Using errtol_s: 26.434712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.389821e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.633538e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.890447e+00\n Vprtstp: contraction number = 9.890447e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.620089e-06\n Vprtstp: contraction number = 3.367316e-01\n Vnewton: Using errtol_s: 8.901403\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.490909e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.681180e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.377400e+00\n Vprtstp: contraction number = 3.377400e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.943597e-06\n Vprtstp: contraction number = 3.414810e-01\n Vnewton: Using errtol_s: 3.039660\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.599923e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.725680e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.164729e+00\n Vprtstp: contraction number = 1.164729e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.015127e-06\n Vprtstp: contraction number = 3.448595e-01\n Vnewton: Using errtol_s: 1.048256\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.707684e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.769734e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.047354e-01\n Vprtstp: contraction number = 4.047354e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.527500e-07\n Vprtstp: contraction number = 3.474933e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.008436e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.037400e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.214467e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.450408e+00\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -15323,15 +15323,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.262250874476E-03 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 7.842003689004E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.640500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.527900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -15354,272 +15354,272 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.399211\n+Vacc_SASA: Time elapsed: 1.399569\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.649255e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.697342e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.972100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.945900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.382590e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.897540e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.992539e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.003137e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.020495e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.018901e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.113974e+05\n Vprtstp: contraction number = 2.113974e+05\n Vnewton: Attempting damping, relres = 0.047573\n Vnewton: Attempting damping, relres = 0.515375\n Vnewton: Damping accepted, relres = 0.047573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.757263e-02\n Vprtstp: contraction number = 4.757263e-02\n Vnewton: Using errtol_s: 203448.048803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.126156e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.072630e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.589098e+04\n Vprtstp: contraction number = 4.589098e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.811582e-03\n Vprtstp: contraction number = 2.062443e-01\n Vnewton: Using errtol_s: 41959.996661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.219206e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.117553e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404662e+04\n Vprtstp: contraction number = 1.404662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.960291e-03\n Vprtstp: contraction number = 3.017139e-01\n Vnewton: Using errtol_s: 12659.913691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.292811e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.162584e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.279840e+03\n Vprtstp: contraction number = 5.279840e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111524e-03\n Vprtstp: contraction number = 3.754781e-01\n Vnewton: Using errtol_s: 4753.520446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.363907e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.211057e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.336921e+03\n Vprtstp: contraction number = 2.336921e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.918609e-04\n Vprtstp: contraction number = 4.425102e-01\n Vnewton: Using errtol_s: 2103.481419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.434712e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.252641e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194576e+03\n Vprtstp: contraction number = 1.194576e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.514070e-04\n Vprtstp: contraction number = 5.111344e-01\n Vnewton: Using errtol_s: 1075.161658\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.507097e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.297641e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.792983e+02\n Vprtstp: contraction number = 6.792983e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.429594e-04\n Vprtstp: contraction number = 5.686374e-01\n Vnewton: Using errtol_s: 611.377148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.590713e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.353597e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.154648e+02\n Vprtstp: contraction number = 4.154648e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.743449e-05\n Vprtstp: contraction number = 6.116036e-01\n Vnewton: Using errtol_s: 373.920435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.688287e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.457368e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660684e+02\n Vprtstp: contraction number = 2.660684e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.599388e-05\n Vprtstp: contraction number = 6.404095e-01\n Vnewton: Using errtol_s: 239.462182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.779738e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.595695e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755593e+02\n Vprtstp: contraction number = 1.755593e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.694626e-05\n Vprtstp: contraction number = 6.598268e-01\n Vnewton: Using errtol_s: 158.003576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.865072e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.726996e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183176e+02\n Vprtstp: contraction number = 1.183176e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.489979e-05\n Vprtstp: contraction number = 6.739462e-01\n Vnewton: Using errtol_s: 106.485913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.944080e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.859352e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.102710e+01\n Vprtstp: contraction number = 8.102710e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705205e-05\n Vprtstp: contraction number = 6.848271e-01\n Vnewton: Using errtol_s: 72.924443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.016943e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.991343e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.628393e+01\n Vprtstp: contraction number = 5.628393e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.184488e-05\n Vprtstp: contraction number = 6.946308e-01\n Vnewton: Using errtol_s: 50.655566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.089291e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.114277e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955755e+01\n Vprtstp: contraction number = 3.955755e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.324836e-06\n Vprtstp: contraction number = 7.028213e-01\n Vnewton: Using errtol_s: 35.601810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.160940e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.208959e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.808103e+01\n Vprtstp: contraction number = 2.808103e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.909617e-06\n Vprtstp: contraction number = 7.098779e-01\n Vnewton: Using errtol_s: 25.272937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.238156e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.333859e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.010039e+01\n Vprtstp: contraction number = 2.010039e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 4.230100e-06\n Vprtstp: contraction number = 7.157995e-01\n Vnewton: Using errtol_s: 18.090355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.319377e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.458339e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.449222e+01\n Vprtstp: contraction number = 1.449222e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 3.049867e-06\n Vprtstp: contraction number = 7.209918e-01\n Vnewton: Using errtol_s: 13.042997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.401846e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.599717e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051084e+01\n Vprtstp: contraction number = 1.051084e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 2.211992e-06\n Vprtstp: contraction number = 7.252749e-01\n Vnewton: Using errtol_s: 9.459758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.477559e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.734845e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.663626e+00\n Vprtstp: contraction number = 7.663626e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.612800e-06\n Vprtstp: contraction number = 7.291164e-01\n Vnewton: Using errtol_s: 6.897264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.553174e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.856480e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.612195e+00\n Vprtstp: contraction number = 5.612195e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 1.181079e-06\n Vprtstp: contraction number = 7.323158e-01\n Vnewton: Using errtol_s: 5.050976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.632224e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.956856e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.124624e+00\n Vprtstp: contraction number = 4.124624e+00\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 8.680215e-07\n Vprtstp: contraction number = 7.349396e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.707398e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.734500e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.062767e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.085408e+01\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -15628,17 +15628,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.028844380467E+00 kT\n Vpmg_energy:  qfEnergy = 9.611210700866E+03 kT\n Vpmg_energy:  dielEnergy = 4.863079386675E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.310000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.331000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -15684,171 +15684,171 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0377574 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.428825\n+Vacc_SASA: Time elapsed: 1.379125\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.866968e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.065245e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.069400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.770400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.289090e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.011140e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.914425e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.298722e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 6079198.405761\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.938404e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.319168e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.898758e+05\n Vprtstp: contraction number = 5.898758e+05\n Vnewton: Attempting damping, relres = 0.088148\n Vnewton: Attempting damping, relres = 0.541560\n Vnewton: Damping accepted, relres = 0.088148\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.814828e-02\n Vprtstp: contraction number = 8.814828e-02\n Vnewton: Using errtol_s: 535870.896065\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.038896e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.374689e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.077049e+05\n Vprtstp: contraction number = 1.077049e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.598309e-02\n Vprtstp: contraction number = 1.813205e-01\n Vnewton: Using errtol_s: 97164.364787\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.128779e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.416940e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.746148e+04\n Vprtstp: contraction number = 2.746148e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.065921e-03\n Vprtstp: contraction number = 2.543889e-01\n Vnewton: Using errtol_s: 24717.539236\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.214655e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.467276e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.490060e+03\n Vprtstp: contraction number = 8.490060e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.256932e-03\n Vprtstp: contraction number = 3.091382e-01\n Vnewton: Using errtol_s: 7641.136045\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.297497e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.510195e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.906153e+03\n Vprtstp: contraction number = 2.906153e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.302464e-04\n Vprtstp: contraction number = 3.422990e-01\n Vnewton: Using errtol_s: 2615.553137\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.385279e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.557021e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.038756e+03\n Vprtstp: contraction number = 1.038756e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.537840e-04\n Vprtstp: contraction number = 3.574324e-01\n Vnewton: Using errtol_s: 934.883311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.465008e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.604456e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.756989e+02\n Vprtstp: contraction number = 3.756989e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.562081e-05\n Vprtstp: contraction number = 3.616814e-01\n Vnewton: Using errtol_s: 338.129920\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.545851e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.648416e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.372077e+02\n Vprtstp: contraction number = 1.372077e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.031307e-05\n Vprtstp: contraction number = 3.652064e-01\n Vnewton: Using errtol_s: 123.487196\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.635746e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.695127e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.308624e+01\n Vprtstp: contraction number = 5.308624e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.859206e-06\n Vprtstp: contraction number = 3.869039e-01\n Vnewton: Using errtol_s: 47.777672\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.721555e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.742163e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.247149e+01\n Vprtstp: contraction number = 2.247149e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.326814e-06\n Vprtstp: contraction number = 4.233015e-01\n Vnewton: Using errtol_s: 20.224360\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.805028e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.789115e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.031380e+01\n Vprtstp: contraction number = 1.031380e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.526916e-06\n Vprtstp: contraction number = 4.589724e-01\n Vnewton: Using errtol_s: 9.282423\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.888893e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.831977e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.018395e+00\n Vprtstp: contraction number = 5.018395e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.429527e-07\n Vprtstp: contraction number = 4.865709e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.058058e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.084147e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.714651e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.962939e+00\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -15857,15 +15857,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.101910647011E+00 kT\n Vpmg_energy:  qfEnergy = 7.806992325165E+04 kT\n Vpmg_energy:  dielEnergy = 3.916747531828E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.445200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.313300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -15888,261 +15888,261 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.007559\n+Vacc_SASA: Time elapsed: 3.033793\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.375057e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.496020e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.012400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.103000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.453980e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.381560e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.339054e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.247995e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.360862e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.269914e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.298565e+05\n Vprtstp: contraction number = 4.298565e+05\n Vnewton: Attempting damping, relres = 0.048079\n Vnewton: Attempting damping, relres = 0.515481\n Vnewton: Damping accepted, relres = 0.048079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.807904e-02\n Vprtstp: contraction number = 4.807904e-02\n Vnewton: Using errtol_s: 418259.137179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.461273e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.412611e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.275297e+04\n Vprtstp: contraction number = 9.275297e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.791706e-03\n Vprtstp: contraction number = 2.036585e-01\n Vnewton: Using errtol_s: 85182.030508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.539490e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.463070e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.830324e+04\n Vprtstp: contraction number = 2.830324e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.931540e-03\n Vprtstp: contraction number = 2.993901e-01\n Vnewton: Using errtol_s: 25502.653903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.617281e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.570365e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066383e+04\n Vprtstp: contraction number = 1.066383e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.103407e-03\n Vprtstp: contraction number = 3.763916e-01\n Vnewton: Using errtol_s: 9598.985602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.696338e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.636118e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725476e+03\n Vprtstp: contraction number = 4.725476e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.889004e-04\n Vprtstp: contraction number = 4.430826e-01\n Vnewton: Using errtol_s: 4253.143226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.770812e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.697631e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402868e+03\n Vprtstp: contraction number = 2.402868e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.485940e-04\n Vprtstp: contraction number = 5.084757e-01\n Vnewton: Using errtol_s: 2162.620089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.851358e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.847153e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352802e+03\n Vprtstp: contraction number = 1.352802e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.399556e-04\n Vprtstp: contraction number = 5.629888e-01\n Vnewton: Using errtol_s: 1217.530795\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.931185e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.894857e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164880e+02\n Vprtstp: contraction number = 8.164880e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.447037e-05\n Vprtstp: contraction number = 6.035512e-01\n Vnewton: Using errtol_s: 734.842122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.010390e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.939866e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157033e+02\n Vprtstp: contraction number = 5.157033e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.335238e-05\n Vprtstp: contraction number = 6.316106e-01\n Vnewton: Using errtol_s: 464.134076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.089298e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.987392e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352095e+02\n Vprtstp: contraction number = 3.352095e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.467926e-05\n Vprtstp: contraction number = 6.500040e-01\n Vnewton: Using errtol_s: 301.688999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.164692e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.031723e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.222234e+02\n Vprtstp: contraction number = 2.222234e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.299022e-05\n Vprtstp: contraction number = 6.629387e-01\n Vnewton: Using errtol_s: 200.001301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.237023e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.076929e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.495221e+02\n Vprtstp: contraction number = 1.495221e+02\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.546887e-05\n Vprtstp: contraction number = 6.728456e-01\n Vnewton: Using errtol_s: 134.569993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.317818e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.121084e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018836e+02\n Vprtstp: contraction number = 1.018836e+02\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.054041e-05\n Vprtstp: contraction number = 6.813949e-01\n Vnewton: Using errtol_s: 91.695311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.396269e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.165924e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.012825e+01\n Vprtstp: contraction number = 7.012825e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.255144e-06\n Vprtstp: contraction number = 6.883171e-01\n Vnewton: Using errtol_s: 63.115450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.469480e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.211482e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.869976e+01\n Vprtstp: contraction number = 4.869976e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.038252e-06\n Vprtstp: contraction number = 6.944386e-01\n Vnewton: Using errtol_s: 43.829803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.543226e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.255573e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.408035e+01\n Vprtstp: contraction number = 3.408035e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 3.525795e-06\n Vprtstp: contraction number = 6.998052e-01\n Vnewton: Using errtol_s: 30.672326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.616905e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.305323e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401453e+01\n Vprtstp: contraction number = 2.401453e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 2.484432e-06\n Vprtstp: contraction number = 7.046444e-01\n Vnewton: Using errtol_s: 21.613084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.690705e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.367384e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.702723e+01\n Vprtstp: contraction number = 1.702723e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.761558e-06\n Vprtstp: contraction number = 7.090385e-01\n Vnewton: Using errtol_s: 15.324508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.764323e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.412485e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214065e+01\n Vprtstp: contraction number = 1.214065e+01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.256015e-06\n Vprtstp: contraction number = 7.130137e-01\n Vnewton: Using errtol_s: 10.926584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.843955e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.459962e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.699962e+00\n Vprtstp: contraction number = 8.699962e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 9.000575e-07\n Vprtstp: contraction number = 7.165978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.571729e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.598887e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.250154e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.276626e+01\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -16151,17 +16151,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.017893422646E+00 kT\n Vpmg_energy:  qfEnergy = 9.611562953522E+03 kT\n Vpmg_energy:  dielEnergy = 4.865716990042E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.516000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.939000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -16207,171 +16207,171 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0371069 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.016294\n+Vacc_SASA: Time elapsed: 3.003942\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.415784e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.782025e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.999100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.957200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.084290e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.885090e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.277694e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.900034e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 6935084.404705\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.294325e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.918418e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.727592e+05\n Vprtstp: contraction number = 6.727592e+05\n Vnewton: Attempting damping, relres = 0.088102\n Vnewton: Attempting damping, relres = 0.541455\n Vnewton: Damping accepted, relres = 0.088102\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.810224e-02\n Vprtstp: contraction number = 8.810224e-02\n Vnewton: Using errtol_s: 610996.445538\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.387839e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.972805e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.225330e+05\n Vprtstp: contraction number = 1.225330e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.593368e-02\n Vprtstp: contraction number = 1.808544e-01\n Vnewton: Using errtol_s: 110501.406789\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.472258e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.017866e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.085731e+04\n Vprtstp: contraction number = 3.085731e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.004954e-03\n Vprtstp: contraction number = 2.513515e-01\n Vnewton: Using errtol_s: 27774.696268\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.556507e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.063742e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.402021e+03\n Vprtstp: contraction number = 9.402021e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.220185e-03\n Vprtstp: contraction number = 3.046688e-01\n Vnewton: Using errtol_s: 8462.082872\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.637517e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.110137e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.175895e+03\n Vprtstp: contraction number = 3.175895e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.121575e-04\n Vprtstp: contraction number = 3.377829e-01\n Vnewton: Using errtol_s: 2858.347084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.720819e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.152438e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.121720e+03\n Vprtstp: contraction number = 1.121720e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.455722e-04\n Vprtstp: contraction number = 3.531955e-01\n Vnewton: Using errtol_s: 1009.555317\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.806328e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.197848e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.008316e+02\n Vprtstp: contraction number = 4.008316e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.201806e-05\n Vprtstp: contraction number = 3.573352e-01\n Vnewton: Using errtol_s: 360.749636\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.890072e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.242930e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.444166e+02\n Vprtstp: contraction number = 1.444166e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.874168e-05\n Vprtstp: contraction number = 3.602918e-01\n Vnewton: Using errtol_s: 129.975153\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.974391e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.291261e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.512662e+01\n Vprtstp: contraction number = 5.512662e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.154062e-06\n Vprtstp: contraction number = 3.817193e-01\n Vnewton: Using errtol_s: 49.614025\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.058879e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.336780e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.308362e+01\n Vprtstp: contraction number = 2.308362e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.995677e-06\n Vprtstp: contraction number = 4.187379e-01\n Vnewton: Using errtol_s: 20.775274\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.145257e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.379405e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051871e+01\n Vprtstp: contraction number = 1.051871e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.365066e-06\n Vprtstp: contraction number = 4.556784e-01\n Vnewton: Using errtol_s: 9.466845\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.230025e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.427714e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.098076e+00\n Vprtstp: contraction number = 5.098076e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 6.616025e-07\n Vprtstp: contraction number = 4.846672e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.027227e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.051078e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.665509e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.889984e+00\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -16380,27 +16380,27 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.129100275217E+00 kT\n Vpmg_energy:  qfEnergy = 7.806947604587E+04 kT\n Vpmg_energy:  dielEnergy = 3.916855498576E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.337700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.644500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.332927e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.493962e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:27:50 2025\n+# Creation Date and Time:  Sun Jan  7 09:40:27 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -16753,250 +16753,250 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.402717\n+Vacc_SASA: Time elapsed: 1.373415\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.642852e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.650957e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.859300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.983600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.310790e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.895840e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.023807e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.047477e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.220656e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.225288e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.136321e+05\n Vprtstp: contraction number = 2.136321e+05\n Vnewton: Attempting damping, relres = 0.047663\n Vnewton: Attempting damping, relres = 0.515490\n Vnewton: Damping accepted, relres = 0.047663\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.766304e-02\n Vprtstp: contraction number = 4.766304e-02\n Vnewton: Using errtol_s: 204994.485638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.158139e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.744522e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.587025e+04\n Vprtstp: contraction number = 4.587025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.727679e-03\n Vprtstp: contraction number = 2.040927e-01\n Vnewton: Using errtol_s: 41837.880528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.940766e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.237648e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.391016e+04\n Vprtstp: contraction number = 1.391016e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.912173e-03\n Vprtstp: contraction number = 2.993697e-01\n Vnewton: Using errtol_s: 12524.995351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.659427e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.697411e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.237707e+03\n Vprtstp: contraction number = 5.237707e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.096054e-03\n Vprtstp: contraction number = 3.763697e-01\n Vnewton: Using errtol_s: 4714.028550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.373820e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.150263e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.331453e+03\n Vprtstp: contraction number = 2.331453e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.878779e-04\n Vprtstp: contraction number = 4.451223e-01\n Vnewton: Using errtol_s: 2098.319320\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.062465e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.655902e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189035e+03\n Vprtstp: contraction number = 1.189035e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.488161e-04\n Vprtstp: contraction number = 5.099966e-01\n Vnewton: Using errtol_s: 1070.135650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.744516e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.097771e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.678182e+02\n Vprtstp: contraction number = 6.678182e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.397467e-04\n Vprtstp: contraction number = 5.616468e-01\n Vnewton: Using errtol_s: 601.038216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.447905e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.543840e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.994733e+02\n Vprtstp: contraction number = 3.994733e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.359319e-05\n Vprtstp: contraction number = 5.981764e-01\n Vnewton: Using errtol_s: 359.526862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.161294e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.042690e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.488647e+02\n Vprtstp: contraction number = 2.488647e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.207703e-05\n Vprtstp: contraction number = 6.229817e-01\n Vnewton: Using errtol_s: 223.978670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.915644e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.504395e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.588671e+02\n Vprtstp: contraction number = 1.588671e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.324425e-05\n Vprtstp: contraction number = 6.383669e-01\n Vnewton: Using errtol_s: 142.980568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.614924e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.982719e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.030284e+02\n Vprtstp: contraction number = 1.030284e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.155954e-05\n Vprtstp: contraction number = 6.485194e-01\n Vnewton: Using errtol_s: 92.725673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.037263e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.480091e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.760657e+01\n Vprtstp: contraction number = 6.760657e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.414722e-05\n Vprtstp: contraction number = 6.561932e-01\n Vnewton: Using errtol_s: 60.845953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.112098e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.937874e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.480217e+01\n Vprtstp: contraction number = 4.480217e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.375216e-06\n Vprtstp: contraction number = 6.626894e-01\n Vnewton: Using errtol_s: 40.321969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.189612e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.429423e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990735e+01\n Vprtstp: contraction number = 2.990735e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 6.258355e-06\n Vprtstp: contraction number = 6.675424e-01\n Vnewton: Using errtol_s: 26.916626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.268378e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.901119e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.008505e+01\n Vprtstp: contraction number = 2.008505e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 4.202958e-06\n Vprtstp: contraction number = 6.715755e-01\n Vnewton: Using errtol_s: 18.076547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.346047e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.390774e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356100e+01\n Vprtstp: contraction number = 1.356100e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 2.837748e-06\n Vprtstp: contraction number = 6.751787e-01\n Vnewton: Using errtol_s: 12.204901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.425204e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.894376e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.198733e+00\n Vprtstp: contraction number = 9.198733e+00\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 1.924909e-06\n Vprtstp: contraction number = 6.783227e-01\n Vnewton: Using errtol_s: 8.278861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.503554e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.035122e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.265697e+00\n Vprtstp: contraction number = 6.265697e+00\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.311147e-06\n Vprtstp: contraction number = 6.811478e-01\n Vnewton: Using errtol_s: 5.639128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.577752e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.081833e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.284635e+00\n Vprtstp: contraction number = 4.284635e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 8.965941e-07\n Vprtstp: contraction number = 6.838241e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.438854e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.466244e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.155085e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.380791e+00\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -17005,15 +17005,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.751162440734E-01 kT\n Vpmg_energy:  qfEnergy = 1.947112425311E+03 kT\n Vpmg_energy:  dielEnergy = 9.674060402300E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.231000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.042000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -17061,160 +17061,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0113169 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.356663\n+Vacc_SASA: Time elapsed: 1.363382\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.748616e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.877733e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.093600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.859500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.564000e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.972260e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.848105e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.334101e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2854416.159669\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.877233e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.349081e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.073946e+05\n Vprtstp: contraction number = 3.073946e+05\n Vnewton: Attempting damping, relres = 0.097301\n Vnewton: Attempting damping, relres = 0.546102\n Vnewton: Damping accepted, relres = 0.097301\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.730086e-02\n Vprtstp: contraction number = 9.730086e-02\n Vnewton: Using errtol_s: 277737.152012\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.990653e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.407043e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.422127e+04\n Vprtstp: contraction number = 5.422127e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.709795e-02\n Vprtstp: contraction number = 1.757225e-01\n Vnewton: Using errtol_s: 48804.661136\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.077479e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.453740e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.206353e+04\n Vprtstp: contraction number = 1.206353e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.803701e-03\n Vprtstp: contraction number = 2.224653e-01\n Vnewton: Using errtol_s: 10857.344468\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.168919e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.501137e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.177380e+03\n Vprtstp: contraction number = 3.177380e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.001847e-03\n Vprtstp: contraction number = 2.633874e-01\n Vnewton: Using errtol_s: 2859.687867\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.260434e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.548744e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.523572e+02\n Vprtstp: contraction number = 9.523572e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.002837e-04\n Vprtstp: contraction number = 2.997301e-01\n Vnewton: Using errtol_s: 857.134538\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.350634e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.591517e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.079890e+02\n Vprtstp: contraction number = 3.079890e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.711021e-05\n Vprtstp: contraction number = 3.233949e-01\n Vnewton: Using errtol_s: 277.192960\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.438835e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.638525e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.041211e+02\n Vprtstp: contraction number = 1.041211e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.282966e-05\n Vprtstp: contraction number = 3.380660e-01\n Vnewton: Using errtol_s: 93.709510\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.528257e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.689764e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.682551e+01\n Vprtstp: contraction number = 3.682551e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.161114e-05\n Vprtstp: contraction number = 3.536784e-01\n Vnewton: Using errtol_s: 33.143025\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.623661e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.747318e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.414772e+01\n Vprtstp: contraction number = 1.414772e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.460791e-06\n Vprtstp: contraction number = 3.841820e-01\n Vnewton: Using errtol_s: 12.732955\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.713650e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.794941e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.014294e+00\n Vprtstp: contraction number = 6.014294e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.896313e-06\n Vprtstp: contraction number = 4.251068e-01\n Vnewton: Using errtol_s: 5.412865\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.801338e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.845022e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.770154e+00\n Vprtstp: contraction number = 2.770154e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.734323e-07\n Vprtstp: contraction number = 4.605951e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.028493e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.058908e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.468404e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.716781e+00\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -17223,17 +17223,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.831261294961E-01 kT\n Vpmg_energy:  qfEnergy = 1.781344550664E+04 kT\n Vpmg_energy:  dielEnergy = 8.939288545980E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.471000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.447700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -17254,272 +17254,272 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.394309\n+Vacc_SASA: Time elapsed: 1.409556\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.619044e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.692867e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.651300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.913000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.316270e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.872980e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.067552e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.074360e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.090316e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.092450e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.113974e+05\n Vprtstp: contraction number = 2.113974e+05\n Vnewton: Attempting damping, relres = 0.047573\n Vnewton: Attempting damping, relres = 0.515375\n Vnewton: Damping accepted, relres = 0.047573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.757263e-02\n Vprtstp: contraction number = 4.757263e-02\n Vnewton: Using errtol_s: 203448.048803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.184821e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.145471e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.589098e+04\n Vprtstp: contraction number = 4.589098e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.811582e-03\n Vprtstp: contraction number = 2.062443e-01\n Vnewton: Using errtol_s: 41959.996661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.257471e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.197572e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404662e+04\n Vprtstp: contraction number = 1.404662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.960291e-03\n Vprtstp: contraction number = 3.017139e-01\n Vnewton: Using errtol_s: 12659.913691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.331484e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.247654e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.279840e+03\n Vprtstp: contraction number = 5.279840e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111524e-03\n Vprtstp: contraction number = 3.754781e-01\n Vnewton: Using errtol_s: 4753.520446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.406438e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.290414e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.336921e+03\n Vprtstp: contraction number = 2.336921e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.918609e-04\n Vprtstp: contraction number = 4.425102e-01\n Vnewton: Using errtol_s: 2103.481419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.480531e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.334864e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194576e+03\n Vprtstp: contraction number = 1.194576e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.514070e-04\n Vprtstp: contraction number = 5.111344e-01\n Vnewton: Using errtol_s: 1075.161658\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.550120e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.377390e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.792983e+02\n Vprtstp: contraction number = 6.792983e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.429594e-04\n Vprtstp: contraction number = 5.686374e-01\n Vnewton: Using errtol_s: 611.377148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.623593e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.426675e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.154648e+02\n Vprtstp: contraction number = 4.154648e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.743449e-05\n Vprtstp: contraction number = 6.116036e-01\n Vnewton: Using errtol_s: 373.920435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.699870e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.469164e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660684e+02\n Vprtstp: contraction number = 2.660684e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.599388e-05\n Vprtstp: contraction number = 6.404095e-01\n Vnewton: Using errtol_s: 239.462182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.776701e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.512970e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755593e+02\n Vprtstp: contraction number = 1.755593e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.694626e-05\n Vprtstp: contraction number = 6.598268e-01\n Vnewton: Using errtol_s: 158.003576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.851623e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.561073e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183176e+02\n Vprtstp: contraction number = 1.183176e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.489979e-05\n Vprtstp: contraction number = 6.739462e-01\n Vnewton: Using errtol_s: 106.485913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.929754e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.611997e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.102710e+01\n Vprtstp: contraction number = 8.102710e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705205e-05\n Vprtstp: contraction number = 6.848271e-01\n Vnewton: Using errtol_s: 72.924443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.003810e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.659784e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.628393e+01\n Vprtstp: contraction number = 5.628393e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.184488e-05\n Vprtstp: contraction number = 6.946308e-01\n Vnewton: Using errtol_s: 50.655566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.074520e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.707924e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955755e+01\n Vprtstp: contraction number = 3.955755e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.324836e-06\n Vprtstp: contraction number = 7.028213e-01\n Vnewton: Using errtol_s: 35.601810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.145736e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.753894e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.808103e+01\n Vprtstp: contraction number = 2.808103e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.909617e-06\n Vprtstp: contraction number = 7.098779e-01\n Vnewton: Using errtol_s: 25.272937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.218901e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.798995e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.010039e+01\n Vprtstp: contraction number = 2.010039e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 4.230100e-06\n Vprtstp: contraction number = 7.157995e-01\n Vnewton: Using errtol_s: 18.090355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.291797e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.845896e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.449222e+01\n Vprtstp: contraction number = 1.449222e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 3.049867e-06\n Vprtstp: contraction number = 7.209918e-01\n Vnewton: Using errtol_s: 13.042997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.362422e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.896078e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051084e+01\n Vprtstp: contraction number = 1.051084e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 2.211992e-06\n Vprtstp: contraction number = 7.252749e-01\n Vnewton: Using errtol_s: 9.459758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.433741e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.940183e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.663626e+00\n Vprtstp: contraction number = 7.663626e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.612800e-06\n Vprtstp: contraction number = 7.291164e-01\n Vnewton: Using errtol_s: 6.897264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.506444e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.984218e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.612195e+00\n Vprtstp: contraction number = 5.612195e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 1.181079e-06\n Vprtstp: contraction number = 7.323158e-01\n Vnewton: Using errtol_s: 5.050976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.576523e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.035739e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.124624e+00\n Vprtstp: contraction number = 4.124624e+00\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 8.680215e-07\n Vprtstp: contraction number = 7.349396e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.568888e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.596051e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.057543e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.079826e+01\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -17528,15 +17528,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.114658040660E-01 kT\n Vpmg_energy:  qfEnergy = 3.255454137160E+02 kT\n Vpmg_energy:  dielEnergy = 1.687649926413E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.059000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.610800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -17584,160 +17584,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00476673 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.374228\n+Vacc_SASA: Time elapsed: 1.447246\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.687236e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.837226e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.547000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.329900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.578900e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.225370e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.835998e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.345372e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1723088.414735\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.865886e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.359831e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.042446e+05\n Vprtstp: contraction number = 2.042446e+05\n Vnewton: Attempting damping, relres = 0.108739\n Vnewton: Attempting damping, relres = 0.550663\n Vnewton: Damping accepted, relres = 0.108739\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.087385e-01\n Vprtstp: contraction number = 1.087385e-01\n Vnewton: Using errtol_s: 187366.060856\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.984562e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.415383e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.786866e+04\n Vprtstp: contraction number = 3.786866e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.981324e-02\n Vprtstp: contraction number = 1.822100e-01\n Vnewton: Using errtol_s: 34139.969757\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.078461e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.462535e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.828513e+03\n Vprtstp: contraction number = 8.828513e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.612234e-03\n Vprtstp: contraction number = 2.327854e-01\n Vnewton: Using errtol_s: 7947.287090\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.164619e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.511333e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.384276e+03\n Vprtstp: contraction number = 2.384276e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.245382e-03\n Vprtstp: contraction number = 2.700171e-01\n Vnewton: Using errtol_s: 2145.903122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.250629e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.555739e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.047320e+02\n Vprtstp: contraction number = 7.047320e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.680970e-04\n Vprtstp: contraction number = 2.955696e-01\n Vnewton: Using errtol_s: 634.263634\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.332073e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.603977e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.207559e+02\n Vprtstp: contraction number = 2.207559e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.153050e-04\n Vprtstp: contraction number = 3.132463e-01\n Vnewton: Using errtol_s: 198.680750\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.404910e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.651669e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.166503e+01\n Vprtstp: contraction number = 7.166503e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.743196e-05\n Vprtstp: contraction number = 3.246343e-01\n Vnewton: Using errtol_s: 64.498581\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.486288e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.697784e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.385676e+01\n Vprtstp: contraction number = 2.385676e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.246082e-05\n Vprtstp: contraction number = 3.328924e-01\n Vnewton: Using errtol_s: 21.471088\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.569933e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.747333e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.086151e+00\n Vprtstp: contraction number = 8.086151e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.223542e-06\n Vprtstp: contraction number = 3.389459e-01\n Vnewton: Using errtol_s: 7.277536\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.653387e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.796030e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.777094e+00\n Vprtstp: contraction number = 2.777094e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.450526e-06\n Vprtstp: contraction number = 3.434383e-01\n Vnewton: Using errtol_s: 2.499385\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.730944e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.841849e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.633001e-01\n Vprtstp: contraction number = 9.633001e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.031489e-07\n Vprtstp: contraction number = 3.468734e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.624686e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.920584e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.362075e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.629002e+00\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -17746,17 +17746,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.878540629656E-01 kT\n Vpmg_energy:  qfEnergy = 3.319538441543E+03 kT\n Vpmg_energy:  dielEnergy = 1.644040185021E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.881100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.435700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -17777,261 +17777,261 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.997815\n+Vacc_SASA: Time elapsed: 3.036026\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.378074e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.503254e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.115000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.108000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.295670e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.113260e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.165730e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.257513e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.186382e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.274869e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.298565e+05\n Vprtstp: contraction number = 4.298565e+05\n Vnewton: Attempting damping, relres = 0.048079\n Vnewton: Attempting damping, relres = 0.515481\n Vnewton: Damping accepted, relres = 0.048079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.807904e-02\n Vprtstp: contraction number = 4.807904e-02\n Vnewton: Using errtol_s: 418259.137179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.284779e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.349368e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.275297e+04\n Vprtstp: contraction number = 9.275297e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.791706e-03\n Vprtstp: contraction number = 2.036585e-01\n Vnewton: Using errtol_s: 85182.030508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.370703e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.395823e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.830324e+04\n Vprtstp: contraction number = 2.830324e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.931540e-03\n Vprtstp: contraction number = 2.993901e-01\n Vnewton: Using errtol_s: 25502.653903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.451852e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.440551e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066383e+04\n Vprtstp: contraction number = 1.066383e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.103407e-03\n Vprtstp: contraction number = 3.763916e-01\n Vnewton: Using errtol_s: 9598.985602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.533875e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.486663e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725476e+03\n Vprtstp: contraction number = 4.725476e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.889004e-04\n Vprtstp: contraction number = 4.430826e-01\n Vnewton: Using errtol_s: 4253.143226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.624658e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.533778e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402868e+03\n Vprtstp: contraction number = 2.402868e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.485940e-04\n Vprtstp: contraction number = 5.084757e-01\n Vnewton: Using errtol_s: 2162.620089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.709890e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.579276e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352802e+03\n Vprtstp: contraction number = 1.352802e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.399556e-04\n Vprtstp: contraction number = 5.629888e-01\n Vnewton: Using errtol_s: 1217.530795\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.794313e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.624833e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164880e+02\n Vprtstp: contraction number = 8.164880e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.447037e-05\n Vprtstp: contraction number = 6.035512e-01\n Vnewton: Using errtol_s: 734.842122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.874573e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.672860e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157033e+02\n Vprtstp: contraction number = 5.157033e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.335238e-05\n Vprtstp: contraction number = 6.316106e-01\n Vnewton: Using errtol_s: 464.134076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.949072e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.718708e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352095e+02\n Vprtstp: contraction number = 3.352095e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.467926e-05\n Vprtstp: contraction number = 6.500040e-01\n Vnewton: Using errtol_s: 301.688999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.031146e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.762917e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.222234e+02\n Vprtstp: contraction number = 2.222234e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.299022e-05\n Vprtstp: contraction number = 6.629387e-01\n Vnewton: Using errtol_s: 200.001301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.110129e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.811689e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.495221e+02\n Vprtstp: contraction number = 1.495221e+02\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.546887e-05\n Vprtstp: contraction number = 6.728456e-01\n Vnewton: Using errtol_s: 134.569993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.188819e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.854803e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018836e+02\n Vprtstp: contraction number = 1.018836e+02\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.054041e-05\n Vprtstp: contraction number = 6.813949e-01\n Vnewton: Using errtol_s: 91.695311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.269953e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.898666e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.012825e+01\n Vprtstp: contraction number = 7.012825e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.255144e-06\n Vprtstp: contraction number = 6.883171e-01\n Vnewton: Using errtol_s: 63.115450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.346036e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.947049e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.869976e+01\n Vprtstp: contraction number = 4.869976e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.038252e-06\n Vprtstp: contraction number = 6.944386e-01\n Vnewton: Using errtol_s: 43.829803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.423911e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.994485e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.408035e+01\n Vprtstp: contraction number = 3.408035e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 3.525795e-06\n Vprtstp: contraction number = 6.998052e-01\n Vnewton: Using errtol_s: 30.672326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.506939e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.041549e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401453e+01\n Vprtstp: contraction number = 2.401453e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 2.484432e-06\n Vprtstp: contraction number = 7.046444e-01\n Vnewton: Using errtol_s: 21.613084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.591676e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.092918e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.702723e+01\n Vprtstp: contraction number = 1.702723e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.761558e-06\n Vprtstp: contraction number = 7.090385e-01\n Vnewton: Using errtol_s: 15.324508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.680351e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.139440e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214065e+01\n Vprtstp: contraction number = 1.214065e+01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.256015e-06\n Vprtstp: contraction number = 7.130137e-01\n Vnewton: Using errtol_s: 10.926584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.768367e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.183637e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.699962e+00\n Vprtstp: contraction number = 8.699962e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 9.000575e-07\n Vprtstp: contraction number = 7.165978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.674824e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.701793e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.651344e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.888785e+00\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -18040,15 +18040,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.211144338750E-01 kT\n Vpmg_energy:  qfEnergy = 2.301973448783E+03 kT\n Vpmg_energy:  dielEnergy = 1.153004707320E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.933000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.120000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -18096,160 +18096,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0260263 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.997258\n+Vacc_SASA: Time elapsed: 3.011793\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.474097e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.679051e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.947800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.997900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.265370e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.169720e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.214703e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.617401e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4514465.797290\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.240101e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.632510e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.961912e+05\n Vprtstp: contraction number = 4.961912e+05\n Vnewton: Attempting damping, relres = 0.099852\n Vnewton: Attempting damping, relres = 0.546981\n Vnewton: Damping accepted, relres = 0.099852\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.985216e-02\n Vprtstp: contraction number = 9.985216e-02\n Vnewton: Using errtol_s: 450779.157003\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.359801e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.692444e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.942393e+04\n Vprtstp: contraction number = 8.942393e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.783565e-02\n Vprtstp: contraction number = 1.786206e-01\n Vnewton: Using errtol_s: 80518.432475\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.450351e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.739380e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.031115e+04\n Vprtstp: contraction number = 2.031115e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.049611e-03\n Vprtstp: contraction number = 2.270515e-01\n Vnewton: Using errtol_s: 18281.831872\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.539849e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.787248e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.419185e+03\n Vprtstp: contraction number = 5.419185e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.080391e-03\n Vprtstp: contraction number = 2.667887e-01\n Vnewton: Using errtol_s: 4877.386053\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.627958e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.831873e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.625333e+03\n Vprtstp: contraction number = 1.625333e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.240293e-04\n Vprtstp: contraction number = 2.999187e-01\n Vnewton: Using errtol_s: 1462.819304\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.720560e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.882680e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.216368e+02\n Vprtstp: contraction number = 5.216368e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.039939e-04\n Vprtstp: contraction number = 3.209397e-01\n Vnewton: Using errtol_s: 469.476847\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.813037e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.930601e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.735595e+02\n Vprtstp: contraction number = 1.735595e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.460082e-05\n Vprtstp: contraction number = 3.327198e-01\n Vnewton: Using errtol_s: 156.204227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.912131e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.979410e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.923935e+01\n Vprtstp: contraction number = 5.923935e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.180993e-05\n Vprtstp: contraction number = 3.413193e-01\n Vnewton: Using errtol_s: 53.315519\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.999939e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.025449e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.118946e+01\n Vprtstp: contraction number = 2.118946e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.224316e-06\n Vprtstp: contraction number = 3.576919e-01\n Vnewton: Using errtol_s: 19.070529\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.087313e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.086730e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.237698e+00\n Vprtstp: contraction number = 8.237698e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.642261e-06\n Vprtstp: contraction number = 3.887637e-01\n Vnewton: Using errtol_s: 7.413930\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.175975e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.140723e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.509994e+00\n Vprtstp: contraction number = 3.509994e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.997494e-07\n Vprtstp: contraction number = 4.260891e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.040444e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.065952e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.108793e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.364743e+00\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -18258,27 +18258,27 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 3.259341430721E-01 kT\n Vpmg_energy:  qfEnergy = 2.116108930828E+04 kT\n Vpmg_energy:  dielEnergy = 1.059930084642E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.759400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.169100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.284070e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 6.259866e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:28:33 2025\n+# Creation Date and Time:  Sun Jan  7 09:40:53 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -18631,129 +18631,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.362576\n+Vacc_SASA: Time elapsed: 1.384119\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.740004e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.807414e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.008800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.125100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.287460e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.049500e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.106450e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.157209e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.349005e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.399846e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.776390e+05\n Vprtstp: contraction number = 1.776390e+05\n Vnewton: Attempting damping, relres = 0.041319\n Vnewton: Attempting damping, relres = 0.513474\n Vnewton: Damping accepted, relres = 0.041319\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.131938e-02\n Vprtstp: contraction number = 4.131938e-02\n Vnewton: Using errtol_s: 177710.973970\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.374883e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.989780e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677180e+04\n Vprtstp: contraction number = 2.677180e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.962101e-03\n Vprtstp: contraction number = 1.442931e-01\n Vnewton: Using errtol_s: 25642.465478\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.213239e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.489047e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.966549e+03\n Vprtstp: contraction number = 4.966549e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.056655e-03\n Vprtstp: contraction number = 1.772286e-01\n Vnewton: Using errtol_s: 4544.578762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.026477e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.938209e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011325e+03\n Vprtstp: contraction number = 1.011325e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.118038e-04\n Vprtstp: contraction number = 2.004475e-01\n Vnewton: Using errtol_s: 910.949292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.822068e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.403315e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.253595e+02\n Vprtstp: contraction number = 2.253595e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.715911e-05\n Vprtstp: contraction number = 2.226547e-01\n Vnewton: Using errtol_s: 202.827138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.604383e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.900382e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.445207e+01\n Vprtstp: contraction number = 5.445207e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.139456e-05\n Vprtstp: contraction number = 2.416194e-01\n Vnewton: Using errtol_s: 49.006980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.418202e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.349891e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420316e+01\n Vprtstp: contraction number = 1.420316e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.972126e-06\n Vprtstp: contraction number = 2.608373e-01\n Vnewton: Using errtol_s: 12.782849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.232061e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.843868e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.022184e+00\n Vprtstp: contraction number = 4.022184e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.416744e-07\n Vprtstp: contraction number = 2.831893e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.837740e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.097668e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.125188e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.367864e+00\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -18762,17 +18762,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.432004946158E-01 kT\n Vpmg_energy:  qfEnergy = 1.213065901878E+03 kT\n Vpmg_energy:  dielEnergy = 6.590634025531E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.938000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.766400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -18818,127 +18818,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00605008 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.353326\n+Vacc_SASA: Time elapsed: 1.381821\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.839027e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.043412e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.042100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.067300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.377840e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.020190e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.106297e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.596170e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3435589.940646\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.134452e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.752494e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.946642e+05\n Vprtstp: contraction number = 2.946642e+05\n Vnewton: Attempting damping, relres = 0.078398\n Vnewton: Attempting damping, relres = 0.536416\n Vnewton: Damping accepted, relres = 0.078398\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.839769e-02\n Vprtstp: contraction number = 7.839769e-02\n Vnewton: Using errtol_s: 269342.316546\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.254152e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.341927e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.926470e+04\n Vprtstp: contraction number = 3.926470e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.037644e-02\n Vprtstp: contraction number = 1.323565e-01\n Vnewton: Using errtol_s: 35649.206105\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.351727e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.825276e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.330351e+03\n Vprtstp: contraction number = 6.330351e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.659520e-03\n Vprtstp: contraction number = 1.599315e-01\n Vnewton: Using errtol_s: 5701.430665\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.444851e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.031038e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.149005e+03\n Vprtstp: contraction number = 1.149005e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.009992e-04\n Vprtstp: contraction number = 1.813772e-01\n Vnewton: Using errtol_s: 1034.109707\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.538013e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.078513e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.271091e+02\n Vprtstp: contraction number = 2.271091e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.949440e-05\n Vprtstp: contraction number = 1.976564e-01\n Vnewton: Using errtol_s: 204.398353\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.621638e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.128209e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.795044e+01\n Vprtstp: contraction number = 4.795044e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.256128e-05\n Vprtstp: contraction number = 2.111338e-01\n Vnewton: Using errtol_s: 43.155404\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.711852e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.176384e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.083630e+01\n Vprtstp: contraction number = 1.083630e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.838717e-06\n Vprtstp: contraction number = 2.259895e-01\n Vnewton: Using errtol_s: 9.752668\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.804874e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.225465e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677103e+00\n Vprtstp: contraction number = 2.677103e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.013038e-07\n Vprtstp: contraction number = 2.470496e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.763939e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.031855e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.034746e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.274251e+00\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -18947,15 +18947,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.646975834938E-01 kT\n Vpmg_energy:  qfEnergy = 1.061546373318E+04 kT\n Vpmg_energy:  dielEnergy = 5.342705444088E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.689100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.462100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -18978,129 +18978,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.390393\n+Vacc_SASA: Time elapsed: 1.411593\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.733327e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.824324e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.871100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.962500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.109710e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.938880e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.082224e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.470161e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.106370e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.488617e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.716926e+05\n Vprtstp: contraction number = 1.716926e+05\n Vnewton: Attempting damping, relres = 0.040940\n Vnewton: Attempting damping, relres = 0.513162\n Vnewton: Damping accepted, relres = 0.040940\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.093968e-02\n Vprtstp: contraction number = 4.093968e-02\n Vnewton: Using errtol_s: 175081.721880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.211698e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.544229e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.487025e+04\n Vprtstp: contraction number = 2.487025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.724811e-03\n Vprtstp: contraction number = 1.398353e-01\n Vnewton: Using errtol_s: 24482.603484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.280489e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.588439e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.528470e+03\n Vprtstp: contraction number = 4.528470e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.801406e-04\n Vprtstp: contraction number = 1.712092e-01\n Vnewton: Using errtol_s: 4191.647712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.358964e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.634513e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.122748e+02\n Vprtstp: contraction number = 9.122748e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923658e-04\n Vprtstp: contraction number = 1.962635e-01\n Vnewton: Using errtol_s: 822.667398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.438678e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.682803e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052635e+02\n Vprtstp: contraction number = 2.052635e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.319998e-05\n Vprtstp: contraction number = 2.245720e-01\n Vnewton: Using errtol_s: 184.748098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.516769e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.731111e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.154123e+01\n Vprtstp: contraction number = 5.154123e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.084685e-05\n Vprtstp: contraction number = 2.510845e-01\n Vnewton: Using errtol_s: 46.387392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.597268e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.774398e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.435770e+01\n Vprtstp: contraction number = 1.435770e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.021563e-06\n Vprtstp: contraction number = 2.785660e-01\n Vnewton: Using errtol_s: 12.921949\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.674793e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.818983e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.361187e+00\n Vprtstp: contraction number = 4.361187e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.178062e-07\n Vprtstp: contraction number = 3.037522e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.613248e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.853751e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.869576e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.097378e+00\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -19109,15 +19109,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.317231145309E-01 kT\n Vpmg_energy:  qfEnergy = 2.397951074417E+03 kT\n Vpmg_energy:  dielEnergy = 1.196103394551E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.079000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.041000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -19165,149 +19165,149 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0714014 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.377313\n+Vacc_SASA: Time elapsed: 1.383442\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.873713e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.056949e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.931300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.977000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.191640e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.852300e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.956863e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.086145e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3849668.809256\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.982334e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.103530e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.552766e+05\n Vprtstp: contraction number = 3.552766e+05\n Vnewton: Attempting damping, relres = 0.084988\n Vnewton: Attempting damping, relres = 0.539692\n Vnewton: Damping accepted, relres = 0.084988\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.498801e-02\n Vprtstp: contraction number = 8.498801e-02\n Vnewton: Using errtol_s: 327175.687931\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.092975e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.158640e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.008831e+04\n Vprtstp: contraction number = 5.008831e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.180515e-02\n Vprtstp: contraction number = 1.389037e-01\n Vnewton: Using errtol_s: 45445.906193\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.185665e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.207766e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.515214e+03\n Vprtstp: contraction number = 8.515214e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.991773e-03\n Vprtstp: contraction number = 1.687207e-01\n Vnewton: Using errtol_s: 7667.665331\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.273468e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.255298e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.650417e+03\n Vprtstp: contraction number = 1.650417e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.858749e-04\n Vprtstp: contraction number = 1.937344e-01\n Vnewton: Using errtol_s: 1485.490751\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.356943e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.303944e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.445276e+02\n Vprtstp: contraction number = 3.445276e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 8.054589e-05\n Vprtstp: contraction number = 2.087357e-01\n Vnewton: Using errtol_s: 310.075011\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.444702e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.354656e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.228113e+01\n Vprtstp: contraction number = 9.228113e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.157878e-05\n Vprtstp: contraction number = 2.679067e-01\n Vnewton: Using errtol_s: 83.071163\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.533196e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.401003e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.340270e+01\n Vprtstp: contraction number = 3.340270e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.809088e-06\n Vprtstp: contraction number = 3.618873e-01\n Vnewton: Using errtol_s: 30.062402\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.625330e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.445084e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.311951e+01\n Vprtstp: contraction number = 1.311951e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.067793e-06\n Vprtstp: contraction number = 3.928491e-01\n Vnewton: Using errtol_s: 11.809988\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.712950e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.489938e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.550050e+00\n Vprtstp: contraction number = 5.550050e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.297525e-06\n Vprtstp: contraction number = 4.229508e-01\n Vnewton: Using errtol_s: 4.995043\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.794540e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.537926e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.408064e+00\n Vprtstp: contraction number = 2.408064e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 5.629926e-07\n Vprtstp: contraction number = 4.338972e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.172921e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.420249e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.878750e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.100013e+00\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -19316,17 +19316,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.477515515257E-01 kT\n Vpmg_energy:  qfEnergy = 1.844029166481E+04 kT\n Vpmg_energy:  dielEnergy = 9.209478522286E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.563100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.392700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -19347,129 +19347,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.003385\n+Vacc_SASA: Time elapsed: 3.034601\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.524584e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.625526e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.948800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.009100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.535990e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.003800e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.256488e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.960907e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.289883e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.976465e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528464e+05\n Vprtstp: contraction number = 3.528464e+05\n Vnewton: Attempting damping, relres = 0.041605\n Vnewton: Attempting damping, relres = 0.513349\n Vnewton: Damping accepted, relres = 0.041605\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160535e-02\n Vprtstp: contraction number = 4.160535e-02\n Vnewton: Using errtol_s: 361941.817774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.405801e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.035089e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.210930e+04\n Vprtstp: contraction number = 5.210930e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.921711e-03\n Vprtstp: contraction number = 1.423305e-01\n Vnewton: Using errtol_s: 51515.371182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.490147e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.077226e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.570568e+03\n Vprtstp: contraction number = 9.570568e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.018950e-03\n Vprtstp: contraction number = 1.720701e-01\n Vnewton: Using errtol_s: 8864.257334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.578684e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.126424e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.944504e+03\n Vprtstp: contraction number = 1.944504e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.015521e-04\n Vprtstp: contraction number = 1.978037e-01\n Vnewton: Using errtol_s: 1753.383252\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.671197e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.172833e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.357668e+02\n Vprtstp: contraction number = 4.357668e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.508379e-05\n Vprtstp: contraction number = 2.236831e-01\n Vnewton: Using errtol_s: 392.202227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.761374e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.215989e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.074784e+02\n Vprtstp: contraction number = 1.074784e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.111924e-05\n Vprtstp: contraction number = 2.466350e-01\n Vnewton: Using errtol_s: 96.730784\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.844752e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.262117e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.903808e+01\n Vprtstp: contraction number = 2.903808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.004146e-06\n Vprtstp: contraction number = 2.701755e-01\n Vnewton: Using errtol_s: 26.134288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.934716e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.308950e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.552738e+00\n Vprtstp: contraction number = 8.552738e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.848266e-07\n Vprtstp: contraction number = 2.945351e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.530476e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.809045e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.348609e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.574111e+00\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -19478,15 +19478,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.111204276616E+00 kT\n Vpmg_energy:  qfEnergy = 3.618165500075E+03 kT\n Vpmg_energy:  dielEnergy = 1.858858240156E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.043000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.051000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -19534,138 +19534,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0800356 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.005396\n+Vacc_SASA: Time elapsed: 3.015319\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.646344e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.981649e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.970900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.911200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.282170e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.887000e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.401101e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.817896e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7226173.981930\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.427473e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.834571e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.363534e+05\n Vprtstp: contraction number = 6.363534e+05\n Vnewton: Attempting damping, relres = 0.081351\n Vnewton: Attempting damping, relres = 0.537664\n Vnewton: Damping accepted, relres = 0.081351\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.135112e-02\n Vprtstp: contraction number = 8.135112e-02\n Vnewton: Using errtol_s: 587857.310633\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.538880e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.889091e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.753275e+04\n Vprtstp: contraction number = 8.753275e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.104343e-02\n Vprtstp: contraction number = 1.357502e-01\n Vnewton: Using errtol_s: 79801.757672\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.624723e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.932306e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.461031e+04\n Vprtstp: contraction number = 1.461031e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.821090e-03\n Vprtstp: contraction number = 1.649025e-01\n Vnewton: Using errtol_s: 13159.512971\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.711173e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.980402e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.736183e+03\n Vprtstp: contraction number = 2.736183e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.408124e-04\n Vprtstp: contraction number = 1.871475e-01\n Vnewton: Using errtol_s: 2462.769628\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.797646e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.034037e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.483227e+02\n Vprtstp: contraction number = 5.483227e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.829255e-05\n Vprtstp: contraction number = 2.003817e-01\n Vnewton: Using errtol_s: 493.493873\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.881900e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.085851e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.327802e+02\n Vprtstp: contraction number = 1.327802e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.654140e-05\n Vprtstp: contraction number = 2.422139e-01\n Vnewton: Using errtol_s: 119.531057\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.968806e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.128905e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.724135e+01\n Vprtstp: contraction number = 4.724135e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.883780e-06\n Vprtstp: contraction number = 3.557002e-01\n Vnewton: Using errtol_s: 42.517221\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.052539e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.176151e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.799945e+01\n Vprtstp: contraction number = 1.799945e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.242401e-06\n Vprtstp: contraction number = 3.811157e-01\n Vnewton: Using errtol_s: 16.203980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.136840e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.221340e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.792899e+00\n Vprtstp: contraction number = 7.792899e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 9.705840e-07\n Vprtstp: contraction number = 4.328325e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.110257e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.367534e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.404193e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.628535e+00\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -19674,27 +19674,27 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.120796256198E+00 kT\n Vpmg_energy:  qfEnergy = 2.906327571511E+04 kT\n Vpmg_energy:  dielEnergy = 1.455577325600E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.384400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.381300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 6.240693e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 4.285501e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:29:05 2025\n+# Creation Date and Time:  Sun Jan  7 09:41:14 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -20047,129 +20047,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.414800\n+Vacc_SASA: Time elapsed: 1.379222\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.795958e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.787202e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.092600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.019100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.186390e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.863270e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.150956e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.181364e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.355413e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.366779e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.776390e+05\n Vprtstp: contraction number = 1.776390e+05\n Vnewton: Attempting damping, relres = 0.041319\n Vnewton: Attempting damping, relres = 0.513474\n Vnewton: Damping accepted, relres = 0.041319\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.131938e-02\n Vprtstp: contraction number = 4.131938e-02\n Vnewton: Using errtol_s: 177710.973970\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.165492e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.900812e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677180e+04\n Vprtstp: contraction number = 2.677180e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.962101e-03\n Vprtstp: contraction number = 1.442931e-01\n Vnewton: Using errtol_s: 25642.465478\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.882826e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.371921e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.966549e+03\n Vprtstp: contraction number = 4.966549e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.056655e-03\n Vprtstp: contraction number = 1.772286e-01\n Vnewton: Using errtol_s: 4544.578762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.577439e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.824436e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011325e+03\n Vprtstp: contraction number = 1.011325e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.118038e-04\n Vprtstp: contraction number = 2.004475e-01\n Vnewton: Using errtol_s: 910.949292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.307695e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.242832e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.253595e+02\n Vprtstp: contraction number = 2.253595e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.715911e-05\n Vprtstp: contraction number = 2.226547e-01\n Vnewton: Using errtol_s: 202.827138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.034670e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.719947e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.445207e+01\n Vprtstp: contraction number = 5.445207e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.139456e-05\n Vprtstp: contraction number = 2.416194e-01\n Vnewton: Using errtol_s: 49.006980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.750122e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.167555e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420316e+01\n Vprtstp: contraction number = 1.420316e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.972126e-06\n Vprtstp: contraction number = 2.608373e-01\n Vnewton: Using errtol_s: 12.782849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.480194e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.614263e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.022184e+00\n Vprtstp: contraction number = 4.022184e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.416744e-07\n Vprtstp: contraction number = 2.831893e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.968174e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.216037e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.816013e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.039198e+00\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -20178,15 +20178,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.829504544268E-01 kT\n Vpmg_energy:  qfEnergy = 9.542693128993E+03 kT\n Vpmg_energy:  dielEnergy = 4.766198316119E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.912000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.887000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -20234,127 +20234,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0290577 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.353743\n+Vacc_SASA: Time elapsed: 1.356651\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.872826e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.138172e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.067300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.975000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.948030e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.862200e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.023018e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.368409e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 6495890.956801\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.037748e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.556064e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.477908e+05\n Vprtstp: contraction number = 5.477908e+05\n Vnewton: Attempting damping, relres = 0.076573\n Vnewton: Attempting damping, relres = 0.536204\n Vnewton: Damping accepted, relres = 0.076573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.657334e-02\n Vprtstp: contraction number = 7.657334e-02\n Vnewton: Using errtol_s: 497412.042043\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.129260e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.110781e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.388713e+04\n Vprtstp: contraction number = 7.388713e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.027070e-02\n Vprtstp: contraction number = 1.341289e-01\n Vnewton: Using errtol_s: 66717.354364\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.213838e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.583510e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.213780e+04\n Vprtstp: contraction number = 1.213780e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.681990e-03\n Vprtstp: contraction number = 1.637659e-01\n Vnewton: Using errtol_s: 10926.025346\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.298270e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.005271e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.238925e+03\n Vprtstp: contraction number = 2.238925e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.102037e-04\n Vprtstp: contraction number = 1.844265e-01\n Vnewton: Using errtol_s: 2015.049122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.383605e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.053042e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.343882e+02\n Vprtstp: contraction number = 4.343882e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.018448e-05\n Vprtstp: contraction number = 1.940160e-01\n Vnewton: Using errtol_s: 390.951807\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.469066e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.098026e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.935633e+01\n Vprtstp: contraction number = 7.935633e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.099479e-05\n Vprtstp: contraction number = 1.826848e-01\n Vnewton: Using errtol_s: 71.420957\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.553007e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.156084e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.530287e+01\n Vprtstp: contraction number = 1.530287e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.120201e-06\n Vprtstp: contraction number = 1.928369e-01\n Vnewton: Using errtol_s: 13.772596\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.638009e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.203744e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.453153e+00\n Vprtstp: contraction number = 3.453153e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.784317e-07\n Vprtstp: contraction number = 2.256539e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.901932e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.126504e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.064297e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.285426e+00\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -20363,15 +20363,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.465943688462E-01 kT\n Vpmg_energy:  qfEnergy = 7.516233054559E+04 kT\n Vpmg_energy:  dielEnergy = 3.774235798852E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.372600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.370800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -20394,129 +20394,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.396914\n+Vacc_SASA: Time elapsed: 1.409987\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.692486e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.805452e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.945500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.875000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.969540e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.347530e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.906556e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.452394e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.922372e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.469354e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.716926e+05\n Vprtstp: contraction number = 1.716926e+05\n Vnewton: Attempting damping, relres = 0.040940\n Vnewton: Attempting damping, relres = 0.513162\n Vnewton: Damping accepted, relres = 0.040940\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.093968e-02\n Vprtstp: contraction number = 4.093968e-02\n Vnewton: Using errtol_s: 175081.721880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.004621e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.526108e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.487025e+04\n Vprtstp: contraction number = 2.487025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.724811e-03\n Vprtstp: contraction number = 1.398353e-01\n Vnewton: Using errtol_s: 24482.603484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.074641e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.567814e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.528470e+03\n Vprtstp: contraction number = 4.528470e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.801406e-04\n Vprtstp: contraction number = 1.712092e-01\n Vnewton: Using errtol_s: 4191.647712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.147880e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.613002e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.122748e+02\n Vprtstp: contraction number = 9.122748e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923658e-04\n Vprtstp: contraction number = 1.962635e-01\n Vnewton: Using errtol_s: 822.667398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.217895e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.657905e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052635e+02\n Vprtstp: contraction number = 2.052635e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.319998e-05\n Vprtstp: contraction number = 2.245720e-01\n Vnewton: Using errtol_s: 184.748098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.292339e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.701865e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.154123e+01\n Vprtstp: contraction number = 5.154123e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.084685e-05\n Vprtstp: contraction number = 2.510845e-01\n Vnewton: Using errtol_s: 46.387392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.362644e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.751233e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.435770e+01\n Vprtstp: contraction number = 1.435770e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.021563e-06\n Vprtstp: contraction number = 2.785660e-01\n Vnewton: Using errtol_s: 12.921949\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.434574e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.792444e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.361187e+00\n Vprtstp: contraction number = 4.361187e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.178062e-07\n Vprtstp: contraction number = 3.037522e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.920794e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.144095e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.767397e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.035415e+00\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -20525,15 +20525,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.849546283812E-03 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 5.146958313419E-02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.026000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.149000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -20581,127 +20581,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00106753 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.378529\n+Vacc_SASA: Time elapsed: 1.435252\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.642169e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.804848e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.955300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.914500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.960120e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.878010e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.686238e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.032891e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 652367.043511\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.701120e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.047409e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.625442e+04\n Vprtstp: contraction number = 6.625442e+04\n Vnewton: Attempting damping, relres = 0.091545\n Vnewton: Attempting damping, relres = 0.542935\n Vnewton: Damping accepted, relres = 0.091545\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.154497e-02\n Vprtstp: contraction number = 9.154497e-02\n Vnewton: Using errtol_s: 59720.919943\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.773529e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.103485e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.669735e+03\n Vprtstp: contraction number = 8.669735e+03\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.196277e-02\n Vprtstp: contraction number = 1.306764e-01\n Vnewton: Using errtol_s: 7804.116477\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.839807e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.149117e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.277730e+03\n Vprtstp: contraction number = 1.277730e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.762772e-03\n Vprtstp: contraction number = 1.473548e-01\n Vnewton: Using errtol_s: 1149.974141\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.905668e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.198031e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.050893e+02\n Vprtstp: contraction number = 2.050893e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.829401e-04\n Vprtstp: contraction number = 1.605086e-01\n Vnewton: Using errtol_s: 184.580789\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.970582e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.242973e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.556662e+01\n Vprtstp: contraction number = 3.556662e+01\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.906742e-05\n Vprtstp: contraction number = 1.734198e-01\n Vnewton: Using errtol_s: 32.009971\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.036343e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.287403e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.633566e+00\n Vprtstp: contraction number = 6.633566e+00\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.151612e-06\n Vprtstp: contraction number = 1.865109e-01\n Vnewton: Using errtol_s: 5.970210\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.101503e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.347701e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.319897e+00\n Vprtstp: contraction number = 1.319897e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.820919e-06\n Vprtstp: contraction number = 1.989725e-01\n Vnewton: Using errtol_s: 1.187907\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.167159e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.406564e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.771301e-01\n Vprtstp: contraction number = 2.771301e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.823263e-07\n Vprtstp: contraction number = 2.099634e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.364863e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.586847e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.145957e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.366549e+00\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -20710,17 +20710,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.030046232457E-03 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 4.051425345163E-02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.436500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.434100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -20741,129 +20741,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.003989\n+Vacc_SASA: Time elapsed: 3.003746\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.354283e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.594148e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.994900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.895200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.945310e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.900290e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.581982e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.830104e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.597110e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.848426e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528464e+05\n Vprtstp: contraction number = 3.528464e+05\n Vnewton: Attempting damping, relres = 0.041605\n Vnewton: Attempting damping, relres = 0.513349\n Vnewton: Damping accepted, relres = 0.041605\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160535e-02\n Vprtstp: contraction number = 4.160535e-02\n Vnewton: Using errtol_s: 361941.817774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.687700e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.901695e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.210930e+04\n Vprtstp: contraction number = 5.210930e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.921711e-03\n Vprtstp: contraction number = 1.423305e-01\n Vnewton: Using errtol_s: 51515.371182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.768175e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.951564e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.570568e+03\n Vprtstp: contraction number = 9.570568e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.018950e-03\n Vprtstp: contraction number = 1.720701e-01\n Vnewton: Using errtol_s: 8864.257334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.848346e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.997967e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.944504e+03\n Vprtstp: contraction number = 1.944504e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.015521e-04\n Vprtstp: contraction number = 1.978037e-01\n Vnewton: Using errtol_s: 1753.383252\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.929960e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.051657e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.357668e+02\n Vprtstp: contraction number = 4.357668e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.508379e-05\n Vprtstp: contraction number = 2.236831e-01\n Vnewton: Using errtol_s: 392.202227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.011048e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.093881e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.074784e+02\n Vprtstp: contraction number = 1.074784e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.111924e-05\n Vprtstp: contraction number = 2.466350e-01\n Vnewton: Using errtol_s: 96.730784\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.093775e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.141084e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.903808e+01\n Vprtstp: contraction number = 2.903808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.004146e-06\n Vprtstp: contraction number = 2.701755e-01\n Vnewton: Using errtol_s: 26.134288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.176187e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.184720e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.552738e+00\n Vprtstp: contraction number = 8.552738e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.848266e-07\n Vprtstp: contraction number = 2.945351e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.659367e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.879355e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.936387e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.150206e+00\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -20872,15 +20872,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.211035436477E-01 kT\n Vpmg_energy:  qfEnergy = 9.542244232526E+03 kT\n Vpmg_energy:  dielEnergy = 4.766290532541E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.973000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.046000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -20928,127 +20928,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.033736 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.011393\n+Vacc_SASA: Time elapsed: 3.011177\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.629526e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.855704e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.060200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.935200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.168040e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.017150e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.636632e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.634178e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7064626.020092\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.655851e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.651760e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.009458e+05\n Vprtstp: contraction number = 6.009458e+05\n Vnewton: Attempting damping, relres = 0.077277\n Vnewton: Attempting damping, relres = 0.536445\n Vnewton: Damping accepted, relres = 0.077277\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.727667e-02\n Vprtstp: contraction number = 7.727667e-02\n Vnewton: Using errtol_s: 545930.796082\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.752441e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.710506e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.090350e+04\n Vprtstp: contraction number = 8.090350e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.034337e-02\n Vprtstp: contraction number = 1.338486e-01\n Vnewton: Using errtol_s: 73072.056615\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.837267e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.762633e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.317148e+04\n Vprtstp: contraction number = 1.317148e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.678394e-03\n Vprtstp: contraction number = 1.622676e-01\n Vnewton: Using errtol_s: 11857.226595\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.921396e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.806552e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401584e+03\n Vprtstp: contraction number = 2.401584e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.059541e-04\n Vprtstp: contraction number = 1.822898e-01\n Vnewton: Using errtol_s: 2161.451428\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.006416e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.854679e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.616256e+02\n Vprtstp: contraction number = 4.616256e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.880932e-05\n Vprtstp: contraction number = 1.922161e-01\n Vnewton: Using errtol_s: 415.465831\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.092028e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.900131e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.389879e+01\n Vprtstp: contraction number = 8.389879e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.068835e-05\n Vprtstp: contraction number = 1.817458e-01\n Vnewton: Using errtol_s: 75.509189\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.178412e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.944517e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.600785e+01\n Vprtstp: contraction number = 1.600785e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.039328e-06\n Vprtstp: contraction number = 1.907991e-01\n Vnewton: Using errtol_s: 14.407086\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.264727e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.987439e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.576512e+00\n Vprtstp: contraction number = 3.576512e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.556310e-07\n Vprtstp: contraction number = 2.234222e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.044759e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.290442e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.897640e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.134258e+00\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -21057,27 +21057,27 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.037329097601E-01 kT\n Vpmg_energy:  qfEnergy = 7.516201956521E+04 kT\n Vpmg_energy:  dielEnergy = 3.774250132186E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.332100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.326800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.368751e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 4.051760e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:29:41 2025\n+# Creation Date and Time:  Sun Jan  7 09:41:35 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -21430,129 +21430,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.365296\n+Vacc_SASA: Time elapsed: 1.373624\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.629581e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.791637e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.988600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.063800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.855410e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.403780e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.948788e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.185919e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.098382e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.491511e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.776390e+05\n Vprtstp: contraction number = 1.776390e+05\n Vnewton: Attempting damping, relres = 0.041319\n Vnewton: Attempting damping, relres = 0.513474\n Vnewton: Damping accepted, relres = 0.041319\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.131938e-02\n Vprtstp: contraction number = 4.131938e-02\n Vnewton: Using errtol_s: 177710.973970\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.927950e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.430586e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677180e+04\n Vprtstp: contraction number = 2.677180e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.962101e-03\n Vprtstp: contraction number = 1.442931e-01\n Vnewton: Using errtol_s: 25642.465478\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.676980e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.903224e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.966549e+03\n Vprtstp: contraction number = 4.966549e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.056655e-03\n Vprtstp: contraction number = 1.772286e-01\n Vnewton: Using errtol_s: 4544.578762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.431673e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.362978e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011325e+03\n Vprtstp: contraction number = 1.011325e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.118038e-04\n Vprtstp: contraction number = 2.004475e-01\n Vnewton: Using errtol_s: 910.949292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.182337e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.811324e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.253595e+02\n Vprtstp: contraction number = 2.253595e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.715911e-05\n Vprtstp: contraction number = 2.226547e-01\n Vnewton: Using errtol_s: 202.827138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.924271e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.275597e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.445207e+01\n Vprtstp: contraction number = 5.445207e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.139456e-05\n Vprtstp: contraction number = 2.416194e-01\n Vnewton: Using errtol_s: 49.006980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.661636e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.753337e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420316e+01\n Vprtstp: contraction number = 1.420316e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.972126e-06\n Vprtstp: contraction number = 2.608373e-01\n Vnewton: Using errtol_s: 12.782849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.408832e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.183001e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.022184e+00\n Vprtstp: contraction number = 4.022184e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.416744e-07\n Vprtstp: contraction number = 2.831893e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.116495e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.329218e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.366111e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.653571e+00\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -21561,15 +21561,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.136518672902E-02 kT\n Vpmg_energy:  qfEnergy = 4.355357372613E+01 kT\n Vpmg_energy:  dielEnergy = 4.752320511857E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.166000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.989000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -21617,127 +21617,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00231815 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.353390\n+Vacc_SASA: Time elapsed: 1.357497\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.734821e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.883479e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.072400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.992600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.986740e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.917130e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.003949e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.674959e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2402140.419777\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.019118e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.848940e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.993407e+05\n Vprtstp: contraction number = 1.993407e+05\n Vnewton: Attempting damping, relres = 0.074788\n Vnewton: Attempting damping, relres = 0.535005\n Vnewton: Damping accepted, relres = 0.074788\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.478844e-02\n Vprtstp: contraction number = 7.478844e-02\n Vnewton: Using errtol_s: 179652.345700\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.112234e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.402779e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.540846e+04\n Vprtstp: contraction number = 2.540846e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.520223e-03\n Vprtstp: contraction number = 1.272954e-01\n Vnewton: Using errtol_s: 22868.913120\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.197064e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.832249e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.863220e+03\n Vprtstp: contraction number = 3.863220e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.447432e-03\n Vprtstp: contraction number = 1.520376e-01\n Vnewton: Using errtol_s: 3476.934666\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.281419e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.030073e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.609951e+02\n Vprtstp: contraction number = 6.609951e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.476530e-04\n Vprtstp: contraction number = 1.710982e-01\n Vnewton: Using errtol_s: 594.897360\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.366263e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.078037e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.229316e+02\n Vprtstp: contraction number = 1.229316e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.605831e-05\n Vprtstp: contraction number = 1.859792e-01\n Vnewton: Using errtol_s: 110.638524\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.450989e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.124781e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.422381e+01\n Vprtstp: contraction number = 2.422381e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.075836e-06\n Vprtstp: contraction number = 1.970510e-01\n Vnewton: Using errtol_s: 21.801431\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.538547e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.167217e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.026312e+00\n Vprtstp: contraction number = 5.026312e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.883187e-06\n Vprtstp: contraction number = 2.074947e-01\n Vnewton: Using errtol_s: 4.523681\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.623822e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.215419e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.096485e+00\n Vprtstp: contraction number = 1.096485e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.108154e-07\n Vprtstp: contraction number = 2.181490e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.944812e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.172081e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.836886e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.064430e+00\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -21746,15 +21746,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.937401577775E-02 kT\n Vpmg_energy:  qfEnergy = 4.174168231022E+02 kT\n Vpmg_energy:  dielEnergy = 2.811735250011E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.474800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.488000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -21777,129 +21777,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.402104\n+Vacc_SASA: Time elapsed: 1.425189\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.715636e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.771301e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.960900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.902300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.082140e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.107690e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.895400e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.454735e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.913639e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.474777e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.716926e+05\n Vprtstp: contraction number = 1.716926e+05\n Vnewton: Attempting damping, relres = 0.040940\n Vnewton: Attempting damping, relres = 0.513162\n Vnewton: Damping accepted, relres = 0.040940\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.093968e-02\n Vprtstp: contraction number = 4.093968e-02\n Vnewton: Using errtol_s: 175081.721880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.004361e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.549863e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.487025e+04\n Vprtstp: contraction number = 2.487025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.724811e-03\n Vprtstp: contraction number = 1.398353e-01\n Vnewton: Using errtol_s: 24482.603484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.077175e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.605069e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.528470e+03\n Vprtstp: contraction number = 4.528470e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.801406e-04\n Vprtstp: contraction number = 1.712092e-01\n Vnewton: Using errtol_s: 4191.647712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.151919e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.655833e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.122748e+02\n Vprtstp: contraction number = 9.122748e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923658e-04\n Vprtstp: contraction number = 1.962635e-01\n Vnewton: Using errtol_s: 822.667398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.229403e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.712696e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052635e+02\n Vprtstp: contraction number = 2.052635e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.319998e-05\n Vprtstp: contraction number = 2.245720e-01\n Vnewton: Using errtol_s: 184.748098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.305522e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.767392e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.154123e+01\n Vprtstp: contraction number = 5.154123e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.084685e-05\n Vprtstp: contraction number = 2.510845e-01\n Vnewton: Using errtol_s: 46.387392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.378969e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.824520e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.435770e+01\n Vprtstp: contraction number = 1.435770e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.021563e-06\n Vprtstp: contraction number = 2.785660e-01\n Vnewton: Using errtol_s: 12.921949\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.452679e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.889419e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.361187e+00\n Vprtstp: contraction number = 4.361187e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.178062e-07\n Vprtstp: contraction number = 3.037522e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.212400e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.447666e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.777721e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.023244e+00\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -21908,17 +21908,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.911964187079E-01 kT\n Vpmg_energy:  qfEnergy = 3.802931672989E+03 kT\n Vpmg_energy:  dielEnergy = 1.840794517786E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.059000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.893400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -21964,127 +21964,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00427913 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.381106\n+Vacc_SASA: Time elapsed: 1.436979\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.751276e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.070022e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.932200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.827900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.853170e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.773340e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.714368e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.163872e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3438753.706105\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.729130e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.178980e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.983675e+05\n Vprtstp: contraction number = 2.983675e+05\n Vnewton: Attempting damping, relres = 0.078821\n Vnewton: Attempting damping, relres = 0.537150\n Vnewton: Damping accepted, relres = 0.078821\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.882110e-02\n Vprtstp: contraction number = 7.882110e-02\n Vnewton: Using errtol_s: 271046.361497\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.821684e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.230985e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.000218e+04\n Vprtstp: contraction number = 4.000218e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.049665e-02\n Vprtstp: contraction number = 1.331706e-01\n Vnewton: Using errtol_s: 36095.399051\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.905774e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.278412e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.428391e+03\n Vprtstp: contraction number = 6.428391e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.682686e-03\n Vprtstp: contraction number = 1.603069e-01\n Vnewton: Using errtol_s: 5786.342471\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.992151e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.321361e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.149080e+03\n Vprtstp: contraction number = 1.149080e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.007422e-04\n Vprtstp: contraction number = 1.787275e-01\n Vnewton: Using errtol_s: 1034.178484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.078078e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.363185e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.202083e+02\n Vprtstp: contraction number = 2.202083e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.763359e-05\n Vprtstp: contraction number = 1.916378e-01\n Vnewton: Using errtol_s: 198.187725\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.164392e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.407051e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.389925e+01\n Vprtstp: contraction number = 4.389925e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.148943e-05\n Vprtstp: contraction number = 1.993531e-01\n Vnewton: Using errtol_s: 39.509333\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.250573e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.450364e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.964795e+00\n Vprtstp: contraction number = 8.964795e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.346291e-06\n Vprtstp: contraction number = 2.042129e-01\n Vnewton: Using errtol_s: 8.068316\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.337022e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.498254e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.877921e+00\n Vprtstp: contraction number = 1.877921e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.914947e-07\n Vprtstp: contraction number = 2.094773e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.999589e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.211556e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.677949e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.888953e+00\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -22093,15 +22093,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.727005736130E-01 kT\n Vpmg_energy:  qfEnergy = 2.988671053842E+04 kT\n Vpmg_energy:  dielEnergy = 1.487788509003E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.388500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.390900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -22124,129 +22124,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.008082\n+Vacc_SASA: Time elapsed: 3.025975\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.398017e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.562147e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.880300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.852900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.042760e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.796540e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.778766e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.909947e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.796476e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.928325e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528464e+05\n Vprtstp: contraction number = 3.528464e+05\n Vnewton: Attempting damping, relres = 0.041605\n Vnewton: Attempting damping, relres = 0.513349\n Vnewton: Damping accepted, relres = 0.041605\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160535e-02\n Vprtstp: contraction number = 4.160535e-02\n Vnewton: Using errtol_s: 361941.817774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.895405e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.977779e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.210930e+04\n Vprtstp: contraction number = 5.210930e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.921711e-03\n Vprtstp: contraction number = 1.423305e-01\n Vnewton: Using errtol_s: 51515.371182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.972661e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.027449e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.570568e+03\n Vprtstp: contraction number = 9.570568e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.018950e-03\n Vprtstp: contraction number = 1.720701e-01\n Vnewton: Using errtol_s: 8864.257334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.050995e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.073764e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.944504e+03\n Vprtstp: contraction number = 1.944504e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.015521e-04\n Vprtstp: contraction number = 1.978037e-01\n Vnewton: Using errtol_s: 1753.383252\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.131001e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.117259e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.357668e+02\n Vprtstp: contraction number = 4.357668e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.508379e-05\n Vprtstp: contraction number = 2.236831e-01\n Vnewton: Using errtol_s: 392.202227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.211087e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.160707e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.074784e+02\n Vprtstp: contraction number = 1.074784e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.111924e-05\n Vprtstp: contraction number = 2.466350e-01\n Vnewton: Using errtol_s: 96.730784\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.291172e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.204181e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.903808e+01\n Vprtstp: contraction number = 2.903808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.004146e-06\n Vprtstp: contraction number = 2.701755e-01\n Vnewton: Using errtol_s: 26.134288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.372453e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.251142e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.552738e+00\n Vprtstp: contraction number = 8.552738e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.848266e-07\n Vprtstp: contraction number = 2.945351e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.628660e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.857247e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.760555e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.963501e+00\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -22255,17 +22255,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 3.095882318015E-01 kT\n Vpmg_energy:  qfEnergy = 3.878073055635E+03 kT\n Vpmg_energy:  dielEnergy = 1.902406349449E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.066000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.004000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -22311,127 +22311,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0124605 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.007479\n+Vacc_SASA: Time elapsed: 3.004882\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.656084e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.844812e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.900400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.867200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.289360e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.452590e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.834176e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.699509e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 5736524.194850\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.861487e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.734471e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.767730e+05\n Vprtstp: contraction number = 4.767730e+05\n Vnewton: Attempting damping, relres = 0.075286\n Vnewton: Attempting damping, relres = 0.535307\n Vnewton: Damping accepted, relres = 0.075286\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.528638e-02\n Vprtstp: contraction number = 7.528638e-02\n Vnewton: Using errtol_s: 431882.117004\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.968261e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.844353e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.255964e+04\n Vprtstp: contraction number = 6.255964e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.827684e-03\n Vprtstp: contraction number = 1.305373e-01\n Vnewton: Using errtol_s: 56376.745785\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.059343e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.891242e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.936134e+03\n Vprtstp: contraction number = 9.936134e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.558974e-03\n Vprtstp: contraction number = 1.586309e-01\n Vnewton: Using errtol_s: 8943.094496\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.148236e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.936371e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.786775e+03\n Vprtstp: contraction number = 1.786775e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.803288e-04\n Vprtstp: contraction number = 1.798162e-01\n Vnewton: Using errtol_s: 1608.113190\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.233736e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.982524e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.548476e+02\n Vprtstp: contraction number = 3.548476e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.567220e-05\n Vprtstp: contraction number = 1.985960e-01\n Vnewton: Using errtol_s: 319.364924\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.314743e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.028490e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.691838e+01\n Vprtstp: contraction number = 7.691838e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.206774e-05\n Vprtstp: contraction number = 2.167643e-01\n Vnewton: Using errtol_s: 69.226906\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.396972e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.070126e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.836013e+01\n Vprtstp: contraction number = 1.836013e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.880520e-06\n Vprtstp: contraction number = 2.386958e-01\n Vnewton: Using errtol_s: 16.524170\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.474879e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.117106e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.825966e+00\n Vprtstp: contraction number = 4.825966e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.571442e-07\n Vprtstp: contraction number = 2.628499e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.163721e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.421016e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.543038e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.821399e+00\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -22440,27 +22440,27 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 3.027416628019E-01 kT\n Vpmg_energy:  qfEnergy = 3.032769300439E+04 kT\n Vpmg_energy:  dielEnergy = 1.516953015159E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.398700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.388000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.578196e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 4.181127e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:30:18 2025\n+# Creation Date and Time:  Sun Jan  7 09:41:55 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -22813,129 +22813,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.358883\n+Vacc_SASA: Time elapsed: 1.373323\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.624182e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.763861e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.039600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.001800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.924040e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.799470e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.950473e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.147968e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.096989e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.310545e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.776390e+05\n Vprtstp: contraction number = 1.776390e+05\n Vnewton: Attempting damping, relres = 0.041319\n Vnewton: Attempting damping, relres = 0.513474\n Vnewton: Damping accepted, relres = 0.041319\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.131938e-02\n Vprtstp: contraction number = 4.131938e-02\n Vnewton: Using errtol_s: 177710.973970\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.932095e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.883922e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677180e+04\n Vprtstp: contraction number = 2.677180e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.962101e-03\n Vprtstp: contraction number = 1.442931e-01\n Vnewton: Using errtol_s: 25642.465478\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.678559e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.374997e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.966549e+03\n Vprtstp: contraction number = 4.966549e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.056655e-03\n Vprtstp: contraction number = 1.772286e-01\n Vnewton: Using errtol_s: 4544.578762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.430367e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.823899e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011325e+03\n Vprtstp: contraction number = 1.011325e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.118038e-04\n Vprtstp: contraction number = 2.004475e-01\n Vnewton: Using errtol_s: 910.949292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.170056e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.300413e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.253595e+02\n Vprtstp: contraction number = 2.253595e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.715911e-05\n Vprtstp: contraction number = 2.226547e-01\n Vnewton: Using errtol_s: 202.827138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.910452e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.721575e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.445207e+01\n Vprtstp: contraction number = 5.445207e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.139456e-05\n Vprtstp: contraction number = 2.416194e-01\n Vnewton: Using errtol_s: 49.006980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.650678e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.178981e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420316e+01\n Vprtstp: contraction number = 1.420316e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.972126e-06\n Vprtstp: contraction number = 2.608373e-01\n Vnewton: Using errtol_s: 12.782849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.399291e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.635797e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.022184e+00\n Vprtstp: contraction number = 4.022184e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.416744e-07\n Vprtstp: contraction number = 2.831893e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.077144e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.297918e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.836620e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.050898e+00\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -22944,15 +22944,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.578940273076E+00 kT\n Vpmg_energy:  qfEnergy = 1.464055888829E+04 kT\n Vpmg_energy:  dielEnergy = 7.268608527503E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.052000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.865000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -23000,138 +23000,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.246197 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.358949\n+Vacc_SASA: Time elapsed: 1.361481\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.850708e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.186921e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.119000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.950400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.038080e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.901720e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.012292e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.406695e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7187187.181934\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.027365e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.581833e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.181171e+05\n Vprtstp: contraction number = 6.181171e+05\n Vnewton: Attempting damping, relres = 0.078820\n Vnewton: Attempting damping, relres = 0.536981\n Vnewton: Damping accepted, relres = 0.078820\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.881989e-02\n Vprtstp: contraction number = 7.881989e-02\n Vnewton: Using errtol_s: 566493.329521\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.119937e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.116497e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.371738e+04\n Vprtstp: contraction number = 8.371738e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.055690e-02\n Vprtstp: contraction number = 1.339370e-01\n Vnewton: Using errtol_s: 75874.442084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.204428e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.579404e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.390337e+04\n Vprtstp: contraction number = 1.390337e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.741620e-03\n Vprtstp: contraction number = 1.649745e-01\n Vnewton: Using errtol_s: 12517.346695\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.290110e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.016494e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.648048e+03\n Vprtstp: contraction number = 2.648048e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.316551e-04\n Vprtstp: contraction number = 1.904291e-01\n Vnewton: Using errtol_s: 2383.666964\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.373897e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.064739e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.422627e+02\n Vprtstp: contraction number = 5.422627e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.790546e-05\n Vprtstp: contraction number = 2.047472e-01\n Vnewton: Using errtol_s: 488.049223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.455904e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.111521e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.184576e+02\n Vprtstp: contraction number = 1.184576e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.483378e-05\n Vprtstp: contraction number = 2.184475e-01\n Vnewton: Using errtol_s: 106.613126\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.536424e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.160750e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.976808e+01\n Vprtstp: contraction number = 2.976808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.727649e-06\n Vprtstp: contraction number = 2.512947e-01\n Vnewton: Using errtol_s: 26.791312\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.622694e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.203045e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.888808e+00\n Vprtstp: contraction number = 8.888808e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.113097e-06\n Vprtstp: contraction number = 2.986056e-01\n Vnewton: Using errtol_s: 8.000035\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.704862e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.252794e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.963970e+00\n Vprtstp: contraction number = 2.963970e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.711568e-07\n Vprtstp: contraction number = 3.334452e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.646190e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.878829e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.473204e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.696729e+00\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -23140,15 +23140,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.679263931619E+00 kT\n Vpmg_energy:  qfEnergy = 1.125861211589E+05 kT\n Vpmg_energy:  dielEnergy = 5.606777456856E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.343700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.326900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -23171,129 +23171,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.391820\n+Vacc_SASA: Time elapsed: 1.410319\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.725426e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.797279e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.914000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.940800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.025050e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.577030e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.974164e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.498512e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.993068e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.533694e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.716926e+05\n Vprtstp: contraction number = 1.716926e+05\n Vnewton: Attempting damping, relres = 0.040940\n Vnewton: Attempting damping, relres = 0.513162\n Vnewton: Damping accepted, relres = 0.040940\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.093968e-02\n Vprtstp: contraction number = 4.093968e-02\n Vnewton: Using errtol_s: 175081.721880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.083819e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.686187e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.487025e+04\n Vprtstp: contraction number = 2.487025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.724811e-03\n Vprtstp: contraction number = 1.398353e-01\n Vnewton: Using errtol_s: 24482.603484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.151782e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.818819e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.528470e+03\n Vprtstp: contraction number = 4.528470e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.801406e-04\n Vprtstp: contraction number = 1.712092e-01\n Vnewton: Using errtol_s: 4191.647712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.220872e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.943273e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.122748e+02\n Vprtstp: contraction number = 9.122748e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923658e-04\n Vprtstp: contraction number = 1.962635e-01\n Vnewton: Using errtol_s: 822.667398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.292002e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.090401e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052635e+02\n Vprtstp: contraction number = 2.052635e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.319998e-05\n Vprtstp: contraction number = 2.245720e-01\n Vnewton: Using errtol_s: 184.748098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.364300e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.224003e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.154123e+01\n Vprtstp: contraction number = 5.154123e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.084685e-05\n Vprtstp: contraction number = 2.510845e-01\n Vnewton: Using errtol_s: 46.387392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.436276e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.361683e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.435770e+01\n Vprtstp: contraction number = 1.435770e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.021563e-06\n Vprtstp: contraction number = 2.785660e-01\n Vnewton: Using errtol_s: 12.921949\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.506414e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.502258e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.361187e+00\n Vprtstp: contraction number = 4.361187e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.178062e-07\n Vprtstp: contraction number = 3.037522e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.947496e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.177194e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.114730e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.143817e+01\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -23302,17 +23302,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.880126377174E-02 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 3.532414743910E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.920000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.526000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -23358,127 +23358,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.000694544 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.375820\n+Vacc_SASA: Time elapsed: 1.392516\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.657093e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.836751e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.934300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.909500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.930670e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.352150e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.757701e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.825912e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 947577.428093\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.772729e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.854334e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.028571e+05\n Vprtstp: contraction number = 1.028571e+05\n Vnewton: Attempting damping, relres = 0.100178\n Vnewton: Attempting damping, relres = 0.546680\n Vnewton: Damping accepted, relres = 0.100178\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.001782e-01\n Vprtstp: contraction number = 1.001782e-01\n Vnewton: Using errtol_s: 94926.584698\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.846884e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.995558e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.470559e+04\n Vprtstp: contraction number = 1.470559e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.405726e-02\n Vprtstp: contraction number = 1.403226e-01\n Vnewton: Using errtol_s: 13320.343474\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.913476e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.121689e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.349875e+03\n Vprtstp: contraction number = 2.349875e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.232971e-03\n Vprtstp: contraction number = 1.588482e-01\n Vnewton: Using errtol_s: 2115.913123\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.981676e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.247036e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.041926e+02\n Vprtstp: contraction number = 4.041926e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.839085e-04\n Vprtstp: contraction number = 1.719272e-01\n Vnewton: Using errtol_s: 363.783073\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.049789e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.376510e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.386262e+01\n Vprtstp: contraction number = 7.386262e+01\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.015424e-05\n Vprtstp: contraction number = 1.827368e-01\n Vnewton: Using errtol_s: 66.476570\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.118250e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.495689e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.423266e+01\n Vprtstp: contraction number = 1.423266e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.351805e-05\n Vprtstp: contraction number = 1.926905e-01\n Vnewton: Using errtol_s: 12.809401\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.186392e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.609332e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.877145e+00\n Vprtstp: contraction number = 2.877145e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.732685e-06\n Vprtstp: contraction number = 2.021508e-01\n Vnewton: Using errtol_s: 2.589431\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.255913e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.724631e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.073349e-01\n Vprtstp: contraction number = 6.073349e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.768409e-07\n Vprtstp: contraction number = 2.110894e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.578279e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.797265e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.985944e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.024797e+01\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -23487,15 +23487,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.348045314741E-02 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 3.080172074466E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.451300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.578900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -23518,129 +23518,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.001745\n+Vacc_SASA: Time elapsed: 3.237961\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.354282e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.810634e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.848900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.025400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.960300e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.344880e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.674757e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.236184e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.692898e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.265043e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528464e+05\n Vprtstp: contraction number = 3.528464e+05\n Vnewton: Attempting damping, relres = 0.041605\n Vnewton: Attempting damping, relres = 0.513349\n Vnewton: Damping accepted, relres = 0.041605\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160535e-02\n Vprtstp: contraction number = 4.160535e-02\n Vnewton: Using errtol_s: 361941.817774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.783443e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.397801e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.210930e+04\n Vprtstp: contraction number = 5.210930e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.921711e-03\n Vprtstp: contraction number = 1.423305e-01\n Vnewton: Using errtol_s: 51515.371182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.864007e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.524896e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.570568e+03\n Vprtstp: contraction number = 9.570568e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.018950e-03\n Vprtstp: contraction number = 1.720701e-01\n Vnewton: Using errtol_s: 8864.257334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.940707e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.650610e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.944504e+03\n Vprtstp: contraction number = 1.944504e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.015521e-04\n Vprtstp: contraction number = 1.978037e-01\n Vnewton: Using errtol_s: 1753.383252\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.023376e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.800593e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.357668e+02\n Vprtstp: contraction number = 4.357668e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.508379e-05\n Vprtstp: contraction number = 2.236831e-01\n Vnewton: Using errtol_s: 392.202227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.103471e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.946235e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.074784e+02\n Vprtstp: contraction number = 1.074784e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.111924e-05\n Vprtstp: contraction number = 2.466350e-01\n Vnewton: Using errtol_s: 96.730784\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.180326e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.067541e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.903808e+01\n Vprtstp: contraction number = 2.903808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.004146e-06\n Vprtstp: contraction number = 2.701755e-01\n Vnewton: Using errtol_s: 26.134288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.260446e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.183790e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.552738e+00\n Vprtstp: contraction number = 8.552738e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.848266e-07\n Vprtstp: contraction number = 2.945351e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.551644e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.771097e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.021696e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.047732e+01\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -23649,17 +23649,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.727728107537E+00 kT\n Vpmg_energy:  qfEnergy = 1.464487511349E+04 kT\n Vpmg_energy:  dielEnergy = 7.268391520583E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.070000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.927000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -23705,138 +23705,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.239586 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.020682\n+Vacc_SASA: Time elapsed: 3.211159\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.677640e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.069239e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.939100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.918500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.259130e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.288310e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.724310e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.692288e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8056801.731105\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.749291e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.720963e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.019948e+05\n Vprtstp: contraction number = 7.019948e+05\n Vnewton: Attempting damping, relres = 0.080001\n Vnewton: Attempting damping, relres = 0.537427\n Vnewton: Damping accepted, relres = 0.080001\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.000142e-02\n Vprtstp: contraction number = 8.000142e-02\n Vnewton: Using errtol_s: 644555.552257\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.852845e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.829126e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.545628e+04\n Vprtstp: contraction number = 9.545628e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.074028e-02\n Vprtstp: contraction number = 1.342512e-01\n Vnewton: Using errtol_s: 86532.331514\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.932411e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.937905e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.576216e+04\n Vprtstp: contraction number = 1.576216e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.761379e-03\n Vprtstp: contraction number = 1.639975e-01\n Vnewton: Using errtol_s: 14191.084898\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.015531e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.045563e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.960538e+03\n Vprtstp: contraction number = 2.960538e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.307659e-04\n Vprtstp: contraction number = 1.877880e-01\n Vnewton: Using errtol_s: 2664.915408\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.100907e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.155883e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.967294e+02\n Vprtstp: contraction number = 5.967294e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.666049e-05\n Vprtstp: contraction number = 2.015337e-01\n Vnewton: Using errtol_s: 537.070343\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.183420e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.291282e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.275865e+02\n Vprtstp: contraction number = 1.275865e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.425245e-05\n Vprtstp: contraction number = 2.138065e-01\n Vnewton: Using errtol_s: 114.829153\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.265040e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.432312e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.141071e+01\n Vprtstp: contraction number = 3.141071e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.508796e-06\n Vprtstp: contraction number = 2.461890e-01\n Vnewton: Using errtol_s: 28.269675\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.350453e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.570846e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.244202e+00\n Vprtstp: contraction number = 9.244202e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.032654e-06\n Vprtstp: contraction number = 2.943044e-01\n Vnewton: Using errtol_s: 8.319891\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.434164e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.710578e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.069585e+00\n Vprtstp: contraction number = 3.069585e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.428937e-07\n Vprtstp: contraction number = 3.320508e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.860855e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.115180e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.106188e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.132327e+01\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -23845,27 +23845,27 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.898743294947E+00 kT\n Vpmg_energy:  qfEnergy = 1.125893253171E+05 kT\n Vpmg_energy:  dielEnergy = 5.606732677067E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.675500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.278500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.538515e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 6.825532e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:30:55 2025\n+# Creation Date and Time:  Sun Jan  7 09:42:21 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -24218,129 +24218,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.360608\n+Vacc_SASA: Time elapsed: 1.378952\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.711457e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.794579e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.007300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.022000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.234420e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.422230e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.072044e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.250529e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.339748e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.496167e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.776390e+05\n Vprtstp: contraction number = 1.776390e+05\n Vnewton: Attempting damping, relres = 0.041319\n Vnewton: Attempting damping, relres = 0.513474\n Vnewton: Damping accepted, relres = 0.041319\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.131938e-02\n Vprtstp: contraction number = 4.131938e-02\n Vnewton: Using errtol_s: 177710.973970\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.354107e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.538564e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677180e+04\n Vprtstp: contraction number = 2.677180e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.962101e-03\n Vprtstp: contraction number = 1.442931e-01\n Vnewton: Using errtol_s: 25642.465478\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.154834e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.905441e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.966549e+03\n Vprtstp: contraction number = 4.966549e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.056655e-03\n Vprtstp: contraction number = 1.772286e-01\n Vnewton: Using errtol_s: 4544.578762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.914874e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.291915e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011325e+03\n Vprtstp: contraction number = 1.011325e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.118038e-04\n Vprtstp: contraction number = 2.004475e-01\n Vnewton: Using errtol_s: 910.949292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.683909e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.357615e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.253595e+02\n Vprtstp: contraction number = 2.253595e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.715911e-05\n Vprtstp: contraction number = 2.226547e-01\n Vnewton: Using errtol_s: 202.827138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.448621e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.198905e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.445207e+01\n Vprtstp: contraction number = 5.445207e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.139456e-05\n Vprtstp: contraction number = 2.416194e-01\n Vnewton: Using errtol_s: 49.006980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.182151e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.524605e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420316e+01\n Vprtstp: contraction number = 1.420316e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.972126e-06\n Vprtstp: contraction number = 2.608373e-01\n Vnewton: Using errtol_s: 12.782849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.890888e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.056942e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.022184e+00\n Vprtstp: contraction number = 4.022184e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.416744e-07\n Vprtstp: contraction number = 2.831893e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.464365e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.718429e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.312948e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.597456e+00\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -24349,17 +24349,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.439783180216E-02 kT\n Vpmg_energy:  qfEnergy = 2.890574221449E+02 kT\n Vpmg_energy:  dielEnergy = 1.267284045292E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.445000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.674500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -24405,127 +24405,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00201917 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.352615\n+Vacc_SASA: Time elapsed: 1.369750\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.773912e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.852389e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.013500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.080600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.268270e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.468770e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.058166e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.372977e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1602777.342155\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.083779e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.406595e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.455767e+05\n Vprtstp: contraction number = 1.455767e+05\n Vnewton: Attempting damping, relres = 0.082108\n Vnewton: Attempting damping, relres = 0.538752\n Vnewton: Damping accepted, relres = 0.082108\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.210786e-02\n Vprtstp: contraction number = 8.210786e-02\n Vnewton: Using errtol_s: 131600.616465\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.188990e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.551749e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.947215e+04\n Vprtstp: contraction number = 1.947215e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.093564e-02\n Vprtstp: contraction number = 1.331863e-01\n Vnewton: Using errtol_s: 17527.393818\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.272251e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.694336e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.986234e+03\n Vprtstp: contraction number = 2.986234e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.676878e-03\n Vprtstp: contraction number = 1.533407e-01\n Vnewton: Using errtol_s: 2687.662365\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.358506e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.823663e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.993905e+02\n Vprtstp: contraction number = 4.993905e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.804220e-04\n Vprtstp: contraction number = 1.672286e-01\n Vnewton: Using errtol_s: 449.454038\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.449313e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.923552e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.039598e+01\n Vprtstp: contraction number = 9.039598e+01\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.075969e-05\n Vprtstp: contraction number = 1.810118e-01\n Vnewton: Using errtol_s: 81.356480\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.537930e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.060236e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755931e+01\n Vprtstp: contraction number = 1.755931e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.860000e-06\n Vprtstp: contraction number = 1.942486e-01\n Vnewton: Using errtol_s: 15.803384\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.624164e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.185811e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.630601e+00\n Vprtstp: contraction number = 3.630601e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.038674e-06\n Vprtstp: contraction number = 2.067621e-01\n Vnewton: Using errtol_s: 3.267541\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.712351e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.291638e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.904977e-01\n Vprtstp: contraction number = 7.904977e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.438845e-07\n Vprtstp: contraction number = 2.177319e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.273228e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.531542e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.021499e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.049791e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -24534,15 +24534,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.337785270449E-02 kT\n Vpmg_energy:  qfEnergy = 2.452499065480E+03 kT\n Vpmg_energy:  dielEnergy = 1.155272442741E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.483100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.514400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -24565,129 +24565,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.408043\n+Vacc_SASA: Time elapsed: 1.410952\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.790862e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.787770e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.953800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.030000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.439760e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.435440e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.993908e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.603245e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.025269e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.630463e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.716926e+05\n Vprtstp: contraction number = 1.716926e+05\n Vnewton: Attempting damping, relres = 0.040940\n Vnewton: Attempting damping, relres = 0.513162\n Vnewton: Damping accepted, relres = 0.040940\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.093968e-02\n Vprtstp: contraction number = 4.093968e-02\n Vnewton: Using errtol_s: 175081.721880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.128334e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.751676e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.487025e+04\n Vprtstp: contraction number = 2.487025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.724811e-03\n Vprtstp: contraction number = 1.398353e-01\n Vnewton: Using errtol_s: 24482.603484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.205055e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.835554e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.528470e+03\n Vprtstp: contraction number = 4.528470e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.801406e-04\n Vprtstp: contraction number = 1.712092e-01\n Vnewton: Using errtol_s: 4191.647712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.281863e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.953565e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.122748e+02\n Vprtstp: contraction number = 9.122748e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923658e-04\n Vprtstp: contraction number = 1.962635e-01\n Vnewton: Using errtol_s: 822.667398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.359263e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.028699e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052635e+02\n Vprtstp: contraction number = 2.052635e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.319998e-05\n Vprtstp: contraction number = 2.245720e-01\n Vnewton: Using errtol_s: 184.748098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.433389e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.110331e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.154123e+01\n Vprtstp: contraction number = 5.154123e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.084685e-05\n Vprtstp: contraction number = 2.510845e-01\n Vnewton: Using errtol_s: 46.387392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.508903e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.235401e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.435770e+01\n Vprtstp: contraction number = 1.435770e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.021563e-06\n Vprtstp: contraction number = 2.785660e-01\n Vnewton: Using errtol_s: 12.921949\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.591798e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.367176e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.361187e+00\n Vprtstp: contraction number = 4.361187e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.178062e-07\n Vprtstp: contraction number = 3.037522e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.666432e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.940883e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.398696e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.679345e+00\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -24696,15 +24696,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.047547930931E+00 kT\n Vpmg_energy:  qfEnergy = 1.326714299389E+04 kT\n Vpmg_energy:  dielEnergy = 6.630706107593E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.973000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.707700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -24752,138 +24752,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.20724 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.410423\n+Vacc_SASA: Time elapsed: 1.388671\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.061213e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.145527e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.032500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.979700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.417500e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.422920e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.895156e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.689263e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 6744887.867090\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.918510e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.721465e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.873341e+05\n Vprtstp: contraction number = 5.873341e+05\n Vnewton: Attempting damping, relres = 0.079798\n Vnewton: Attempting damping, relres = 0.537526\n Vnewton: Damping accepted, relres = 0.079798\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.979817e-02\n Vprtstp: contraction number = 7.979817e-02\n Vnewton: Using errtol_s: 538229.715979\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.033692e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.862657e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.003940e+04\n Vprtstp: contraction number = 8.003940e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.075173e-02\n Vprtstp: contraction number = 1.347366e-01\n Vnewton: Using errtol_s: 72519.230886\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.122390e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.952970e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.324771e+04\n Vprtstp: contraction number = 1.324771e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.768162e-03\n Vprtstp: contraction number = 1.644537e-01\n Vnewton: Using errtol_s: 11926.055102\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.207649e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.048507e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.493439e+03\n Vprtstp: contraction number = 2.493439e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.328041e-04\n Vprtstp: contraction number = 1.882203e-01\n Vnewton: Using errtol_s: 2244.726103\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.293318e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.198620e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.093161e+02\n Vprtstp: contraction number = 5.093161e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.796477e-05\n Vprtstp: contraction number = 2.042186e-01\n Vnewton: Using errtol_s: 458.414752\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.384650e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.329261e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.115992e+02\n Vprtstp: contraction number = 1.115992e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.489139e-05\n Vprtstp: contraction number = 2.191046e-01\n Vnewton: Using errtol_s: 100.440778\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.473739e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.392560e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.141695e+01\n Vprtstp: contraction number = 3.141695e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.192112e-06\n Vprtstp: contraction number = 2.815124e-01\n Vnewton: Using errtol_s: 28.275326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.564235e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.481026e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.143181e+01\n Vprtstp: contraction number = 1.143181e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.525422e-06\n Vprtstp: contraction number = 3.638791e-01\n Vnewton: Using errtol_s: 10.288800\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.651686e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.557007e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.900145e+00\n Vprtstp: contraction number = 4.900145e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 6.538480e-07\n Vprtstp: contraction number = 4.286342e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.370770e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.643250e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.988396e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.027333e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -24892,17 +24892,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.068066451634E+00 kT\n Vpmg_energy:  qfEnergy = 1.027128342703E+05 kT\n Vpmg_energy:  dielEnergy = 5.130929239454E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.277400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.055300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -24923,129 +24923,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.999169\n+Vacc_SASA: Time elapsed: 3.005655\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.440220e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.608003e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.865500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.948900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.234260e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.589010e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.102630e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.081883e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.127644e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.113811e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528464e+05\n Vprtstp: contraction number = 3.528464e+05\n Vnewton: Attempting damping, relres = 0.041605\n Vnewton: Attempting damping, relres = 0.513349\n Vnewton: Damping accepted, relres = 0.041605\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160535e-02\n Vprtstp: contraction number = 4.160535e-02\n Vnewton: Using errtol_s: 361941.817774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.229907e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.293010e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.210930e+04\n Vprtstp: contraction number = 5.210930e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.921711e-03\n Vprtstp: contraction number = 1.423305e-01\n Vnewton: Using errtol_s: 51515.371182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.310303e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.434712e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.570568e+03\n Vprtstp: contraction number = 9.570568e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.018950e-03\n Vprtstp: contraction number = 1.720701e-01\n Vnewton: Using errtol_s: 8864.257334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.387950e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.515406e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.944504e+03\n Vprtstp: contraction number = 1.944504e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.015521e-04\n Vprtstp: contraction number = 1.978037e-01\n Vnewton: Using errtol_s: 1753.383252\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.469889e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.650627e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.357668e+02\n Vprtstp: contraction number = 4.357668e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.508379e-05\n Vprtstp: contraction number = 2.236831e-01\n Vnewton: Using errtol_s: 392.202227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.549669e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.768813e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.074784e+02\n Vprtstp: contraction number = 1.074784e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.111924e-05\n Vprtstp: contraction number = 2.466350e-01\n Vnewton: Using errtol_s: 96.730784\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.628295e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.904261e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.903808e+01\n Vprtstp: contraction number = 2.903808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.004146e-06\n Vprtstp: contraction number = 2.701755e-01\n Vnewton: Using errtol_s: 26.134288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.707065e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.005435e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.552738e+00\n Vprtstp: contraction number = 8.552738e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.848266e-07\n Vprtstp: contraction number = 2.945351e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.715773e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.962728e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.047663e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.076555e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -25054,17 +25054,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.318490670487E+00 kT\n Vpmg_energy:  qfEnergy = 1.359627523071E+04 kT\n Vpmg_energy:  dielEnergy = 6.777157121148E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.267000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.469100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -25110,138 +25110,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.207145 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.005258\n+Vacc_SASA: Time elapsed: 3.043207\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.732064e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.057367e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.975400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.939000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.304630e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.451890e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.174686e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.566108e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8257970.099902\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.197648e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.597381e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.174738e+05\n Vprtstp: contraction number = 7.174738e+05\n Vnewton: Attempting damping, relres = 0.079654\n Vnewton: Attempting damping, relres = 0.537366\n Vnewton: Damping accepted, relres = 0.079654\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.965353e-02\n Vprtstp: contraction number = 7.965353e-02\n Vnewton: Using errtol_s: 657776.459467\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.293282e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.768794e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.738355e+04\n Vprtstp: contraction number = 9.738355e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.068030e-02\n Vprtstp: contraction number = 1.340844e-01\n Vnewton: Using errtol_s: 88197.583593\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.376943e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.932223e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.590859e+04\n Vprtstp: contraction number = 1.590859e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.734478e-03\n Vprtstp: contraction number = 1.623998e-01\n Vnewton: Using errtol_s: 14323.269837\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.459616e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.091201e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.927974e+03\n Vprtstp: contraction number = 2.927974e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.191803e-04\n Vprtstp: contraction number = 1.840209e-01\n Vnewton: Using errtol_s: 2635.781086\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.542875e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.197441e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.843569e+02\n Vprtstp: contraction number = 5.843569e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.369066e-05\n Vprtstp: contraction number = 1.995445e-01\n Vnewton: Using errtol_s: 525.955563\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.627881e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.340976e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.235877e+02\n Vprtstp: contraction number = 1.235877e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.346947e-05\n Vprtstp: contraction number = 2.114827e-01\n Vnewton: Using errtol_s: 111.230501\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.713366e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.487356e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.351690e+01\n Vprtstp: contraction number = 3.351690e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.652870e-06\n Vprtstp: contraction number = 2.711962e-01\n Vnewton: Using errtol_s: 30.165292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.798026e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.621655e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.181991e+01\n Vprtstp: contraction number = 1.181991e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.288222e-06\n Vprtstp: contraction number = 3.526602e-01\n Vnewton: Using errtol_s: 10.638098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.885301e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.745646e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.017523e+00\n Vprtstp: contraction number = 5.017523e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.468381e-07\n Vprtstp: contraction number = 4.244906e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.870792e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.130178e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.315517e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.343525e+01\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -25250,27 +25250,27 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.366252621548E+00 kT\n Vpmg_energy:  qfEnergy = 1.051945297594E+05 kT\n Vpmg_energy:  dielEnergy = 5.247887253466E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.297300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.609500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.990253e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.911588e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:31:28 2025\n+# Creation Date and Time:  Sun Jan  7 09:42:47 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -25623,129 +25623,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.362232\n+Vacc_SASA: Time elapsed: 1.383932\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.654296e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.774028e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.150400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.997400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.047580e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.397270e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.998452e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.215402e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.146889e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.539747e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.776390e+05\n Vprtstp: contraction number = 1.776390e+05\n Vnewton: Attempting damping, relres = 0.041319\n Vnewton: Attempting damping, relres = 0.513474\n Vnewton: Damping accepted, relres = 0.041319\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.131938e-02\n Vprtstp: contraction number = 4.131938e-02\n Vnewton: Using errtol_s: 177710.973970\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.968709e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.107273e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677180e+04\n Vprtstp: contraction number = 2.677180e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.962101e-03\n Vprtstp: contraction number = 1.442931e-01\n Vnewton: Using errtol_s: 25642.465478\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.692748e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.418639e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.966549e+03\n Vprtstp: contraction number = 4.966549e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.056655e-03\n Vprtstp: contraction number = 1.772286e-01\n Vnewton: Using errtol_s: 4544.578762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.408697e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.926407e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011325e+03\n Vprtstp: contraction number = 1.011325e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.118038e-04\n Vprtstp: contraction number = 2.004475e-01\n Vnewton: Using errtol_s: 910.949292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.154014e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.033326e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.253595e+02\n Vprtstp: contraction number = 2.253595e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.715911e-05\n Vprtstp: contraction number = 2.226547e-01\n Vnewton: Using errtol_s: 202.827138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.917553e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.418546e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.445207e+01\n Vprtstp: contraction number = 5.445207e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.139456e-05\n Vprtstp: contraction number = 2.416194e-01\n Vnewton: Using errtol_s: 49.006980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.703599e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.073704e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420316e+01\n Vprtstp: contraction number = 1.420316e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.972126e-06\n Vprtstp: contraction number = 2.608373e-01\n Vnewton: Using errtol_s: 12.782849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.531663e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.196002e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.022184e+00\n Vprtstp: contraction number = 4.022184e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.416744e-07\n Vprtstp: contraction number = 2.831893e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.246538e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.480877e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.079220e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.106532e+01\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -25754,15 +25754,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.504309500280E-01 kT\n Vpmg_energy:  qfEnergy = 1.755208046486E+03 kT\n Vpmg_energy:  dielEnergy = 8.724652508101E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.991000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.533500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -25810,127 +25810,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00318265 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.354305\n+Vacc_SASA: Time elapsed: 1.357282\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.848240e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.975835e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.062000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.986000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.127020e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.383750e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.034700e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.528431e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2662068.021804\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.052707e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.559065e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.456208e+05\n Vprtstp: contraction number = 2.456208e+05\n Vnewton: Attempting damping, relres = 0.083386\n Vnewton: Attempting damping, relres = 0.539586\n Vnewton: Damping accepted, relres = 0.083386\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.338571e-02\n Vprtstp: contraction number = 8.338571e-02\n Vnewton: Using errtol_s: 221978.424581\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.143086e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.723209e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.405567e+04\n Vprtstp: contraction number = 3.405567e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.151500e-02\n Vprtstp: contraction number = 1.380932e-01\n Vnewton: Using errtol_s: 30653.716000\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.228122e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.854062e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.435916e+03\n Vprtstp: contraction number = 5.435916e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.837816e-03\n Vprtstp: contraction number = 1.596019e-01\n Vnewton: Using errtol_s: 4892.390079\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.312067e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.996627e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.557902e+02\n Vprtstp: contraction number = 9.557902e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.231381e-04\n Vprtstp: contraction number = 1.758273e-01\n Vnewton: Using errtol_s: 860.215698\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.395041e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.110029e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.830694e+02\n Vprtstp: contraction number = 1.830694e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.189280e-05\n Vprtstp: contraction number = 1.915367e-01\n Vnewton: Using errtol_s: 164.762841\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.476856e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.260231e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.747370e+01\n Vprtstp: contraction number = 3.747370e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.266923e-05\n Vprtstp: contraction number = 2.046964e-01\n Vnewton: Using errtol_s: 33.726360\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.559711e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.400645e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.392089e+00\n Vprtstp: contraction number = 8.392089e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.837224e-06\n Vprtstp: contraction number = 2.239460e-01\n Vnewton: Using errtol_s: 7.552883\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.643390e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.537872e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.064121e+00\n Vprtstp: contraction number = 2.064121e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.978444e-07\n Vprtstp: contraction number = 2.459603e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.817093e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.058579e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.140654e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.167783e+01\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -25939,15 +25939,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.014738094319E-01 kT\n Vpmg_energy:  qfEnergy = 1.339968414661E+04 kT\n Vpmg_energy:  dielEnergy = 6.688675559504E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.472000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.059600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -25970,129 +25970,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.389694\n+Vacc_SASA: Time elapsed: 1.402773\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.743232e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.818061e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.970800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.925300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.436560e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.504460e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.919837e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.883683e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.944542e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.920674e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.716926e+05\n Vprtstp: contraction number = 1.716926e+05\n Vnewton: Attempting damping, relres = 0.040940\n Vnewton: Attempting damping, relres = 0.513162\n Vnewton: Damping accepted, relres = 0.040940\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.093968e-02\n Vprtstp: contraction number = 4.093968e-02\n Vnewton: Using errtol_s: 175081.721880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.040163e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.084128e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.487025e+04\n Vprtstp: contraction number = 2.487025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.724811e-03\n Vprtstp: contraction number = 1.398353e-01\n Vnewton: Using errtol_s: 24482.603484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.111053e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.204488e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.528470e+03\n Vprtstp: contraction number = 4.528470e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.801406e-04\n Vprtstp: contraction number = 1.712092e-01\n Vnewton: Using errtol_s: 4191.647712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.187307e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.334759e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.122748e+02\n Vprtstp: contraction number = 9.122748e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923658e-04\n Vprtstp: contraction number = 1.962635e-01\n Vnewton: Using errtol_s: 822.667398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.262520e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.467376e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052635e+02\n Vprtstp: contraction number = 2.052635e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.319998e-05\n Vprtstp: contraction number = 2.245720e-01\n Vnewton: Using errtol_s: 184.748098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.339369e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.590949e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.154123e+01\n Vprtstp: contraction number = 5.154123e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.084685e-05\n Vprtstp: contraction number = 2.510845e-01\n Vnewton: Using errtol_s: 46.387392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.414756e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.719080e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.435770e+01\n Vprtstp: contraction number = 1.435770e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.021563e-06\n Vprtstp: contraction number = 2.785660e-01\n Vnewton: Using errtol_s: 12.921949\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.490950e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.794630e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.361187e+00\n Vprtstp: contraction number = 4.361187e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.178062e-07\n Vprtstp: contraction number = 3.037522e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.352170e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.624455e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.038711e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.067363e+01\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -26101,17 +26101,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.301986990892E-02 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 1.769795919653E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.510000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.473500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -26157,127 +26157,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0030275 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.379773\n+Vacc_SASA: Time elapsed: 1.386779\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.781352e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.850844e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.004200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.967800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.195750e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.163760e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.759327e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.135928e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1183078.697095\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.779030e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.165920e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.216317e+05\n Vprtstp: contraction number = 1.216317e+05\n Vnewton: Attempting damping, relres = 0.092815\n Vnewton: Attempting damping, relres = 0.543699\n Vnewton: Damping accepted, relres = 0.092815\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.281548e-02\n Vprtstp: contraction number = 9.281548e-02\n Vnewton: Using errtol_s: 109808.011526\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.857523e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.307016e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.637169e+04\n Vprtstp: contraction number = 1.637169e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.245819e-02\n Vprtstp: contraction number = 1.342253e-01\n Vnewton: Using errtol_s: 14739.016153\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.924542e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.433516e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.481814e+03\n Vprtstp: contraction number = 2.481814e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.888035e-03\n Vprtstp: contraction number = 1.515497e-01\n Vnewton: Using errtol_s: 2233.693882\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.991222e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.516773e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.090266e+02\n Vprtstp: contraction number = 4.090266e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.111589e-04\n Vprtstp: contraction number = 1.648057e-01\n Vnewton: Using errtol_s: 368.125449\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.058337e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.605223e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.284721e+01\n Vprtstp: contraction number = 7.284721e+01\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.541690e-05\n Vprtstp: contraction number = 1.780984e-01\n Vnewton: Using errtol_s: 65.562559\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.124462e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.725634e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.403461e+01\n Vprtstp: contraction number = 1.403461e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.067651e-05\n Vprtstp: contraction number = 1.926581e-01\n Vnewton: Using errtol_s: 12.631156\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.191318e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.801437e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.928656e+00\n Vprtstp: contraction number = 2.928656e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.227908e-06\n Vprtstp: contraction number = 2.086737e-01\n Vnewton: Using errtol_s: 2.635791\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.257238e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.920882e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.633899e-01\n Vprtstp: contraction number = 6.633899e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.046587e-07\n Vprtstp: contraction number = 2.265168e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.537301e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.785558e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.967341e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.222829e+00\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -26286,17 +26286,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.998648605542E-02 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 1.756152878975E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.435700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.263000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -26317,129 +26317,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.991572\n+Vacc_SASA: Time elapsed: 3.052464\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.449465e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.678569e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.018400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.952500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.315920e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.503620e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.685599e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.432338e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.707848e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.467237e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528464e+05\n Vprtstp: contraction number = 3.528464e+05\n Vnewton: Attempting damping, relres = 0.041605\n Vnewton: Attempting damping, relres = 0.513349\n Vnewton: Damping accepted, relres = 0.041605\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160535e-02\n Vprtstp: contraction number = 4.160535e-02\n Vnewton: Using errtol_s: 361941.817774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.806872e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.640732e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.210930e+04\n Vprtstp: contraction number = 5.210930e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.921711e-03\n Vprtstp: contraction number = 1.423305e-01\n Vnewton: Using errtol_s: 51515.371182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.884498e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.776158e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.570568e+03\n Vprtstp: contraction number = 9.570568e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.018950e-03\n Vprtstp: contraction number = 1.720701e-01\n Vnewton: Using errtol_s: 8864.257334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.965694e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.927523e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.944504e+03\n Vprtstp: contraction number = 1.944504e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.015521e-04\n Vprtstp: contraction number = 1.978037e-01\n Vnewton: Using errtol_s: 1753.383252\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.046546e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.075890e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.357668e+02\n Vprtstp: contraction number = 4.357668e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.508379e-05\n Vprtstp: contraction number = 2.236831e-01\n Vnewton: Using errtol_s: 392.202227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.126660e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.230802e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.074784e+02\n Vprtstp: contraction number = 1.074784e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.111924e-05\n Vprtstp: contraction number = 2.466350e-01\n Vnewton: Using errtol_s: 96.730784\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.208644e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.387381e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.903808e+01\n Vprtstp: contraction number = 2.903808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.004146e-06\n Vprtstp: contraction number = 2.701755e-01\n Vnewton: Using errtol_s: 26.134288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.288403e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.534218e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.552738e+00\n Vprtstp: contraction number = 8.552738e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.848266e-07\n Vprtstp: contraction number = 2.945351e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.719621e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.976541e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.218754e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.246254e+01\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -26448,15 +26448,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 3.337014891966E-01 kT\n Vpmg_energy:  qfEnergy = 1.757508966493E+03 kT\n Vpmg_energy:  dielEnergy = 8.741342460079E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.060000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.555000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -26504,127 +26504,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0125584 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.007161\n+Vacc_SASA: Time elapsed: 3.040233\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.543326e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.793646e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.967600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.904200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.410740e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.072600e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.740366e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.057865e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3725039.964738\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.765642e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.077442e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.491722e+05\n Vprtstp: contraction number = 3.491722e+05\n Vnewton: Attempting damping, relres = 0.084831\n Vnewton: Attempting damping, relres = 0.540016\n Vnewton: Damping accepted, relres = 0.084831\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.483081e-02\n Vprtstp: contraction number = 8.483081e-02\n Vnewton: Using errtol_s: 315998.155182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.900642e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.216070e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.811279e+04\n Vprtstp: contraction number = 4.811279e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.162816e-02\n Vprtstp: contraction number = 1.370747e-01\n Vnewton: Using errtol_s: 43315.357930\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.007257e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.363183e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.589005e+03\n Vprtstp: contraction number = 7.589005e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.833655e-03\n Vprtstp: contraction number = 1.576909e-01\n Vnewton: Using errtol_s: 6830.439897\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.106592e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.490814e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.299757e+03\n Vprtstp: contraction number = 1.299757e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.140354e-04\n Vprtstp: contraction number = 1.712619e-01\n Vnewton: Using errtol_s: 1169.794412\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.209110e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.585498e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.408127e+02\n Vprtstp: contraction number = 2.408127e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.818247e-05\n Vprtstp: contraction number = 1.852736e-01\n Vnewton: Using errtol_s: 216.732029\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.316068e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.736945e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.749053e+01\n Vprtstp: contraction number = 4.749053e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.147411e-05\n Vprtstp: contraction number = 1.972090e-01\n Vnewton: Using errtol_s: 42.741516\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.423482e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.871473e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.028045e+01\n Vprtstp: contraction number = 1.028045e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.483842e-06\n Vprtstp: contraction number = 2.164736e-01\n Vnewton: Using errtol_s: 9.252409\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.530617e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.024486e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.462555e+00\n Vprtstp: contraction number = 2.462555e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.949733e-07\n Vprtstp: contraction number = 2.395375e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.882011e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.154198e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.045393e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.069941e+01\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -26633,27 +26633,27 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 3.088724409746E-01 kT\n Vpmg_energy:  qfEnergy = 1.340160252589E+04 kT\n Vpmg_energy:  dielEnergy = 6.690276790581E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.414000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.274400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.656923e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.133949e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:32:00 2025\n+# Creation Date and Time:  Sun Jan  7 09:43:14 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -27006,129 +27006,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.413154\n+Vacc_SASA: Time elapsed: 1.370177\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.791981e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.782348e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.977300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.006700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.346460e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.374890e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.219386e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.230685e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.481828e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.544020e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.776390e+05\n Vprtstp: contraction number = 1.776390e+05\n Vnewton: Attempting damping, relres = 0.041319\n Vnewton: Attempting damping, relres = 0.513474\n Vnewton: Damping accepted, relres = 0.041319\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.131938e-02\n Vprtstp: contraction number = 4.131938e-02\n Vnewton: Using errtol_s: 177710.973970\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.754116e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.456098e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677180e+04\n Vprtstp: contraction number = 2.677180e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.962101e-03\n Vprtstp: contraction number = 1.442931e-01\n Vnewton: Using errtol_s: 25642.465478\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.825660e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.773019e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.966549e+03\n Vprtstp: contraction number = 4.966549e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.056655e-03\n Vprtstp: contraction number = 1.772286e-01\n Vnewton: Using errtol_s: 4544.578762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.929468e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.515991e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011325e+03\n Vprtstp: contraction number = 1.011325e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.118038e-04\n Vprtstp: contraction number = 2.004475e-01\n Vnewton: Using errtol_s: 910.949292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.078790e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.794787e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.253595e+02\n Vprtstp: contraction number = 2.253595e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.715911e-05\n Vprtstp: contraction number = 2.226547e-01\n Vnewton: Using errtol_s: 202.827138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.206605e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.147870e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.445207e+01\n Vprtstp: contraction number = 5.445207e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.139456e-05\n Vprtstp: contraction number = 2.416194e-01\n Vnewton: Using errtol_s: 49.006980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.403105e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.460145e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420316e+01\n Vprtstp: contraction number = 1.420316e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.972126e-06\n Vprtstp: contraction number = 2.608373e-01\n Vnewton: Using errtol_s: 12.782849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.053022e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.034914e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.022184e+00\n Vprtstp: contraction number = 4.022184e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.416744e-07\n Vprtstp: contraction number = 2.831893e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.429522e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.695883e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.995146e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.279668e+00\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -27137,17 +27137,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.018818357311E-03 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 1.967662971668E+00 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.617000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.532600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 4.700000e-05\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -27193,127 +27193,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.000195471 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.359903\n+Vacc_SASA: Time elapsed: 1.363340\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.782124e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.804564e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.020900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.037500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.297630e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.503690e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.370918e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.335264e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1020818.402503\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.402227e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.370345e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.825199e+04\n Vprtstp: contraction number = 9.825199e+04\n Vnewton: Attempting damping, relres = 0.087060\n Vnewton: Attempting damping, relres = 0.541082\n Vnewton: Damping accepted, relres = 0.087060\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.706019e-02\n Vprtstp: contraction number = 8.706019e-02\n Vnewton: Using errtol_s: 88872.645048\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.533864e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.539317e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.300904e+04\n Vprtstp: contraction number = 1.300904e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.147153e-02\n Vprtstp: contraction number = 1.317655e-01\n Vnewton: Using errtol_s: 11710.349561\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.651563e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.680097e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.956340e+03\n Vprtstp: contraction number = 1.956340e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.724829e-03\n Vprtstp: contraction number = 1.503573e-01\n Vnewton: Using errtol_s: 1760.737119\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.764524e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.820746e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.204124e+02\n Vprtstp: contraction number = 3.204124e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.824911e-04\n Vprtstp: contraction number = 1.637792e-01\n Vnewton: Using errtol_s: 288.372159\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.871057e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.933346e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.671470e+01\n Vprtstp: contraction number = 5.671470e+01\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.000230e-05\n Vprtstp: contraction number = 1.770048e-01\n Vnewton: Using errtol_s: 51.043267\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.982765e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.053482e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.076760e+01\n Vprtstp: contraction number = 1.076760e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.493208e-06\n Vprtstp: contraction number = 1.898554e-01\n Vnewton: Using errtol_s: 9.690841\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.098187e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.171946e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.170593e+00\n Vprtstp: contraction number = 2.170593e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.913693e-06\n Vprtstp: contraction number = 2.015855e-01\n Vnewton: Using errtol_s: 1.953533\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.220626e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.313848e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.603679e-01\n Vprtstp: contraction number = 4.603679e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.058813e-07\n Vprtstp: contraction number = 2.120932e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.496271e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.757382e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.096711e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.125920e+01\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -27322,15 +27322,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.464558654899E-03 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 1.022303323465E+00 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.669500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.481900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -27353,129 +27353,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.396909\n+Vacc_SASA: Time elapsed: 1.407543\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.821330e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.809454e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.932800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.902300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.554100e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.415810e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.534518e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.644848e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.566990e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.664975e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.716926e+05\n Vprtstp: contraction number = 1.716926e+05\n Vnewton: Attempting damping, relres = 0.040940\n Vnewton: Attempting damping, relres = 0.513162\n Vnewton: Damping accepted, relres = 0.040940\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.093968e-02\n Vprtstp: contraction number = 4.093968e-02\n Vnewton: Using errtol_s: 175081.721880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.697117e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.812743e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.487025e+04\n Vprtstp: contraction number = 2.487025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.724811e-03\n Vprtstp: contraction number = 1.398353e-01\n Vnewton: Using errtol_s: 24482.603484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.806754e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.894793e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.528470e+03\n Vprtstp: contraction number = 4.528470e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.801406e-04\n Vprtstp: contraction number = 1.712092e-01\n Vnewton: Using errtol_s: 4191.647712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.917556e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.045021e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.122748e+02\n Vprtstp: contraction number = 9.122748e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923658e-04\n Vprtstp: contraction number = 1.962635e-01\n Vnewton: Using errtol_s: 822.667398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.027574e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.171147e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052635e+02\n Vprtstp: contraction number = 2.052635e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.319998e-05\n Vprtstp: contraction number = 2.245720e-01\n Vnewton: Using errtol_s: 184.748098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.143200e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.285323e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.154123e+01\n Vprtstp: contraction number = 5.154123e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.084685e-05\n Vprtstp: contraction number = 2.510845e-01\n Vnewton: Using errtol_s: 46.387392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.248760e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.397536e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.435770e+01\n Vprtstp: contraction number = 1.435770e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.021563e-06\n Vprtstp: contraction number = 2.785660e-01\n Vnewton: Using errtol_s: 12.921949\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.361564e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.533236e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.361187e+00\n Vprtstp: contraction number = 4.361187e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.178062e-07\n Vprtstp: contraction number = 3.037522e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.195186e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.477710e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.831053e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.010507e+01\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -27484,17 +27484,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.242044176092E+00 kT\n Vpmg_energy:  qfEnergy = 9.791375610764E+03 kT\n Vpmg_energy:  dielEnergy = 4.948343269624E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.322000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.611900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -27540,127 +27540,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0380116 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.393363\n+Vacc_SASA: Time elapsed: 1.406219\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.082271e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.164142e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.984700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.998600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.452720e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.213430e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.691484e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.873385e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 6064250.335946\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.722068e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.897527e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.053112e+05\n Vprtstp: contraction number = 5.053112e+05\n Vnewton: Attempting damping, relres = 0.075900\n Vnewton: Attempting damping, relres = 0.535745\n Vnewton: Damping accepted, relres = 0.075900\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.590004e-02\n Vprtstp: contraction number = 7.590004e-02\n Vnewton: Using errtol_s: 460276.842537\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.864234e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.005940e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.689298e+04\n Vprtstp: contraction number = 6.689298e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.982301e-03\n Vprtstp: contraction number = 1.315191e-01\n Vnewton: Using errtol_s: 60535.174769\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.988067e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.163473e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.083906e+04\n Vprtstp: contraction number = 1.083906e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.608994e-03\n Vprtstp: contraction number = 1.611846e-01\n Vnewton: Using errtol_s: 9757.339468\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.116911e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.329564e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.965105e+03\n Vprtstp: contraction number = 1.965105e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.916449e-04\n Vprtstp: contraction number = 1.812592e-01\n Vnewton: Using errtol_s: 1768.607683\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.239805e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.437953e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.700829e+02\n Vprtstp: contraction number = 3.700829e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.492457e-05\n Vprtstp: contraction number = 1.883269e-01\n Vnewton: Using errtol_s: 333.076316\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.357115e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.562431e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.574998e+01\n Vprtstp: contraction number = 6.574998e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.758048e-06\n Vprtstp: contraction number = 1.776627e-01\n Vnewton: Using errtol_s: 59.175244\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.475359e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.719275e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.293454e+01\n Vprtstp: contraction number = 1.293454e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.919626e-06\n Vprtstp: contraction number = 1.967224e-01\n Vnewton: Using errtol_s: 11.641095\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.594199e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.863721e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.078562e+00\n Vprtstp: contraction number = 3.078562e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.568945e-07\n Vprtstp: contraction number = 2.380122e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.004351e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.032092e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.123425e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.149385e+01\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -27669,15 +27669,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.156457994238E+00 kT\n Vpmg_energy:  qfEnergy = 7.809362574174E+04 kT\n Vpmg_energy:  dielEnergy = 3.917972751481E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.388300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.442400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -27700,129 +27700,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.061464\n+Vacc_SASA: Time elapsed: 3.020804\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.628914e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.608174e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.055500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.948800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.648940e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.400130e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.091171e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.386049e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.123255e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.417167e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528464e+05\n Vprtstp: contraction number = 3.528464e+05\n Vnewton: Attempting damping, relres = 0.041605\n Vnewton: Attempting damping, relres = 0.513349\n Vnewton: Damping accepted, relres = 0.041605\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160535e-02\n Vprtstp: contraction number = 4.160535e-02\n Vnewton: Using errtol_s: 361941.817774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.265112e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.563278e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.210930e+04\n Vprtstp: contraction number = 5.210930e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.921711e-03\n Vprtstp: contraction number = 1.423305e-01\n Vnewton: Using errtol_s: 51515.371182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.393452e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.695737e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.570568e+03\n Vprtstp: contraction number = 9.570568e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.018950e-03\n Vprtstp: contraction number = 1.720701e-01\n Vnewton: Using errtol_s: 8864.257334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.518811e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.826184e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.944504e+03\n Vprtstp: contraction number = 1.944504e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.015521e-04\n Vprtstp: contraction number = 1.978037e-01\n Vnewton: Using errtol_s: 1753.383252\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.634137e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.965390e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.357668e+02\n Vprtstp: contraction number = 4.357668e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.508379e-05\n Vprtstp: contraction number = 2.236831e-01\n Vnewton: Using errtol_s: 392.202227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.755954e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.071600e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.074784e+02\n Vprtstp: contraction number = 1.074784e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.111924e-05\n Vprtstp: contraction number = 2.466350e-01\n Vnewton: Using errtol_s: 96.730784\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.871694e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.152775e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.903808e+01\n Vprtstp: contraction number = 2.903808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.004146e-06\n Vprtstp: contraction number = 2.701755e-01\n Vnewton: Using errtol_s: 26.134288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.983084e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.293196e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.552738e+00\n Vprtstp: contraction number = 8.552738e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.848266e-07\n Vprtstp: contraction number = 2.945351e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.919598e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.021051e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.041780e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.068327e+01\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -27831,17 +27831,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.221311774650E+00 kT\n Vpmg_energy:  qfEnergy = 9.790964149822E+03 kT\n Vpmg_energy:  dielEnergy = 4.950799444075E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.675000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.672900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -27887,127 +27887,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0371815 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.014448\n+Vacc_SASA: Time elapsed: 3.036001\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.797234e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.965942e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.898000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.002500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.307140e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.625570e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.490428e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.857181e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 6913573.322497\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.519296e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.893291e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.778762e+05\n Vprtstp: contraction number = 5.778762e+05\n Vnewton: Attempting damping, relres = 0.075994\n Vnewton: Attempting damping, relres = 0.535763\n Vnewton: Damping accepted, relres = 0.075994\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.599436e-02\n Vprtstp: contraction number = 7.599436e-02\n Vnewton: Using errtol_s: 525392.598640\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.662800e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.064092e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.670486e+04\n Vprtstp: contraction number = 7.670486e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.002063e-02\n Vprtstp: contraction number = 1.318602e-01\n Vnewton: Using errtol_s: 69278.365005\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.783297e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.172708e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.241801e+04\n Vprtstp: contraction number = 1.241801e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.616751e-03\n Vprtstp: contraction number = 1.613422e-01\n Vnewton: Using errtol_s: 11177.524829\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.897421e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.317582e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.271971e+03\n Vprtstp: contraction number = 2.271971e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.957685e-04\n Vprtstp: contraction number = 1.829401e-01\n Vnewton: Using errtol_s: 2044.817292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.017455e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.430268e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.414335e+02\n Vprtstp: contraction number = 4.414335e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.746599e-05\n Vprtstp: contraction number = 1.942938e-01\n Vnewton: Using errtol_s: 397.295336\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.141602e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.537003e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.690501e+01\n Vprtstp: contraction number = 8.690501e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.131327e-05\n Vprtstp: contraction number = 1.968689e-01\n Vnewton: Using errtol_s: 78.215105\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.250274e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.663725e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.879618e+01\n Vprtstp: contraction number = 1.879618e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.446866e-06\n Vprtstp: contraction number = 2.162828e-01\n Vnewton: Using errtol_s: 16.916585\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.368994e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.802441e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.583329e+00\n Vprtstp: contraction number = 4.583329e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.966529e-07\n Vprtstp: contraction number = 2.438437e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.858591e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.011756e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.075238e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.104913e+01\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -28016,27 +28016,27 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.139698158758E+00 kT\n Vpmg_energy:  qfEnergy = 7.809316280828E+04 kT\n Vpmg_energy:  dielEnergy = 3.918099666156E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.164200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.538800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.504623e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.960103e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:32:30 2025\n+# Creation Date and Time:  Sun Jan  7 09:43:40 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -28389,129 +28389,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.415303\n+Vacc_SASA: Time elapsed: 1.384410\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.808592e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.779185e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.969800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.073900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.339870e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.484060e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.180512e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.231624e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.454684e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.548697e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.776390e+05\n Vprtstp: contraction number = 1.776390e+05\n Vnewton: Attempting damping, relres = 0.041319\n Vnewton: Attempting damping, relres = 0.513474\n Vnewton: Damping accepted, relres = 0.041319\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.131938e-02\n Vprtstp: contraction number = 4.131938e-02\n Vnewton: Using errtol_s: 177710.973970\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.753397e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.044809e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677180e+04\n Vprtstp: contraction number = 2.677180e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.962101e-03\n Vprtstp: contraction number = 1.442931e-01\n Vnewton: Using errtol_s: 25642.465478\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.800568e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.389692e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.966549e+03\n Vprtstp: contraction number = 4.966549e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.056655e-03\n Vprtstp: contraction number = 1.772286e-01\n Vnewton: Using errtol_s: 4544.578762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.879611e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.841118e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011325e+03\n Vprtstp: contraction number = 1.011325e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.118038e-04\n Vprtstp: contraction number = 2.004475e-01\n Vnewton: Using errtol_s: 910.949292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.948300e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.235927e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.253595e+02\n Vprtstp: contraction number = 2.253595e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.715911e-05\n Vprtstp: contraction number = 2.226547e-01\n Vnewton: Using errtol_s: 202.827138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.982265e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.595656e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.445207e+01\n Vprtstp: contraction number = 5.445207e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.139456e-05\n Vprtstp: contraction number = 2.416194e-01\n Vnewton: Using errtol_s: 49.006980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.085870e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.070914e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420316e+01\n Vprtstp: contraction number = 1.420316e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.972126e-06\n Vprtstp: contraction number = 2.608373e-01\n Vnewton: Using errtol_s: 12.782849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.023179e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.200728e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.022184e+00\n Vprtstp: contraction number = 4.022184e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.416744e-07\n Vprtstp: contraction number = 2.831893e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.991647e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.256944e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.060565e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.088847e+01\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -28520,15 +28520,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.085287424313E-01 kT\n Vpmg_energy:  qfEnergy = 2.020959449622E+03 kT\n Vpmg_energy:  dielEnergy = 1.003436009271E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.302100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.462700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -28576,127 +28576,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0111702 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.360901\n+Vacc_SASA: Time elapsed: 1.375770\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.937705e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.995690e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.980500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.068000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.231470e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.316080e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.339135e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.513040e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2843800.208997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.368112e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.546027e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.648041e+05\n Vprtstp: contraction number = 2.648041e+05\n Vnewton: Attempting damping, relres = 0.084229\n Vnewton: Attempting damping, relres = 0.539926\n Vnewton: Damping accepted, relres = 0.084229\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.422893e-02\n Vprtstp: contraction number = 8.422893e-02\n Vnewton: Using errtol_s: 239530.237257\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.511728e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.715474e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.601789e+04\n Vprtstp: contraction number = 3.601789e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.140061e-02\n Vprtstp: contraction number = 1.353527e-01\n Vnewton: Using errtol_s: 32421.054732\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.627885e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.851571e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.547762e+03\n Vprtstp: contraction number = 5.547762e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.755765e-03\n Vprtstp: contraction number = 1.540062e-01\n Vnewton: Using errtol_s: 4993.043762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.743324e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.973184e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.234937e+02\n Vprtstp: contraction number = 9.234937e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.922661e-04\n Vprtstp: contraction number = 1.664609e-01\n Vnewton: Using errtol_s: 831.146494\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.875004e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.085219e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.647026e+02\n Vprtstp: contraction number = 1.647026e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.212477e-05\n Vprtstp: contraction number = 1.783469e-01\n Vnewton: Using errtol_s: 148.232430\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.998813e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.214196e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.095227e+01\n Vprtstp: contraction number = 3.095227e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.795714e-06\n Vprtstp: contraction number = 1.879282e-01\n Vnewton: Using errtol_s: 27.857053\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.113544e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.324301e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.500935e+00\n Vprtstp: contraction number = 6.500935e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.057403e-06\n Vprtstp: contraction number = 2.100309e-01\n Vnewton: Using errtol_s: 5.850843\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.233842e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.433270e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.529139e+00\n Vprtstp: contraction number = 1.529139e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.839389e-07\n Vprtstp: contraction number = 2.352183e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.005342e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.031054e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.009088e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.036030e+01\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -28705,15 +28705,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.004865379330E-01 kT\n Vpmg_energy:  qfEnergy = 1.781523307319E+04 kT\n Vpmg_energy:  dielEnergy = 8.939732950056E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.088400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.724500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -28736,129 +28736,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.395513\n+Vacc_SASA: Time elapsed: 1.405792\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.806119e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.787877e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.945000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.930400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.200460e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.361440e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.554365e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.729945e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.584592e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.758455e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.716926e+05\n Vprtstp: contraction number = 1.716926e+05\n Vnewton: Attempting damping, relres = 0.040940\n Vnewton: Attempting damping, relres = 0.513162\n Vnewton: Damping accepted, relres = 0.040940\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.093968e-02\n Vprtstp: contraction number = 4.093968e-02\n Vnewton: Using errtol_s: 175081.721880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.715562e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.869415e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.487025e+04\n Vprtstp: contraction number = 2.487025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.724811e-03\n Vprtstp: contraction number = 1.398353e-01\n Vnewton: Using errtol_s: 24482.603484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.825526e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.973410e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.528470e+03\n Vprtstp: contraction number = 4.528470e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.801406e-04\n Vprtstp: contraction number = 1.712092e-01\n Vnewton: Using errtol_s: 4191.647712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.932628e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.108696e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.122748e+02\n Vprtstp: contraction number = 9.122748e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923658e-04\n Vprtstp: contraction number = 1.962635e-01\n Vnewton: Using errtol_s: 822.667398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.048021e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.221263e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052635e+02\n Vprtstp: contraction number = 2.052635e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.319998e-05\n Vprtstp: contraction number = 2.245720e-01\n Vnewton: Using errtol_s: 184.748098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.155554e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.322192e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.154123e+01\n Vprtstp: contraction number = 5.154123e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.084685e-05\n Vprtstp: contraction number = 2.510845e-01\n Vnewton: Using errtol_s: 46.387392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.267473e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.427928e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.435770e+01\n Vprtstp: contraction number = 1.435770e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.021563e-06\n Vprtstp: contraction number = 2.785660e-01\n Vnewton: Using errtol_s: 12.921949\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.377824e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.538834e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.361187e+00\n Vprtstp: contraction number = 4.361187e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.178062e-07\n Vprtstp: contraction number = 3.037522e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.169996e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.421179e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.239621e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.508058e+00\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -28867,17 +28867,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.162784451104E-01 kT\n Vpmg_energy:  qfEnergy = 3.383505562700E+02 kT\n Vpmg_energy:  dielEnergy = 1.754184182339E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.773000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.641800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -28923,138 +28923,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00475113 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.373891\n+Vacc_SASA: Time elapsed: 1.389060\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.847956e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.880505e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.998500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.891600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.438430e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.401680e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.685209e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.872263e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1712482.416854\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.713956e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.904504e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.778057e+05\n Vprtstp: contraction number = 1.778057e+05\n Vnewton: Attempting damping, relres = 0.095206\n Vnewton: Attempting damping, relres = 0.544528\n Vnewton: Damping accepted, relres = 0.095206\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.520604e-02\n Vprtstp: contraction number = 9.520604e-02\n Vnewton: Using errtol_s: 163038.671160\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.836946e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.042258e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.588526e+04\n Vprtstp: contraction number = 2.588526e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.365073e-02\n Vprtstp: contraction number = 1.433809e-01\n Vnewton: Using errtol_s: 23376.634124\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.940656e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.144597e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.392675e+03\n Vprtstp: contraction number = 4.392675e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.309227e-03\n Vprtstp: contraction number = 1.691651e-01\n Vnewton: Using errtol_s: 3954.509988\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.049277e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.255833e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.232796e+02\n Vprtstp: contraction number = 8.232796e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 4.326939e-04\n Vprtstp: contraction number = 1.873761e-01\n Vnewton: Using errtol_s: 740.980697\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.154755e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.399300e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.669237e+02\n Vprtstp: contraction number = 1.669237e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 8.772776e-05\n Vprtstp: contraction number = 2.027479e-01\n Vnewton: Using errtol_s: 150.232247\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.263803e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.538675e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.642088e+01\n Vprtstp: contraction number = 3.642088e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.914112e-05\n Vprtstp: contraction number = 2.181877e-01\n Vnewton: Using errtol_s: 32.778836\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.382449e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.682564e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.545476e+00\n Vprtstp: contraction number = 8.545476e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.491102e-06\n Vprtstp: contraction number = 2.346311e-01\n Vnewton: Using errtol_s: 7.690933\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.490674e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.817694e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.153814e+00\n Vprtstp: contraction number = 2.153814e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.131943e-06\n Vprtstp: contraction number = 2.520414e-01\n Vnewton: Using errtol_s: 1.938433\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.595235e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.915684e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.814982e-01\n Vprtstp: contraction number = 5.814982e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.056081e-07\n Vprtstp: contraction number = 2.699853e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.001201e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.028849e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.130797e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.158059e+01\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -29063,15 +29063,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.651168945816E-01 kT\n Vpmg_energy:  qfEnergy = 3.320671858523E+03 kT\n Vpmg_energy:  dielEnergy = 1.644537494834E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.919300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.371700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -29094,129 +29094,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.006082\n+Vacc_SASA: Time elapsed: 3.260458\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.583306e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.853522e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.939900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.909600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.326620e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.411380e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.073064e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.419350e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.102185e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.452381e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528464e+05\n Vprtstp: contraction number = 3.528464e+05\n Vnewton: Attempting damping, relres = 0.041605\n Vnewton: Attempting damping, relres = 0.513349\n Vnewton: Damping accepted, relres = 0.041605\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160535e-02\n Vprtstp: contraction number = 4.160535e-02\n Vnewton: Using errtol_s: 361941.817774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.247802e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.617866e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.210930e+04\n Vprtstp: contraction number = 5.210930e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.921711e-03\n Vprtstp: contraction number = 1.423305e-01\n Vnewton: Using errtol_s: 51515.371182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.350299e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.746427e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.570568e+03\n Vprtstp: contraction number = 9.570568e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.018950e-03\n Vprtstp: contraction number = 1.720701e-01\n Vnewton: Using errtol_s: 8864.257334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.455478e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.876544e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.944504e+03\n Vprtstp: contraction number = 1.944504e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.015521e-04\n Vprtstp: contraction number = 1.978037e-01\n Vnewton: Using errtol_s: 1753.383252\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.572248e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.024470e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.357668e+02\n Vprtstp: contraction number = 4.357668e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.508379e-05\n Vprtstp: contraction number = 2.236831e-01\n Vnewton: Using errtol_s: 392.202227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.686939e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.151950e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.074784e+02\n Vprtstp: contraction number = 1.074784e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.111924e-05\n Vprtstp: contraction number = 2.466350e-01\n Vnewton: Using errtol_s: 96.730784\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.793993e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.308026e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.903808e+01\n Vprtstp: contraction number = 2.903808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.004146e-06\n Vprtstp: contraction number = 2.701755e-01\n Vnewton: Using errtol_s: 26.134288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.895333e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.413179e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.552738e+00\n Vprtstp: contraction number = 8.552738e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.848266e-07\n Vprtstp: contraction number = 2.945351e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.157846e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.416148e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.109847e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.136375e+01\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -29225,15 +29225,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.317973104173E-01 kT\n Vpmg_energy:  qfEnergy = 2.391935061774E+03 kT\n Vpmg_energy:  dielEnergy = 1.197593144317E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.708000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.647100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -29281,127 +29281,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0257349 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.002159\n+Vacc_SASA: Time elapsed: 3.017952\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.711607e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.805141e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.887500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.969200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.282540e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.580860e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.387763e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.942133e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4500132.646352\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.415980e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.976103e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.278020e+05\n Vprtstp: contraction number = 4.278020e+05\n Vnewton: Attempting damping, relres = 0.086415\n Vnewton: Attempting damping, relres = 0.540695\n Vnewton: Damping accepted, relres = 0.086415\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.641451e-02\n Vprtstp: contraction number = 8.641451e-02\n Vnewton: Using errtol_s: 388876.774521\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.557227e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.162490e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.967321e+04\n Vprtstp: contraction number = 5.967321e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.194851e-02\n Vprtstp: contraction number = 1.382697e-01\n Vnewton: Using errtol_s: 53769.886692\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.676697e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.280833e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.609884e+03\n Vprtstp: contraction number = 9.609884e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.922151e-03\n Vprtstp: contraction number = 1.608695e-01\n Vnewton: Using errtol_s: 8649.935921\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.797006e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.413978e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.688280e+03\n Vprtstp: contraction number = 1.688280e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.376534e-04\n Vprtstp: contraction number = 1.756643e-01\n Vnewton: Using errtol_s: 1519.485051\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.915965e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.556559e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.185424e+02\n Vprtstp: contraction number = 3.185424e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.370679e-05\n Vprtstp: contraction number = 1.886751e-01\n Vnewton: Using errtol_s: 286.689023\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.037585e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.679485e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.336866e+01\n Vprtstp: contraction number = 6.336866e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.267337e-05\n Vprtstp: contraction number = 1.989328e-01\n Vnewton: Using errtol_s: 57.031849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.156165e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.846616e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.358194e+01\n Vprtstp: contraction number = 1.358194e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.716310e-06\n Vprtstp: contraction number = 2.143321e-01\n Vnewton: Using errtol_s: 12.223755\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.276575e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.005485e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.189745e+00\n Vprtstp: contraction number = 3.189745e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.379304e-07\n Vprtstp: contraction number = 2.348518e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.928280e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.018881e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.200610e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.229925e+01\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -29410,17 +29410,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 3.132873625516E-01 kT\n Vpmg_energy:  qfEnergy = 2.116420853422E+04 kT\n Vpmg_energy:  dielEnergy = 1.060038494093E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.618900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.721300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.410955e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.170250e+01\n"}, {"source1": "./usr/share/apbs/examples/alkanes/io.mc", "source2": "./usr/share/apbs/examples/alkanes/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:33:00 2025\n+# Creation Date and Time:  Sun Jan  7 09:44:06 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path 2-methylbutane.pdb\n@@ -302,130 +302,130 @@\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (13.5347, 12.2207, 11.3787)\n Vclist_setupGrid:  Grid lower corner = (-6.76736, -6.11036, -5.68936)\n Vclist_assignAtoms:  Have 6745 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.016922\n-initAPOL: Time elapsed: 1.016499\n+Vacc_SASA: Time elapsed: 0.005896\n+initAPOL: Time elapsed: 0.978346\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 15 x 12 x 11 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (13.0267, 11.7717, 11.1107)\n Vclist_setupGrid:  Grid lower corner = (-2.59636, -5.18336, -14.1304)\n Vclist_assignAtoms:  Have 4888 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.004682\n-initAPOL: Time elapsed: 0.799632\n+Vacc_SASA: Time elapsed: 0.004672\n+initAPOL: Time elapsed: 0.801066\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 14 x 12 x 15 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (12.7417, 11.4947, 13.2787)\n Vclist_setupGrid:  Grid lower corner = (-5.24736, -5.15936, -5.87136)\n Vclist_assignAtoms:  Have 6902 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.006510\n-initAPOL: Time elapsed: 1.034510\n+Vacc_SASA: Time elapsed: 0.006534\n+initAPOL: Time elapsed: 1.035984\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 14 x 12 x 13 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (12.4767, 11.4917, 12.3367)\n Vclist_setupGrid:  Grid lower corner = (-4.91836, -5.22036, -4.87936)\n Vclist_assignAtoms:  Have 4977 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.004397\n-initAPOL: Time elapsed: 0.739979\n+Vacc_SASA: Time elapsed: 0.004409\n+initAPOL: Time elapsed: 0.742019\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 9 x 9 x 10 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (10.0327, 10.2387, 10.6647)\n Vclist_setupGrid:  Grid lower corner = (-4.79536, -5.14036, -4.56736)\n Vclist_assignAtoms:  Have 1946 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.002494\n-initAPOL: Time elapsed: 0.456544\n+Vacc_SASA: Time elapsed: 0.002493\n+initAPOL: Time elapsed: 0.457193\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 19 x 15 x 12 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (15.0957, 13.1957, 11.4487)\n Vclist_setupGrid:  Grid lower corner = (-2.59636, -6.60736, -14.1304)\n Vclist_assignAtoms:  Have 9434 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.007378\n-initAPOL: Time elapsed: 1.157490\n+Vacc_SASA: Time elapsed: 0.007407\n+initAPOL: Time elapsed: 1.160090\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 13 x 12 x 14 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (12.0577, 11.5517, 12.5037)\n Vclist_setupGrid:  Grid lower corner = (12.5656, 12.8626, 12.9606)\n Vclist_assignAtoms:  Have 5377 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.004795\n-initAPOL: Time elapsed: 0.834540\n+Vacc_SASA: Time elapsed: 0.004793\n+initAPOL: Time elapsed: 0.835581\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 9 x 9 x 8 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (10.1767, 10.1117, 9.66772)\n Vclist_setupGrid:  Grid lower corner = (12.9396, 12.7376, 12.9816)\n Vclist_assignAtoms:  Have 1014 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.001436\n-initAPOL: Time elapsed: 0.294218\n+Vacc_SASA: Time elapsed: 0.001439\n+initAPOL: Time elapsed: 0.294595\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 13 x 13 x 14 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (12.2347, 12.1667, 12.6837)\n Vclist_setupGrid:  Grid lower corner = (12.5496, 12.8526, 12.8586)\n Vclist_assignAtoms:  Have 6725 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.006289\n-initAPOL: Time elapsed: 1.019203\n+Vacc_SASA: Time elapsed: 0.006297\n+initAPOL: Time elapsed: 1.021061\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 17 x 14 x 11 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (14.1127, 12.8537, 11.1297)\n Vclist_setupGrid:  Grid lower corner = (-2.59636, -6.26536, -14.1304)\n Vclist_assignAtoms:  Have 6650 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.005650\n-initAPOL: Time elapsed: 0.977980\n+Vacc_SASA: Time elapsed: 0.005658\n+initAPOL: Time elapsed: 0.979259\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 10 x 14 x 12 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (10.9097, 12.4407, 11.4747)\n Vclist_setupGrid:  Grid lower corner = (12.9086, 12.7426, 12.8736)\n Vclist_assignAtoms:  Have 3766 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.003739\n-initAPOL: Time elapsed: 0.655390\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.995033e+00\n+Vacc_SASA: Time elapsed: 0.003722\n+initAPOL: Time elapsed: 0.656736\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.965709e+00\n"}, {"source1": "./usr/share/apbs/examples/born/io.mc", "source2": "./usr/share/apbs/examples/born/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:17:27 2025\n+# Creation Date and Time:  Sun Jan  7 09:31:19 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -194,32 +194,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000468\n+Vacc_SASA: Time elapsed: 0.000328\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.534900e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.346900e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.407400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.402000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.327690e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.074000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.921510e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.440610e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.252488e-01\n Vprtstp: contraction number = 1.252488e-01\n Vprtstp: iteration = 2\n@@ -242,31 +242,31 @@\n Vprtstp: contraction number = 2.345457e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.154547e-06\n Vprtstp: contraction number = 2.398447e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.798201e-07\n Vprtstp: contraction number = 2.423636e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.268851e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.494001e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.399054e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.514043e+00\n Vpmg_setPart:  lower corner = (-25, -25, -25)\n Vpmg_setPart:  upper corner = (25, 25, 25)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.750853990251E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.650000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.350000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -315,30 +315,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.111569 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000126\n+Vacc_SASA: Time elapsed: 0.001118\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.450500e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.587800e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.688000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.969000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.223540e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.196210e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.800452e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.779834e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.284366e-01\n Vprtstp: contraction number = 1.284366e-01\n Vprtstp: iteration = 2\n@@ -370,33 +370,33 @@\n Vprtstp: contraction number = 3.689006e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.340984e-06\n Vprtstp: contraction number = 3.689051e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 4.946966e-07\n Vprtstp: contraction number = 3.689058e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.040916e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.231496e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.944002e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.142608e+00\n Vpmg_setPart:  lower corner = (-12.2474, -12.2474, -12.2474)\n Vpmg_setPart:  upper corner = (12.2474, 12.2474, 12.2474)\n Vpmg_setPart:  actual minima = (-12.2474, -12.2474, -12.2474)\n Vpmg_setPart:  actual maxima = (12.2474, 12.2474, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.775144565213E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.270000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.220000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -443,30 +443,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.339539 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001206\n+Vacc_SASA: Time elapsed: 0.000107\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.123600e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.059220e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.771000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.038000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.231080e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.241380e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.148072e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.037960e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.377836e-01\n Vprtstp: contraction number = 1.377836e-01\n Vprtstp: iteration = 2\n@@ -501,33 +501,33 @@\n Vprtstp: contraction number = 3.896678e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.022958e-06\n Vprtstp: contraction number = 3.896627e-01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 3.986147e-07\n Vprtstp: contraction number = 3.896686e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.630477e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.821165e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.815419e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.021007e+00\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-6, -6, -6)\n Vpmg_setPart:  actual maxima = (6, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 3.817909770059E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.640000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.920000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n WARNING\n Vgrid_readGZ:  gzip read/write support is disabled in this build\n Vgrid_readGZ:  configure and compile without the --disable-zlib flag.\n WARNING\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n@@ -552,28 +552,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.009400e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.350500e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.110300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.098000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.376930e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.956300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.002454e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.973436e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -590,33 +590,33 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.908113e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.127116e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.871508e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.971049e+00\n Vpmg_setPart:  lower corner = (-25, -25, -25)\n Vpmg_setPart:  upper corner = (25, 25, 25)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 9.607786035504E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.270000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.850000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 5.600000e-05\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -661,28 +661,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 8.7631 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.923700e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.227200e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.106000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.254000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.333590e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.619100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.216384e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.198573e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114981e-01\n Vprtstp: contraction number = 1.114981e-01\n Vprtstp: iteration = 2\n@@ -699,31 +699,31 @@\n Vprtstp: contraction number = 1.068029e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473476e-06\n Vprtstp: contraction number = 1.075295e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.593050e-07\n Vprtstp: contraction number = 1.081151e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.839755e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.046133e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.967492e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.077636e+00\n Vpmg_setPart:  lower corner = (-12.2474, -12.2474, -12.2474)\n Vpmg_setPart:  upper corner = (12.2474, 12.2474, 12.2474)\n Vpmg_setPart:  actual minima = (-12.2474, -12.2474, -12.2474)\n Vpmg_setPart:  actual maxima = (12.2474, 12.2474, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.961195484637E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.260000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.980000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -770,28 +770,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 26.656 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.307000e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.756100e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.981000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.449000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.136660e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.077120e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.418612e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.413311e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114975e-01\n Vprtstp: contraction number = 1.114975e-01\n Vprtstp: iteration = 2\n@@ -808,39 +808,39 @@\n Vprtstp: contraction number = 1.068029e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473471e-06\n Vprtstp: contraction number = 1.075296e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.593045e-07\n Vprtstp: contraction number = 1.081151e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.941338e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.105877e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.881629e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.041695e+00\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-6, -6, -6)\n Vpmg_setPart:  actual maxima = (6, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 4.003287887017E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.000000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.900000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.613011e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.602024e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:17:31 2025\n+# Creation Date and Time:  Sun Jan  7 09:31:23 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -1028,32 +1028,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000124\n+Vacc_SASA: Time elapsed: 0.000259\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.767500e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.116310e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.868000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.376300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.204670e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.540220e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.614110e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.798290e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.315574e-01\n Vprtstp: contraction number = 1.315574e-01\n Vprtstp: iteration = 2\n@@ -1073,33 +1073,33 @@\n Vprtstp: contraction number = 2.039480e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.384411e-06\n Vprtstp: contraction number = 2.095783e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.318373e-07\n Vprtstp: contraction number = 2.125342e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.158751e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.346373e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.648099e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.904539e+00\n Vpmg_setPart:  lower corner = (-25, -25, -25)\n Vpmg_setPart:  upper corner = (25, 25, 25)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.691034776619E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.420000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.230000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1146,30 +1146,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.111618 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000368\n+Vacc_SASA: Time elapsed: 0.001627\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.729200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.825000e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.203000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.094000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.267210e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.681900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.698427e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.243342e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.204709e-01\n Vprtstp: contraction number = 1.204709e-01\n Vprtstp: iteration = 2\n@@ -1186,16 +1186,16 @@\n Vprtstp: contraction number = 1.476379e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 5.011380e-06\n Vprtstp: contraction number = 1.603001e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.492596e-07\n Vprtstp: contraction number = 1.694662e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.719089e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.914786e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.143362e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.278682e+00\n Vpmg_setPart:  lower corner = (-12.2474, -12.2474, -12.2474)\n Vpmg_setPart:  upper corner = (12.2474, 12.2474, 12.2474)\n Vpmg_setPart:  actual minima = (-12.2474, -12.2474, -12.2474)\n Vpmg_setPart:  actual maxima = (12.2474, 12.2474, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1204,15 +1204,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.775933047078E+03 kT\n Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.360000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1259,30 +1259,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.339781 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000095\n+Vacc_SASA: Time elapsed: 0.000093\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.147100e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.041570e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.243000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.932000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.187760e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.414200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.720606e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.600278e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.298995e-01\n Vprtstp: contraction number = 1.298995e-01\n Vprtstp: iteration = 2\n@@ -1302,31 +1302,31 @@\n Vprtstp: contraction number = 1.916174e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.164097e-06\n Vprtstp: contraction number = 1.993376e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.370219e-07\n Vprtstp: contraction number = 2.019420e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.033631e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.217902e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.224558e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.332610e+00\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-6, -6, -6)\n Vpmg_setPart:  actual maxima = (6, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 3.818523837085E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.400000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.000000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -1349,28 +1349,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.198200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.429800e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.220000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.875000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.234480e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.284000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.969381e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.945016e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -1387,31 +1387,31 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.739099e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.928235e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.143727e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.248073e+00\n Vpmg_setPart:  lower corner = (-25, -25, -25)\n Vpmg_setPart:  upper corner = (25, 25, 25)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 9.607786035504E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.440000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.170000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -1458,28 +1458,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 8.7631 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.748100e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.386700e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.808000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.267000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.065050e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.835500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.891860e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.220748e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114981e-01\n Vprtstp: contraction number = 1.114981e-01\n Vprtstp: iteration = 2\n@@ -1496,33 +1496,33 @@\n Vprtstp: contraction number = 1.068029e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473476e-06\n Vprtstp: contraction number = 1.075295e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.593050e-07\n Vprtstp: contraction number = 1.081151e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.507800e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.670448e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.174684e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.291040e+00\n Vpmg_setPart:  lower corner = (-12.2474, -12.2474, -12.2474)\n Vpmg_setPart:  upper corner = (12.2474, 12.2474, 12.2474)\n Vpmg_setPart:  actual minima = (-12.2474, -12.2474, -12.2474)\n Vpmg_setPart:  actual maxima = (12.2474, 12.2474, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.961195484637E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.850000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.690000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1567,28 +1567,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 26.656 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.064400e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.482000e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.870000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.300000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.332610e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.081500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.062743e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.523815e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114975e-01\n Vprtstp: contraction number = 1.114975e-01\n Vprtstp: iteration = 2\n@@ -1605,39 +1605,39 @@\n Vprtstp: contraction number = 1.068029e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473471e-06\n Vprtstp: contraction number = 1.075296e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.593045e-07\n Vprtstp: contraction number = 1.081151e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.810995e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.015665e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.145937e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.258018e+00\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-6, -6, -6)\n Vpmg_setPart:  actual maxima = (6, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 4.003287887017E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.460000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.180000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.244331e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.665606e+00\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:17:35 2025\n+# Creation Date and Time:  Sun Jan  7 09:31:32 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -1885,32 +1885,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000120\n+Vacc_SASA: Time elapsed: 0.000131\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.690500e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.202300e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.684000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.761000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.291360e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.340700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.414760e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.342240e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.252488e-01\n Vprtstp: contraction number = 1.252488e-01\n Vprtstp: iteration = 2\n@@ -1933,33 +1933,33 @@\n Vprtstp: contraction number = 2.345457e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.154547e-06\n Vprtstp: contraction number = 2.398447e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.798201e-07\n Vprtstp: contraction number = 2.423636e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.323888e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.522460e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.391488e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.497646e+00\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.937713497535E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.500000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.920000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -2006,30 +2006,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0318856 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000782\n+Vacc_SASA: Time elapsed: 0.000090\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.452400e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.444200e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.013000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.005000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.397750e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.663800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.851408e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.680658e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.311479e-01\n Vprtstp: contraction number = 1.311479e-01\n Vprtstp: iteration = 2\n@@ -2061,33 +2061,33 @@\n Vprtstp: contraction number = 3.924056e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.308381e-06\n Vprtstp: contraction number = 3.934819e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 9.098344e-07\n Vprtstp: contraction number = 3.941440e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.980941e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.206757e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.889888e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.008151e+00\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-11.8833, -11.8833, -12.2474)\n Vpmg_setPart:  actual maxima = (7.06083, 7.06083, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.569607552225E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.150000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.490000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -2134,30 +2134,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0917244 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000148\n+Vacc_SASA: Time elapsed: 0.000090\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.237090e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.063000e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.424000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.973000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.285310e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.017600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.177221e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.772450e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.316256e-01\n Vprtstp: contraction number = 1.316256e-01\n Vprtstp: iteration = 2\n@@ -2195,33 +2195,33 @@\n Vprtstp: contraction number = 4.543160e-01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.790206e-06\n Vprtstp: contraction number = 4.616591e-01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.377288e-07\n Vprtstp: contraction number = 4.679511e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.593229e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.807086e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.274561e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.393754e+00\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-6, -6, -6)\n Vpmg_setPart:  actual maxima = (1.17757, 1.17757, 6)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.198283392867E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.050000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.530000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -2242,28 +2242,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.474200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.552600e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.330000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.155000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.339390e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.575200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.000578e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.176369e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -2280,31 +2280,31 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.619540e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.825232e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.147546e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.259737e+00\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.401946508821E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.400000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.020000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -2351,28 +2351,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 2.50448 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.338500e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.623400e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.946000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.355000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.133520e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.329200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.181148e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.464945e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114250e-01\n Vprtstp: contraction number = 1.114250e-01\n Vprtstp: iteration = 2\n@@ -2392,33 +2392,33 @@\n Vprtstp: contraction number = 1.974463e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.739617e-06\n Vprtstp: contraction number = 2.010776e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.579966e-07\n Vprtstp: contraction number = 2.036768e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.815920e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.985633e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.255378e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.377885e+00\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-11.8833, -11.8833, -12.2474)\n Vpmg_setPart:  actual maxima = (7.06083, 7.06083, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.099156934179E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.600000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.400000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -2463,28 +2463,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 7.21011 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.893600e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.331700e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.111000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.126000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.235730e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.875100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.383438e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.847881e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114069e-01\n Vprtstp: contraction number = 1.114069e-01\n Vprtstp: iteration = 2\n@@ -2516,39 +2516,39 @@\n Vprtstp: contraction number = 3.639461e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.623548e-06\n Vprtstp: contraction number = 3.646489e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 5.928874e-07\n Vprtstp: contraction number = 3.651801e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.775155e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.956832e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.942904e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.055295e+00\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-6, -6, -6)\n Vpmg_setPart:  actual maxima = (1.17757, 1.17757, 6)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.244769313627E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.560000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.210000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.661152e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.079084e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:17:41 2025\n+# Creation Date and Time:  Sun Jan  7 09:31:47 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -2796,32 +2796,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000141\n+Vacc_SASA: Time elapsed: 0.000132\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.064200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.741100e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.722000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.780000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.051160e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.535300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.011150e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.319130e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.252488e-01\n Vprtstp: contraction number = 1.252488e-01\n Vprtstp: iteration = 2\n@@ -2844,33 +2844,33 @@\n Vprtstp: contraction number = 2.345457e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.154547e-06\n Vprtstp: contraction number = 2.398447e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.798201e-07\n Vprtstp: contraction number = 2.423636e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.247307e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.400546e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.461126e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.569521e+00\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.937713497535E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.250000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.270000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -2917,30 +2917,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.031798 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000202\n+Vacc_SASA: Time elapsed: 0.000092\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.708200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.757900e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.520000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.797000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.351450e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.758000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.732045e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.749412e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.311630e-01\n Vprtstp: contraction number = 1.311630e-01\n Vprtstp: iteration = 2\n@@ -2972,31 +2972,31 @@\n Vprtstp: contraction number = 3.943689e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.411496e-06\n Vprtstp: contraction number = 3.954554e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 9.552609e-07\n Vprtstp: contraction number = 3.961279e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.138878e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.359994e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.930282e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.046711e+00\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-7.06083, -11.8833, -12.2474)\n Vpmg_setPart:  actual maxima = (11.8833, 7.06083, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.569480660622E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.930000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.440000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -3045,30 +3045,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0914959 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000548\n+Vacc_SASA: Time elapsed: 0.000097\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.371200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.254500e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.018000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.861000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.348180e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.596100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.176812e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.877332e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.316347e-01\n Vprtstp: contraction number = 1.316347e-01\n Vprtstp: iteration = 2\n@@ -3106,33 +3106,33 @@\n Vprtstp: contraction number = 4.560576e-01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.840082e-06\n Vprtstp: contraction number = 4.634922e-01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.644979e-07\n Vprtstp: contraction number = 4.698149e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.651762e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.857600e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.256774e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.369805e+00\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-1.17757, -6, -6)\n Vpmg_setPart:  actual maxima = (6, 1.17757, 6)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.198276421620E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.138000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.120000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -3153,28 +3153,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.435400e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.166700e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.882000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.774000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.295490e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.733200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.006838e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.259313e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -3191,33 +3191,33 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.920207e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.131565e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.120412e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.232590e+00\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.401946508821E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.670000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.260000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -3262,28 +3262,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 2.4976 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.270500e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.516000e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.966000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.162000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.381600e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.770000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.222904e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.509445e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114250e-01\n Vprtstp: contraction number = 1.114250e-01\n Vprtstp: iteration = 2\n@@ -3303,33 +3303,33 @@\n Vprtstp: contraction number = 1.974463e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.739617e-06\n Vprtstp: contraction number = 2.010776e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.579966e-07\n Vprtstp: contraction number = 2.036768e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.222399e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.433962e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.303409e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.415952e+00\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-7.06083, -11.8833, -12.2474)\n Vpmg_setPart:  actual maxima = (11.8833, 7.06083, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.099156934179E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.560000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.290000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -3374,28 +3374,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 7.19142 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.905200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.364000e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.767000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.181000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.382470e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.874900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.468155e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.941806e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114069e-01\n Vprtstp: contraction number = 1.114069e-01\n Vprtstp: iteration = 2\n@@ -3427,39 +3427,39 @@\n Vprtstp: contraction number = 3.639461e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.623548e-06\n Vprtstp: contraction number = 3.646489e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 5.928874e-07\n Vprtstp: contraction number = 3.651801e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.387810e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.592746e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.926609e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.039470e+00\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-1.17757, -6, -6)\n Vpmg_setPart:  actual maxima = (6, 1.17757, 6)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.244769313627E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.020000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.380000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.807139e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.086810e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:17:46 2025\n+# Creation Date and Time:  Sun Jan  7 09:32:00 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -3707,32 +3707,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000138\n+Vacc_SASA: Time elapsed: 0.000126\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.855500e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.738100e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.735000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.996000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.204390e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.231200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.408730e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.268940e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.252488e-01\n Vprtstp: contraction number = 1.252488e-01\n Vprtstp: iteration = 2\n@@ -3755,33 +3755,33 @@\n Vprtstp: contraction number = 2.345457e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.154547e-06\n Vprtstp: contraction number = 2.398447e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.798201e-07\n Vprtstp: contraction number = 2.423636e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.378161e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.574831e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.456187e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.559648e+00\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.937713497591E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.930000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.150000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -3828,30 +3828,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.031798 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000770\n+Vacc_SASA: Time elapsed: 0.000091\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.971400e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.420700e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.762000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.132000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.410600e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.944100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.923639e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.724514e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.311246e-01\n Vprtstp: contraction number = 1.311246e-01\n Vprtstp: iteration = 2\n@@ -3883,33 +3883,33 @@\n Vprtstp: contraction number = 3.922726e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.295236e-06\n Vprtstp: contraction number = 3.933610e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 9.043960e-07\n Vprtstp: contraction number = 3.940319e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.410842e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.637636e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.865641e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.970720e+00\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-11.8833, -7.06083, -12.2474)\n Vpmg_setPart:  actual maxima = (7.06083, 11.8833, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.569607562894E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.810000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.370000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -3956,30 +3956,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0914865 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.002055\n+Vacc_SASA: Time elapsed: 0.000091\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.180400e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.160700e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.173000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.820000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.353890e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.743800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.660164e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.785170e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.312535e-01\n Vprtstp: contraction number = 1.312535e-01\n Vprtstp: iteration = 2\n@@ -4017,31 +4017,31 @@\n Vprtstp: contraction number = 4.543257e-01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.762407e-06\n Vprtstp: contraction number = 4.617179e-01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.248702e-07\n Vprtstp: contraction number = 4.680361e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.978173e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.178329e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.170222e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.281142e+00\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-6, -1.17757, -6)\n Vpmg_setPart:  actual maxima = (1.17757, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.198283391562E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.600000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.880000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -4064,28 +4064,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.214100e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.218000e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.426500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.952000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.443860e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.640500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.089584e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.080757e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -4102,31 +4102,31 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.886464e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.116396e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.076999e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.188604e+00\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.401946508931E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.750000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.740000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -4173,28 +4173,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 2.4976 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.370200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.438900e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.071000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.525000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.223270e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.816800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.299828e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.289896e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.115250e-01\n Vprtstp: contraction number = 1.115250e-01\n Vprtstp: iteration = 2\n@@ -4214,33 +4214,33 @@\n Vprtstp: contraction number = 1.974179e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.739799e-06\n Vprtstp: contraction number = 2.010662e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.580347e-07\n Vprtstp: contraction number = 2.036772e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.263178e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.459049e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.226864e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.342515e+00\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-11.8833, -7.06083, -12.2474)\n Vpmg_setPart:  actual maxima = (7.06083, 11.8833, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.099156934185E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.110000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.290000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -4285,28 +4285,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 7.19142 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.285100e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.439700e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.920000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.144000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.403170e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.928800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.548683e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.644913e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.116239e-01\n Vprtstp: contraction number = 1.116239e-01\n Vprtstp: iteration = 2\n@@ -4338,39 +4338,39 @@\n Vprtstp: contraction number = 3.639660e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.623522e-06\n Vprtstp: contraction number = 3.646624e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 5.928877e-07\n Vprtstp: contraction number = 3.651861e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.351486e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.547236e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.443429e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.553305e+00\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-6, -1.17757, -6)\n Vpmg_setPart:  actual maxima = (1.17757, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.244769313634E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.180000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.730000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.884388e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.109146e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:17:51 2025\n+# Creation Date and Time:  Sun Jan  7 09:32:08 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -4618,32 +4618,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000512\n+Vacc_SASA: Time elapsed: 0.000224\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.578700e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.286000e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.026600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.460100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.301990e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.450280e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.720130e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.152460e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.252488e-01\n Vprtstp: contraction number = 1.252488e-01\n Vprtstp: iteration = 2\n@@ -4666,33 +4666,33 @@\n Vprtstp: contraction number = 2.345457e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.154547e-06\n Vprtstp: contraction number = 2.398447e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.798201e-07\n Vprtstp: contraction number = 2.423636e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.550832e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.754518e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.910155e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.149987e+00\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.937713497591E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.450000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.950000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -4739,30 +4739,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0317109 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000130\n+Vacc_SASA: Time elapsed: 0.000185\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.753100e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.787500e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.957000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.213000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.381500e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.365450e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.105869e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.530920e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.311373e-01\n Vprtstp: contraction number = 1.311373e-01\n Vprtstp: iteration = 2\n@@ -4794,31 +4794,31 @@\n Vprtstp: contraction number = 3.942499e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.398436e-06\n Vprtstp: contraction number = 3.953474e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 9.498453e-07\n Vprtstp: contraction number = 3.960269e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.292518e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.501346e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.732587e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.955003e+00\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-7.06083, -7.06083, -12.2474)\n Vpmg_setPart:  actual maxima = (11.8833, 11.8833, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.569480671365E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.640000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.370000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -4867,30 +4867,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0912591 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000155\n+Vacc_SASA: Time elapsed: 0.000160\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.288840e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.363350e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.304000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.554000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.349210e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.044600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.740404e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.529453e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.312625e-01\n Vprtstp: contraction number = 1.312625e-01\n Vprtstp: iteration = 2\n@@ -4928,33 +4928,33 @@\n Vprtstp: contraction number = 4.561186e-01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.813861e-06\n Vprtstp: contraction number = 4.635791e-01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.523872e-07\n Vprtstp: contraction number = 4.699296e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.850238e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.057444e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.088437e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.212527e+00\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-1.17757, -1.17757, -6)\n Vpmg_setPart:  actual maxima = (6, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.198276420222E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.750000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.670000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -4975,28 +4975,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.462900e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.846800e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.915000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.339500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.303800e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.459060e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.081365e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.181609e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -5013,33 +5013,33 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.854360e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.047725e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.993351e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.160275e+00\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.401946508931E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.190000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.430000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -5084,28 +5084,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 2.49076 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.926600e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.344000e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.496000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.350000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.304380e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.316630e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.288974e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.406531e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.115250e-01\n Vprtstp: contraction number = 1.115250e-01\n Vprtstp: iteration = 2\n@@ -5125,31 +5125,31 @@\n Vprtstp: contraction number = 1.974179e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.739799e-06\n Vprtstp: contraction number = 2.010662e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.580347e-07\n Vprtstp: contraction number = 2.036772e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.240556e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.437278e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.561931e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.788442e+00\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-7.06083, -7.06083, -12.2474)\n Vpmg_setPart:  actual maxima = (11.8833, 11.8833, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.099156934185E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.060000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.180000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -5196,28 +5196,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 7.17281 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.687000e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.394300e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.518000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.824000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.319120e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.816400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.537401e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.679415e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.116239e-01\n Vprtstp: contraction number = 1.116239e-01\n Vprtstp: iteration = 2\n@@ -5249,39 +5249,39 @@\n Vprtstp: contraction number = 3.639660e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.623522e-06\n Vprtstp: contraction number = 3.646624e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 5.928877e-07\n Vprtstp: contraction number = 3.651861e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.498023e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.708191e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.828080e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.962987e+00\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-1.17757, -1.17757, -6)\n Vpmg_setPart:  actual maxima = (6, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.244769313634E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.010000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.120000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.887256e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.861810e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:17:56 2025\n+# Creation Date and Time:  Sun Jan  7 09:32:14 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -5529,32 +5529,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000423\n+Vacc_SASA: Time elapsed: 0.000133\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.438600e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.726900e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.430100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.392000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.504010e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.095000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.344840e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.540850e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.315574e-01\n Vprtstp: contraction number = 1.315574e-01\n Vprtstp: iteration = 2\n@@ -5574,31 +5574,31 @@\n Vprtstp: contraction number = 2.039480e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.384411e-06\n Vprtstp: contraction number = 2.095783e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.318373e-07\n Vprtstp: contraction number = 2.125342e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.187007e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.414751e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.203594e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.304494e+00\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.922758694117E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.610000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.440000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -5647,30 +5647,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0319041 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000199\n+Vacc_SASA: Time elapsed: 0.000092\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.564800e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.541600e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.132000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.805000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.267320e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.831300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.818397e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.540831e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.251607e-01\n Vprtstp: contraction number = 1.251607e-01\n Vprtstp: iteration = 2\n@@ -5693,33 +5693,33 @@\n Vprtstp: contraction number = 2.197650e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.342799e-06\n Vprtstp: contraction number = 2.223851e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.012580e-07\n Vprtstp: contraction number = 2.243508e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.370813e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.567066e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.475875e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.591444e+00\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-11.8833, -11.8833, -12.2474)\n Vpmg_setPart:  actual maxima = (7.06083, 7.06083, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.571571268982E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.290000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.860000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -5766,30 +5766,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0918985 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000105\n+Vacc_SASA: Time elapsed: 0.000096\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.280680e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.124780e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.276000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.251000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.394990e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.099600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.535726e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.250403e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.287586e-01\n Vprtstp: contraction number = 1.287586e-01\n Vprtstp: iteration = 2\n@@ -5821,33 +5821,33 @@\n Vprtstp: contraction number = 3.624968e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.194036e-06\n Vprtstp: contraction number = 3.635428e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.993852e-07\n Vprtstp: contraction number = 3.643446e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.328029e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.539268e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.935683e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.054982e+00\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-6, -6, -6)\n Vpmg_setPart:  actual maxima = (1.17757, 1.17757, 6)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.198500974871E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.110000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.400000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -5868,28 +5868,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.456700e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.403800e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.820000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.679000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.369840e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.312600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.103596e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.310989e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -5906,33 +5906,33 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.914369e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.124093e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.082513e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.191787e+00\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.401946508821E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.180000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.520000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -5977,28 +5977,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 2.50448 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.472300e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.530700e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.743000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.298000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.236910e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.218900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.121394e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.515416e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114250e-01\n Vprtstp: contraction number = 1.114250e-01\n Vprtstp: iteration = 2\n@@ -6018,31 +6018,31 @@\n Vprtstp: contraction number = 1.974463e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.739617e-06\n Vprtstp: contraction number = 2.010776e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.579966e-07\n Vprtstp: contraction number = 2.036768e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.020140e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.199044e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.327957e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.432110e+00\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-11.8833, -11.8833, -12.2474)\n Vpmg_setPart:  actual maxima = (7.06083, 7.06083, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.099156934179E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.820000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.090000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -6089,28 +6089,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 7.21011 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.673700e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.455700e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.858000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.964000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.328180e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.805300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.345189e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.972222e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114069e-01\n Vprtstp: contraction number = 1.114069e-01\n Vprtstp: iteration = 2\n@@ -6142,39 +6142,39 @@\n Vprtstp: contraction number = 3.639461e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.623548e-06\n Vprtstp: contraction number = 3.646489e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 5.928874e-07\n Vprtstp: contraction number = 3.651801e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.237713e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.432620e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.944532e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.056198e+00\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-6, -6, -6)\n Vpmg_setPart:  actual maxima = (1.17757, 1.17757, 6)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.244769313627E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.290000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.390000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.669405e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.917213e+00\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:18:01 2025\n+# Creation Date and Time:  Sun Jan  7 09:32:27 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -6422,32 +6422,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000409\n+Vacc_SASA: Time elapsed: 0.000110\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.658800e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.807200e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.291000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.802000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.333330e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.974900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.145510e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.685650e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.315574e-01\n Vprtstp: contraction number = 1.315574e-01\n Vprtstp: iteration = 2\n@@ -6467,33 +6467,33 @@\n Vprtstp: contraction number = 2.039480e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.384411e-06\n Vprtstp: contraction number = 2.095783e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.318373e-07\n Vprtstp: contraction number = 2.125342e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.217886e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.434081e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.312997e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.427719e+00\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.922758694117E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.070000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.220000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -6540,30 +6540,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0318166 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000099\n+Vacc_SASA: Time elapsed: 0.000088\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.553700e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.102100e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.234000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.971000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.371960e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.042600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.834405e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.661904e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.251837e-01\n Vprtstp: contraction number = 1.251837e-01\n Vprtstp: iteration = 2\n@@ -6586,31 +6586,31 @@\n Vprtstp: contraction number = 2.194352e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.332747e-06\n Vprtstp: contraction number = 2.220306e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.985011e-07\n Vprtstp: contraction number = 2.239743e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.581380e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.794022e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.448539e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.565911e+00\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-7.06083, -11.8833, -12.2474)\n Vpmg_setPart:  actual maxima = (11.8833, 7.06083, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.571611855754E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.060000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.750000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -6659,30 +6659,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0916405 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000136\n+Vacc_SASA: Time elapsed: 0.000299\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.459490e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.061630e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.250000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.240000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.346550e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.900800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.780185e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.332680e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.287503e-01\n Vprtstp: contraction number = 1.287503e-01\n Vprtstp: iteration = 2\n@@ -6714,33 +6714,33 @@\n Vprtstp: contraction number = 3.625355e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.195364e-06\n Vprtstp: contraction number = 3.635887e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.999739e-07\n Vprtstp: contraction number = 3.643923e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.450046e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.661150e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.948133e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.061743e+00\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-1.17757, -6, -6)\n Vpmg_setPart:  actual maxima = (6, 1.17757, 6)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.198504468748E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.580000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.960000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -6761,28 +6761,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.666000e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.531800e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.932000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.203000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.289720e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.090800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.451628e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.416031e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -6799,33 +6799,33 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.995394e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.186232e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.152229e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.270604e+00\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.401946508821E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.070000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.090000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -6870,28 +6870,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 2.4976 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.017300e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.317400e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.286000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.970000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.420100e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.927400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.169479e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.700782e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114250e-01\n Vprtstp: contraction number = 1.114250e-01\n Vprtstp: iteration = 2\n@@ -6911,33 +6911,33 @@\n Vprtstp: contraction number = 1.974463e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.739617e-06\n Vprtstp: contraction number = 2.010776e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.579966e-07\n Vprtstp: contraction number = 2.036768e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.271616e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.493559e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.312478e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.429680e+00\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-7.06083, -11.8833, -12.2474)\n Vpmg_setPart:  actual maxima = (11.8833, 7.06083, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.099156934179E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.270000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.300000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -6982,28 +6982,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 7.19142 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.498500e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.281000e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.266000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.058000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.312590e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.746500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.420777e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.139685e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114069e-01\n Vprtstp: contraction number = 1.114069e-01\n Vprtstp: iteration = 2\n@@ -7035,39 +7035,39 @@\n Vprtstp: contraction number = 3.639461e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.623548e-06\n Vprtstp: contraction number = 3.646489e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 5.928874e-07\n Vprtstp: contraction number = 3.651801e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.490299e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.702404e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.969054e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.080607e+00\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-1.17757, -6, -6)\n Vpmg_setPart:  actual maxima = (6, 1.17757, 6)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.244769313627E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.550000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.220000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.770310e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.010875e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:18:06 2025\n+# Creation Date and Time:  Sun Jan  7 09:32:40 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -7315,32 +7315,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.003541\n+Vacc_SASA: Time elapsed: 0.000120\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.012580e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.928000e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.758000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.785000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.362390e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.957800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.232080e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.707860e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.315574e-01\n Vprtstp: contraction number = 1.315574e-01\n Vprtstp: iteration = 2\n@@ -7360,33 +7360,33 @@\n Vprtstp: contraction number = 2.039480e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.384411e-06\n Vprtstp: contraction number = 2.095783e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.318373e-07\n Vprtstp: contraction number = 2.125342e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.142525e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.349069e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.322619e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.438525e+00\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.922758694192E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.860000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.770000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -7433,30 +7433,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0318166 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000311\n+Vacc_SASA: Time elapsed: 0.000091\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.129440e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.490500e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.511000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.070000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.278290e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.999900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.774143e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.679115e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.252629e-01\n Vprtstp: contraction number = 1.252629e-01\n Vprtstp: iteration = 2\n@@ -7479,33 +7479,33 @@\n Vprtstp: contraction number = 2.198448e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.343869e-06\n Vprtstp: contraction number = 2.224198e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.015100e-07\n Vprtstp: contraction number = 2.243596e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.461739e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.651911e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.495259e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.613634e+00\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-11.8833, -7.06083, -12.2474)\n Vpmg_setPart:  actual maxima = (7.06083, 11.8833, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.571571270505E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.460000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.320000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -7552,30 +7552,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0916602 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000168\n+Vacc_SASA: Time elapsed: 0.000090\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.678480e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.035060e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.931000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.849000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.325930e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.612000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.602569e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.392964e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.283061e-01\n Vprtstp: contraction number = 1.283061e-01\n Vprtstp: iteration = 2\n@@ -7607,33 +7607,33 @@\n Vprtstp: contraction number = 3.626484e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.188308e-06\n Vprtstp: contraction number = 3.636628e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.975574e-07\n Vprtstp: contraction number = 3.644631e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.515970e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.707179e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.954567e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.067454e+00\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-6, -1.17757, -6)\n Vpmg_setPart:  actual maxima = (1.17757, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.198500974608E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.430000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.100000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -7654,28 +7654,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.324800e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.485200e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.579000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.732000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.089500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.785500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.251057e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.476704e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -7692,33 +7692,33 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.487569e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.605159e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.156767e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.269532e+00\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.401946508931E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.270000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.330000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -7763,28 +7763,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 2.4976 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.733400e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.231300e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.115000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.885000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.668100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.756300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.891478e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.764739e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.115250e-01\n Vprtstp: contraction number = 1.115250e-01\n Vprtstp: iteration = 2\n@@ -7804,31 +7804,31 @@\n Vprtstp: contraction number = 1.974179e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.739799e-06\n Vprtstp: contraction number = 2.010662e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.580347e-07\n Vprtstp: contraction number = 2.036772e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.437526e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.569882e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.303186e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.420170e+00\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-11.8833, -7.06083, -12.2474)\n Vpmg_setPart:  actual maxima = (7.06083, 11.8833, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.099156934185E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.090000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.100000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -7875,28 +7875,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 7.19142 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.732900e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.306800e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.559000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.937000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.233810e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.707800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.152217e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.194616e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.116239e-01\n Vprtstp: contraction number = 1.116239e-01\n Vprtstp: iteration = 2\n@@ -7928,39 +7928,39 @@\n Vprtstp: contraction number = 3.639660e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.623522e-06\n Vprtstp: contraction number = 3.646624e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 5.928877e-07\n Vprtstp: contraction number = 3.651861e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.788526e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.959162e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.872954e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.984173e+00\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-6, -1.17757, -6)\n Vpmg_setPart:  actual maxima = (1.17757, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.244769313634E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.240000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.030000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.430489e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.006969e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:18:12 2025\n+# Creation Date and Time:  Sun Jan  7 09:32:53 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -8208,32 +8208,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000116\n+Vacc_SASA: Time elapsed: 0.000172\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.323900e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.043900e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.190000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.312000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.263400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.583100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.773630e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.671960e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.315574e-01\n Vprtstp: contraction number = 1.315574e-01\n Vprtstp: iteration = 2\n@@ -8253,33 +8253,33 @@\n Vprtstp: contraction number = 2.039480e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.384411e-06\n Vprtstp: contraction number = 2.095783e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.318373e-07\n Vprtstp: contraction number = 2.125342e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.329020e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.447502e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.251573e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.362729e+00\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.922758694192E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.480000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.110000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -8326,30 +8326,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0317294 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000095\n+Vacc_SASA: Time elapsed: 0.000098\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.772900e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.508700e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.119000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.885000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.107600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.574300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.693378e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.600595e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.252944e-01\n Vprtstp: contraction number = 1.252944e-01\n Vprtstp: iteration = 2\n@@ -8372,31 +8372,31 @@\n Vprtstp: contraction number = 2.195054e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.334000e-06\n Vprtstp: contraction number = 2.220609e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.987906e-07\n Vprtstp: contraction number = 2.239810e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.476099e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.591927e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.379530e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.493034e+00\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-7.06083, -7.06083, -12.2474)\n Vpmg_setPart:  actual maxima = (11.8833, 11.8833, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.571611857350E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.340000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.110000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -8445,30 +8445,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0914032 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000092\n+Vacc_SASA: Time elapsed: 0.000300\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.101930e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.086690e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.983000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.664000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.019500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.498800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.396223e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.200548e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.282975e-01\n Vprtstp: contraction number = 1.282975e-01\n Vprtstp: iteration = 2\n@@ -8500,31 +8500,31 @@\n Vprtstp: contraction number = 3.626822e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.189511e-06\n Vprtstp: contraction number = 3.637026e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.980984e-07\n Vprtstp: contraction number = 3.645099e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.963745e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.078484e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.928347e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.039309e+00\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-1.17757, -1.17757, -6)\n Vpmg_setPart:  actual maxima = (6, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.198504468496E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.560000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.000000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -8547,28 +8547,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.354500e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.123300e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.436000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.128000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.394300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.166940e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.496300e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.347658e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -8585,33 +8585,33 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.156455e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.276289e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.930193e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.122569e+00\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.401946508931E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.680000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.960000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 4.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -8656,28 +8656,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 2.49076 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.386300e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.601400e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.871000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.063300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.978100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.166870e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.785992e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.457125e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.115250e-01\n Vprtstp: contraction number = 1.115250e-01\n Vprtstp: iteration = 2\n@@ -8697,33 +8697,33 @@\n Vprtstp: contraction number = 1.974179e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.739799e-06\n Vprtstp: contraction number = 2.010662e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.580347e-07\n Vprtstp: contraction number = 2.036772e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.322134e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.439247e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.496634e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.653419e+00\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-7.06083, -7.06083, -12.2474)\n Vpmg_setPart:  actual maxima = (11.8833, 11.8833, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.099156934185E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.680000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.120000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -8768,28 +8768,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 7.17281 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.444300e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.161400e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.173000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.021000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.958800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.317290e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.239728e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.020155e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.116239e-01\n Vprtstp: contraction number = 1.116239e-01\n Vprtstp: iteration = 2\n@@ -8821,29 +8821,29 @@\n Vprtstp: contraction number = 3.639660e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.623522e-06\n Vprtstp: contraction number = 3.646624e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 5.928877e-07\n Vprtstp: contraction number = 3.651861e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.957809e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.073001e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.868195e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.080049e+00\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-1.17757, -1.17757, -6)\n Vpmg_setPart:  actual maxima = (6, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.244769313634E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.620000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.550000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.019878e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.407658e+01\n"}, {"source1": "./usr/share/apbs/examples/hca-bind/io.mc", "source2": "./usr/share/apbs/examples/hca-bind/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:34:15 2025\n+# Creation Date and Time:  Sun Jan  7 09:45:00 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path acet.pqr\n@@ -289,32 +289,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.002457\n+Vacc_SASA: Time elapsed: 0.014008\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.553300e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.390500e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.550000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.310000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.143400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.666600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.653590e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.742030e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.087255e-01\n Vprtstp: contraction number = 1.087255e-01\n Vprtstp: iteration = 2\n@@ -331,32 +331,32 @@\n Vprtstp: contraction number = 1.074047e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.481057e-06\n Vprtstp: contraction number = 1.080656e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.608051e-07\n Vprtstp: contraction number = 1.085746e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.141410e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.263749e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.919730e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.730320e-01\n Vpmg_setPart:  lower corner = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  upper corner = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  actual minima = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  actual maxima = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.785902379684E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.100000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.100000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 6.35359\n Vpbe_ctor2:  solute dimensions = 7.389 x 11.027 x 9.931\n Vpbe_ctor2:  solute charge = -1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -402,30 +402,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.104294 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.002243\n+Vacc_SASA: Time elapsed: 0.009348\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.538600e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.561700e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.577000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.062000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.500300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.111400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.456798e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.902100e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.287269e-01\n Vprtstp: contraction number = 1.287269e-01\n Vprtstp: iteration = 2\n@@ -451,32 +451,32 @@\n Vprtstp: contraction number = 3.073619e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.517211e-06\n Vprtstp: contraction number = 3.092055e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 4.703221e-07\n Vprtstp: contraction number = 3.099912e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.658649e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.781282e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 9.636230e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.035833e+00\n Vpmg_setPart:  lower corner = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  upper corner = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  actual minima = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  actual maxima = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.473001739532E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.100000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.500000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 6.35359\n Vpbe_ctor2:  solute dimensions = 7.389 x 11.027 x 9.931\n Vpbe_ctor2:  solute charge = -1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -522,30 +522,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.504504 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.002642\n+Vacc_SASA: Time elapsed: 0.012310\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.301900e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.903600e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.394000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.292000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.701500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.933100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.254469e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.078953e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.402627e-01\n Vprtstp: contraction number = 1.402627e-01\n Vprtstp: iteration = 2\n@@ -574,30 +574,30 @@\n Vprtstp: contraction number = 3.281873e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.285796e-06\n Vprtstp: contraction number = 3.294777e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.250794e-07\n Vprtstp: contraction number = 3.305964e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.811719e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.926366e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.169374e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.239816e+00\n Vpmg_setPart:  lower corner = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  upper corner = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  actual minima = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  actual maxima = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.210605041355E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.700000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = 1\n@@ -620,32 +620,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.739500\n+Vacc_SASA: Time elapsed: 0.751782\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.906280e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.993870e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.094000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.995000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.982600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.909900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.971262e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.140084e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.838248e-02\n Vprtstp: contraction number = 7.838248e-02\n Vprtstp: iteration = 2\n@@ -707,32 +707,32 @@\n Vprtstp: contraction number = 6.567898e-01\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 1.365716e-06\n Vprtstp: contraction number = 6.589433e-01\n Vprtstp: iteration = 22\n Vprtstp: relative residual = 9.028429e-07\n Vprtstp: contraction number = 6.610767e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.614854e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.728135e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.128372e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.194035e+00\n Vpmg_setPart:  lower corner = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  upper corner = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  actual minima = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  actual maxima = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.689092374656E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.780000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.540000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -778,30 +778,30 @@\n VPMG::extEnergy: extQfEnergy = 4518.73 kT\n VPMG::extEnergy: extDiEnergy = 2191.64 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.727055\n+Vacc_SASA: Time elapsed: 0.743285\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.100910e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.146640e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.114000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.909000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.266200e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.977500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.051780e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.179192e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.397950e-01\n Vprtstp: contraction number = 1.397950e-01\n Vprtstp: iteration = 2\n@@ -842,30 +842,30 @@\n Vprtstp: contraction number = 5.527064e-01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 1.277233e-06\n Vprtstp: contraction number = 5.598610e-01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 7.227170e-07\n Vprtstp: contraction number = 5.658458e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.490410e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.610638e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.464082e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.534233e+00\n Vpmg_setPart:  lower corner = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  upper corner = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  actual minima = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  actual maxima = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.222630775541E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.690000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.400000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = 1\n@@ -913,30 +913,30 @@\n VPMG::extEnergy: extQfEnergy = 110988 kT\n VPMG::extEnergy: extDiEnergy = 56275.9 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.729296\n+Vacc_SASA: Time elapsed: 0.736879\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.005650e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.103320e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.261000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.076000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.199700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.929100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.392538e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.531142e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.115653e-01\n Vprtstp: contraction number = 1.115653e-01\n Vprtstp: iteration = 2\n@@ -962,30 +962,30 @@\n Vprtstp: contraction number = 3.498142e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.355176e-06\n Vprtstp: contraction number = 3.685616e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 9.245419e-07\n Vprtstp: contraction number = 3.925575e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.644307e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.759340e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 9.791720e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.045312e+00\n Vpmg_setPart:  lower corner = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  upper corner = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  actual minima = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  actual maxima = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.441218006192E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.400000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.500000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = -1.01863e-14\n@@ -1008,32 +1008,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.733869\n+Vacc_SASA: Time elapsed: 0.742682\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.971420e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.003000e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.157000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.209000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.087400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.151200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.648151e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.139700e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.658858e-02\n Vprtstp: contraction number = 7.658858e-02\n Vprtstp: iteration = 2\n@@ -1095,30 +1095,30 @@\n Vprtstp: contraction number = 6.561084e-01\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 1.508067e-06\n Vprtstp: contraction number = 6.580134e-01\n Vprtstp: iteration = 22\n Vprtstp: relative residual = 9.954065e-07\n Vprtstp: contraction number = 6.600544e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.608798e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.722237e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.173197e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.248022e+00\n Vpmg_setPart:  lower corner = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  upper corner = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  actual minima = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  actual maxima = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.698545237167E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.260000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.840000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = -1.01863e-14\n@@ -1166,30 +1166,30 @@\n VPMG::extEnergy: extQfEnergy = 4519.43 kT\n VPMG::extEnergy: extDiEnergy = 2191.49 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.736182\n+Vacc_SASA: Time elapsed: 0.751978\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.154300e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.183400e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.553000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.341000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.245600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.867300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.102649e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.446257e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.396668e-01\n Vprtstp: contraction number = 1.396668e-01\n Vprtstp: iteration = 2\n@@ -1230,30 +1230,30 @@\n Vprtstp: contraction number = 5.525486e-01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 1.290655e-06\n Vprtstp: contraction number = 5.600207e-01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 7.308313e-07\n Vprtstp: contraction number = 5.662486e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.472485e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.591820e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.463199e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.532679e+00\n Vpmg_setPart:  lower corner = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  upper corner = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  actual minima = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  actual maxima = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.237049215096E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.410000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.840000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = -1.01863e-14\n@@ -1301,30 +1301,30 @@\n VPMG::extEnergy: extQfEnergy = 110994 kT\n VPMG::extEnergy: extDiEnergy = 56275.1 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.734587\n+Vacc_SASA: Time elapsed: 0.748860\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.047800e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.182190e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.187000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.008000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.057900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.962300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.441688e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.683578e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.163858e-01\n Vprtstp: contraction number = 1.163858e-01\n Vprtstp: iteration = 2\n@@ -1353,38 +1353,38 @@\n Vprtstp: contraction number = 3.950088e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.396547e-06\n Vprtstp: contraction number = 4.328810e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.612158e-07\n Vprtstp: contraction number = 4.734646e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.879840e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.991438e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.234920e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.301381e+00\n Vpmg_setPart:  lower corner = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  upper corner = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  actual minima = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  actual maxima = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.492900778210E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.400000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.150000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.631336e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.810472e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:34:40 2025\n+# Creation Date and Time:  Sun Jan  7 09:45:09 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path acet.pqr\n@@ -1669,32 +1669,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.003714\n+Vacc_SASA: Time elapsed: 0.012576\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.032300e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.044100e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.385000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.411000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.095000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.559300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.982020e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.023480e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.084928e-01\n Vprtstp: contraction number = 1.084928e-01\n Vprtstp: iteration = 2\n@@ -1711,32 +1711,32 @@\n Vprtstp: contraction number = 1.067805e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.430429e-06\n Vprtstp: contraction number = 1.075005e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.545898e-07\n Vprtstp: contraction number = 1.080723e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.183484e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.303817e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.879990e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.852030e-01\n Vpmg_setPart:  lower corner = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  upper corner = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  actual minima = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  actual maxima = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.520701614302E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.500000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.500000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 6.35359\n Vpbe_ctor2:  solute dimensions = 7.389 x 11.027 x 9.931\n Vpbe_ctor2:  solute charge = -1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1782,30 +1782,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.105108 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.002226\n+Vacc_SASA: Time elapsed: 0.012905\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.272800e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.514500e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.346000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.989000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.980500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.365400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.554409e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.142678e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.225646e-01\n Vprtstp: contraction number = 1.225646e-01\n Vprtstp: iteration = 2\n@@ -1822,30 +1822,30 @@\n Vprtstp: contraction number = 1.454441e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 5.669194e-06\n Vprtstp: contraction number = 1.566066e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 9.449546e-07\n Vprtstp: contraction number = 1.666824e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.145930e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.264740e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.196910e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.044360e-01\n Vpmg_setPart:  lower corner = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  upper corner = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  actual minima = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  actual maxima = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.468387819400E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.500000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 6.35359\n Vpbe_ctor2:  solute dimensions = 7.389 x 11.027 x 9.931\n Vpbe_ctor2:  solute charge = -1\n@@ -1893,30 +1893,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.520445 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.002225\n+Vacc_SASA: Time elapsed: 0.011944\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.714200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.394100e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.017000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.882000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.159100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.006900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.876148e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.996662e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.305252e-01\n Vprtstp: contraction number = 1.305252e-01\n Vprtstp: iteration = 2\n@@ -1936,32 +1936,32 @@\n Vprtstp: contraction number = 1.733670e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.357163e-06\n Vprtstp: contraction number = 1.824572e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.550194e-07\n Vprtstp: contraction number = 1.879063e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.315600e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.433056e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.400156e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.468865e+00\n Vpmg_setPart:  lower corner = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  upper corner = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  actual minima = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  actual maxima = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.211840549614E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.100000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.400000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1982,32 +1982,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.741647\n+Vacc_SASA: Time elapsed: 0.762546\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.226980e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.664090e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.211000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.114000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.963600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.997500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.126468e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.346449e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.136636e-02\n Vprtstp: contraction number = 5.136636e-02\n Vprtstp: iteration = 2\n@@ -2027,32 +2027,32 @@\n Vprtstp: contraction number = 2.406804e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.980432e-06\n Vprtstp: contraction number = 2.704556e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.800745e-07\n Vprtstp: contraction number = 2.929030e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.330798e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.441699e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.093085e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.173396e+00\n Vpmg_setPart:  lower corner = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  upper corner = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  actual minima = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  actual maxima = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.766185147917E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.840000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.620000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -2098,30 +2098,30 @@\n VPMG::extEnergy: extQfEnergy = 4619.67 kT\n VPMG::extEnergy: extDiEnergy = 2259.75 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.725525\n+Vacc_SASA: Time elapsed: 0.739567\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.418120e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.761800e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.204000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.889000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.360600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.695100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.421432e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.457155e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.613067e-02\n Vprtstp: contraction number = 9.613067e-02\n Vprtstp: iteration = 2\n@@ -2141,32 +2141,32 @@\n Vprtstp: contraction number = 1.833548e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.811522e-06\n Vprtstp: contraction number = 1.939744e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.707504e-07\n Vprtstp: contraction number = 2.046624e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.321259e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.442288e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.529878e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.668159e+00\n Vpmg_setPart:  lower corner = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  upper corner = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  actual minima = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  actual maxima = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.226315327863E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.920000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.670000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -2212,30 +2212,30 @@\n VPMG::extEnergy: extQfEnergy = 111278 kT\n VPMG::extEnergy: extDiEnergy = 55995.6 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.726387\n+Vacc_SASA: Time elapsed: 0.746299\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.294400e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.701030e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.216000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.953000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.333000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.780400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.689001e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.924961e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.009208e-01\n Vprtstp: contraction number = 1.009208e-01\n Vprtstp: iteration = 2\n@@ -2252,30 +2252,30 @@\n Vprtstp: contraction number = 1.451140e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 3.266673e-06\n Vprtstp: contraction number = 1.668260e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.985159e-07\n Vprtstp: contraction number = 1.832188e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.170130e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.285431e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.741750e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.386320e-01\n Vpmg_setPart:  lower corner = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  upper corner = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  actual minima = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  actual maxima = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.444499098932E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.100000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.200000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = -1.01863e-14\n@@ -2298,32 +2298,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.734529\n+Vacc_SASA: Time elapsed: 0.742757\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.275010e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.195010e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.219000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.980000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.024100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.885900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.180456e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.049965e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.894768e-02\n Vprtstp: contraction number = 4.894768e-02\n Vprtstp: iteration = 2\n@@ -2343,30 +2343,30 @@\n Vprtstp: contraction number = 2.414708e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.098574e-06\n Vprtstp: contraction number = 2.683582e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.050680e-07\n Vprtstp: contraction number = 2.883234e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.312766e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.429045e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 8.371790e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.060380e-01\n Vpmg_setPart:  lower corner = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  upper corner = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  actual minima = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  actual maxima = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.771575298437E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.890000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.680000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = -1.01863e-14\n@@ -2414,30 +2414,30 @@\n VPMG::extEnergy: extQfEnergy = 4620.09 kT\n VPMG::extEnergy: extDiEnergy = 2259.49 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.735861\n+Vacc_SASA: Time elapsed: 0.742129\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.361920e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.429520e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.783000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.600000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.878700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.814000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.406906e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.225486e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.547807e-02\n Vprtstp: contraction number = 9.547807e-02\n Vprtstp: iteration = 2\n@@ -2457,30 +2457,30 @@\n Vprtstp: contraction number = 1.878215e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.896640e-06\n Vprtstp: contraction number = 1.994763e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.991489e-07\n Vprtstp: contraction number = 2.104505e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.329277e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.443469e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.775330e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.458040e-01\n Vpmg_setPart:  lower corner = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  upper corner = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  actual minima = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  actual maxima = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.240652812594E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.430000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.650000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = -1.01863e-14\n@@ -2528,30 +2528,30 @@\n VPMG::extEnergy: extQfEnergy = 111288 kT\n VPMG::extEnergy: extDiEnergy = 55994.2 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.735647\n+Vacc_SASA: Time elapsed: 0.747182\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.432140e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.399330e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.374000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.052000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.398900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.910500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.636078e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.394437e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.031999e-01\n Vprtstp: contraction number = 1.031999e-01\n Vprtstp: iteration = 2\n@@ -2568,28 +2568,28 @@\n Vprtstp: contraction number = 1.434980e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 3.331639e-06\n Vprtstp: contraction number = 1.622112e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.872183e-07\n Vprtstp: contraction number = 1.762551e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.180409e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.298073e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.733500e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.403770e-01\n Vpmg_setPart:  lower corner = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  upper corner = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  actual minima = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  actual maxima = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.496181357535E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.900000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.500000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.755893e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.463850e+01\n"}, {"source1": "./usr/share/apbs/examples/ion-pmf/io.mc", "source2": "./usr/share/apbs/examples/ion-pmf/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:35:32 2025\n+# Creation Date and Time:  Sun Jan  7 09:45:23 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion-pmf.pdb\n@@ -161,28 +161,28 @@\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefSpline...\n Vpmg_fillco:  filling coefficient arrays\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.349800e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.471000e-03\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.264000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.358000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.999600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.859600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.380120e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.323500e-02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194542e-01\n Vprtstp: contraction number = 1.194542e-01\n Vprtstp: iteration = 2\n@@ -202,33 +202,33 @@\n Vprtstp: contraction number = 1.749569e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.117484e-06\n Vprtstp: contraction number = 1.874072e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.180018e-07\n Vprtstp: contraction number = 1.950826e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.305183e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.424096e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.675210e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.373840e-01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.324828953427E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.260000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.000000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 5.560000e-03\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 5.252000e-03\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 4\n Vpbe_ctor2:  solute dimensions = 8 x 4 x 4\n Vpbe_ctor2:  solute charge = 2\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -249,28 +249,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.299700e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.021600e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.957000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.197000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.072300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.969200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.579560e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.815600e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.110640e-01\n Vprtstp: contraction number = 1.110640e-01\n Vprtstp: iteration = 2\n@@ -287,50 +287,50 @@\n Vprtstp: contraction number = 1.067494e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.466502e-06\n Vprtstp: contraction number = 1.074548e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.584103e-07\n Vprtstp: contraction number = 1.080191e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.147240e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.263643e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.701630e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.472930e-01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.232617942545E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.610000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.790000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vpmg_dbForce: No force for uniform dielectric!\n Vpmg_dbForce: No force for uniform dielectric!\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 4.300000e-05\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 5.200000e-05\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 16 x 8 x 8 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.8 max radius\n Vclist_setupGrid:  Grid lengths = (14.792, 10.792, 10.792)\n Vclist_setupGrid:  Grid lower corner = (-8.396, -5.396, -5.396)\n Vclist_assignAtoms:  Have 720 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 181.458\n Vacc_storeParms:  Using 18030-point reference sphere\n forceAPOL: Trying atom surf...\n-forceAPOL: atom surf: Time elapsed: 0.000885\n-forceAPOL: Time elapsed: 1.777965\n-Vacc_SASA: Time elapsed: 0.000001\n-initAPOL: Time elapsed: 4.928775\n+forceAPOL: atom surf: Time elapsed: 0.000955\n+forceAPOL: Time elapsed: 1.776956\n+Vacc_SASA: Time elapsed: 0.000000\n+initAPOL: Time elapsed: 4.926675\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n@@ -339,8 +339,8 @@\n printForce:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.653487e+00\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 6.591553e+00\n"}, {"source1": "./usr/share/apbs/examples/ionize/io.mc", "source2": "./usr/share/apbs/examples/ionize/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:34:57 2025\n+# Creation Date and Time:  Sun Jan  7 09:45:16 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path acetic-acid.xml\n@@ -481,32 +481,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000721\n+Vacc_SASA: Time elapsed: 0.014157\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.072600e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.539300e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.590000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.427400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.384600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.171100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.529280e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.570460e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.188999e-01\n Vprtstp: contraction number = 3.188999e-01\n Vprtstp: iteration = 2\n@@ -535,16 +535,16 @@\n Vprtstp: contraction number = 2.912126e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.816386e-06\n Vprtstp: contraction number = 2.924708e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.271441e-07\n Vprtstp: contraction number = 2.936899e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.842620e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.967365e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.066464e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.161574e+00\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -606,30 +606,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0505207 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000655\n+Vacc_SASA: Time elapsed: 0.010065\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.689500e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.526000e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.539000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.933000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.607400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.968100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.147846e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.355162e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.598074e-01\n Vprtstp: contraction number = 2.598074e-01\n Vprtstp: iteration = 2\n@@ -661,16 +661,16 @@\n Vprtstp: contraction number = 3.326351e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.087103e-06\n Vprtstp: contraction number = 3.343120e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.014192e-07\n Vprtstp: contraction number = 3.360731e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.016661e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.140866e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.158199e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.229054e+00\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -678,15 +678,15 @@\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.039953678525E+03 kT\n Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1.66533e-16\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -707,28 +707,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.531400e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.036800e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.432000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.030000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.330300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.824800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.302568e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.626788e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.679930e-01\n Vprtstp: contraction number = 1.679930e-01\n Vprtstp: iteration = 2\n@@ -745,30 +745,30 @@\n Vprtstp: contraction number = 1.043091e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.862252e-06\n Vprtstp: contraction number = 1.059323e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.994142e-07\n Vprtstp: contraction number = 1.070823e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.175665e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.297200e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.685090e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.364920e-01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 4.800125490193E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.600000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.500000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1.66533e-16\n@@ -814,28 +814,28 @@\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n VPMG::extEnergy: extQmEnergy = 0 kT\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 1.14339 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.370000e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.198800e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.457000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.763000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.126800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.871900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.609203e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.384434e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.651787e-01\n Vprtstp: contraction number = 1.651787e-01\n Vprtstp: iteration = 2\n@@ -852,30 +852,30 @@\n Vprtstp: contraction number = 1.055047e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.934803e-06\n Vprtstp: contraction number = 1.064764e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.073576e-07\n Vprtstp: contraction number = 1.071724e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.162159e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.278212e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.177782e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.259677e+00\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.058572238076E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.800000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1\n@@ -898,32 +898,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001845\n+Vacc_SASA: Time elapsed: 0.010194\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.497000e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.891200e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.501000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.251000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.160700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.836300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.919383e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.758487e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.669750e-01\n Vprtstp: contraction number = 1.669750e-01\n Vprtstp: iteration = 2\n@@ -952,32 +952,32 @@\n Vprtstp: contraction number = 3.348642e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.783762e-06\n Vprtstp: contraction number = 3.348981e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 9.322590e-07\n Vprtstp: contraction number = 3.348918e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.850588e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.972491e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.376865e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.508969e+00\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 6.748221698410E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.700000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.700000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1\n Vpbe_ctor2:  bulk ionic strength = 0.15\n Vpbe_ctor2:  xkappa = 0.128839\n@@ -1023,30 +1023,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.600233 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000644\n+Vacc_SASA: Time elapsed: 0.009590\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.346700e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.468300e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.414000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.501000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.286400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.443000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.914358e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.262165e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.532338e-01\n Vprtstp: contraction number = 1.532338e-01\n Vprtstp: iteration = 2\n@@ -1078,30 +1078,30 @@\n Vprtstp: contraction number = 3.529902e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.276975e-06\n Vprtstp: contraction number = 3.528897e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 4.504551e-07\n Vprtstp: contraction number = 3.527516e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.021832e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.141565e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.952537e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.031340e+00\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.143395002184E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.400000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1\n@@ -1124,28 +1124,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.220400e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.114000e-03\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.288000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.006000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.072000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.805500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.106400e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.321733e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.140338e-01\n Vprtstp: contraction number = 1.140338e-01\n Vprtstp: iteration = 2\n@@ -1162,30 +1162,30 @@\n Vprtstp: contraction number = 1.066400e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.493481e-06\n Vprtstp: contraction number = 1.074330e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.613267e-07\n Vprtstp: contraction number = 1.080206e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.174353e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.288773e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.582920e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.301960e-01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 6.912847895210E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.600000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.000000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1\n@@ -1231,28 +1231,28 @@\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n VPMG::extEnergy: extQmEnergy = 0 kT\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 22.4432 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.423500e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.153500e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.582000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.815000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.614000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.914600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.237738e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.008477e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.151233e-01\n Vprtstp: contraction number = 1.151233e-01\n Vprtstp: iteration = 2\n@@ -1269,30 +1269,30 @@\n Vprtstp: contraction number = 1.065071e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.498104e-06\n Vprtstp: contraction number = 1.072349e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.614370e-07\n Vprtstp: contraction number = 1.077609e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.174698e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.298273e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.670800e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.363280e-01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.159793508256E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.600000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.500000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.15\n Vpbe_ctor2:  solute dimensions = 2.3 x 2.3 x 2.3\n Vpbe_ctor2:  solute charge = 1\n@@ -1315,32 +1315,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000046\n+Vacc_SASA: Time elapsed: 0.000042\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.541300e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.779000e-03\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.458000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.079000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.292900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.783900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.368534e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.086186e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.470644e-01\n Vprtstp: contraction number = 1.470644e-01\n Vprtstp: iteration = 2\n@@ -1366,30 +1366,30 @@\n Vprtstp: contraction number = 2.846821e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.962532e-06\n Vprtstp: contraction number = 2.852652e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 5.602483e-07\n Vprtstp: contraction number = 2.854722e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.653528e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.770180e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 9.403350e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.018786e+00\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.170869129315E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.600000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.100000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.15\n Vpbe_ctor2:  solute dimensions = 2.3 x 2.3 x 2.3\n Vpbe_ctor2:  solute charge = 1\n@@ -1439,28 +1439,28 @@\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n Vacc_SASA: Time elapsed: 0.000044\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.842200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.043600e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.532000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.733000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.991600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.996400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.547767e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.191857e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.382011e-01\n Vprtstp: contraction number = 1.382011e-01\n Vprtstp: iteration = 2\n@@ -1489,16 +1489,16 @@\n Vprtstp: contraction number = 3.143969e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.077403e-06\n Vprtstp: contraction number = 3.146378e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.391862e-07\n Vprtstp: contraction number = 3.148184e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.823275e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.942451e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.055629e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.125897e+00\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1506,15 +1506,15 @@\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.162367825044E+03 kT\n Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.500000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.15\n Vpbe_ctor2:  solute dimensions = 2.3 x 2.3 x 2.3\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1535,28 +1535,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.712700e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.243700e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.026000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.992000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.179000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.884300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.743847e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.308869e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.118955e-01\n Vprtstp: contraction number = 1.118955e-01\n Vprtstp: iteration = 2\n@@ -1573,30 +1573,30 @@\n Vprtstp: contraction number = 1.069169e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.490424e-06\n Vprtstp: contraction number = 1.076150e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.611536e-07\n Vprtstp: contraction number = 1.081260e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.147896e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.266916e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.565150e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.251950e-01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.417301695136E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.600000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.300000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.15\n Vpbe_ctor2:  solute dimensions = 2.3 x 2.3 x 2.3\n Vpbe_ctor2:  solute charge = 1\n@@ -1642,28 +1642,28 @@\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n VPMG::extEnergy: extQmEnergy = 0 kT\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 27.9953 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.280800e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.185600e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.371000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.804000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.073900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.004800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.871535e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.385238e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.111894e-01\n Vprtstp: contraction number = 1.111894e-01\n Vprtstp: iteration = 2\n@@ -1680,44 +1680,44 @@\n Vprtstp: contraction number = 1.067651e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.469870e-06\n Vprtstp: contraction number = 1.074950e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.588283e-07\n Vprtstp: contraction number = 1.080560e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.148020e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.263001e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.914640e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.617110e-01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.406572492944E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.500000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.000000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.986428e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.454530e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:35:16 2025\n+# Creation Date and Time:  Sun Jan  7 09:45:20 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path acetic-acid.xml\n@@ -2194,32 +2194,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001338\n+Vacc_SASA: Time elapsed: 0.011378\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.192400e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.806200e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.891000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.781000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.904800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.906000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.762170e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.336260e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.596091e-01\n Vprtstp: contraction number = 2.596091e-01\n Vprtstp: iteration = 2\n@@ -2239,30 +2239,30 @@\n Vprtstp: contraction number = 1.697798e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.455171e-06\n Vprtstp: contraction number = 1.730577e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.805682e-07\n Vprtstp: contraction number = 1.752050e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.325255e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.442442e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.790130e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.473190e-01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 4.781452735910E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.100000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.200000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1.66533e-16\n@@ -2310,30 +2310,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0553032 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000652\n+Vacc_SASA: Time elapsed: 0.010014\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.313100e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.863100e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.336000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.071000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.565200e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.925300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.687932e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.059171e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.192618e-01\n Vprtstp: contraction number = 2.192618e-01\n Vprtstp: iteration = 2\n@@ -2353,30 +2353,30 @@\n Vprtstp: contraction number = 1.807641e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.267839e-06\n Vprtstp: contraction number = 1.838237e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.807397e-07\n Vprtstp: contraction number = 1.861749e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.319413e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.441512e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.801860e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.490260e-01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.040239618722E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.900000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.100000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1.66533e-16\n@@ -2399,28 +2399,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.469400e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.216600e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.053000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.741000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.137400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.689800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.138590e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.931829e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.679930e-01\n Vprtstp: contraction number = 1.679930e-01\n Vprtstp: iteration = 2\n@@ -2437,30 +2437,30 @@\n Vprtstp: contraction number = 1.043091e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.862252e-06\n Vprtstp: contraction number = 1.059323e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.994142e-07\n Vprtstp: contraction number = 1.070823e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.143616e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.259025e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.558130e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.231700e-01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 4.800125490193E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.700000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.000000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1.66533e-16\n@@ -2506,28 +2506,28 @@\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n VPMG::extEnergy: extQmEnergy = 0 kT\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 1.14339 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.318000e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.326600e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.337000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.094000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.922100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.866600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.412709e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.696111e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.651787e-01\n Vprtstp: contraction number = 1.651787e-01\n Vprtstp: iteration = 2\n@@ -2544,30 +2544,30 @@\n Vprtstp: contraction number = 1.055047e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.934803e-06\n Vprtstp: contraction number = 1.064764e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.073576e-07\n Vprtstp: contraction number = 1.071724e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.151833e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.267921e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.587640e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.280860e-01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.058572238076E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.100000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.200000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1\n@@ -2590,32 +2590,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000623\n+Vacc_SASA: Time elapsed: 0.008846\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.475200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.872800e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.080000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.579000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.941900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.732500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.738263e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.505889e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.505354e-01\n Vprtstp: contraction number = 1.505354e-01\n Vprtstp: iteration = 2\n@@ -2635,30 +2635,30 @@\n Vprtstp: contraction number = 1.898671e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.115563e-06\n Vprtstp: contraction number = 1.948490e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.143002e-07\n Vprtstp: contraction number = 1.971715e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.315606e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.433007e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 8.067160e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.723630e-01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 6.749438220873E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.500000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.800000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1\n@@ -2706,30 +2706,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.607375 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000665\n+Vacc_SASA: Time elapsed: 0.007726\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.315400e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.873400e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.394000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.077000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.937000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.858700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.224834e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.450593e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420228e-01\n Vprtstp: contraction number = 1.420228e-01\n Vprtstp: iteration = 2\n@@ -2749,30 +2749,30 @@\n Vprtstp: contraction number = 1.900725e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.720330e-06\n Vprtstp: contraction number = 1.966740e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.430374e-07\n Vprtstp: contraction number = 1.996219e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.305369e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.422190e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.668830e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.350740e-01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.143498275233E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.400000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.100000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1\n@@ -2795,28 +2795,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.194200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.804000e-03\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.314000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.007000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.736900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.660100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.655618e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.312940e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.140338e-01\n Vprtstp: contraction number = 1.140338e-01\n Vprtstp: iteration = 2\n@@ -2833,30 +2833,30 @@\n Vprtstp: contraction number = 1.066400e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.493481e-06\n Vprtstp: contraction number = 1.074330e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.613267e-07\n Vprtstp: contraction number = 1.080206e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.136328e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.247401e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.023150e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.750780e-01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 6.912847895210E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.700000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.800000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1\n@@ -2902,28 +2902,28 @@\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n VPMG::extEnergy: extQmEnergy = 0 kT\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 22.4432 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.221600e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.283500e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.142000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.231000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.921400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.917100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.919195e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.112183e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.151233e-01\n Vprtstp: contraction number = 1.151233e-01\n Vprtstp: iteration = 2\n@@ -2940,30 +2940,30 @@\n Vprtstp: contraction number = 1.065071e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.498104e-06\n Vprtstp: contraction number = 1.072349e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.614370e-07\n Vprtstp: contraction number = 1.077609e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.154295e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.268117e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.556680e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.297720e-01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.159793508256E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.700000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.300000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.15\n Vpbe_ctor2:  solute dimensions = 2.3 x 2.3 x 2.3\n Vpbe_ctor2:  solute charge = 1\n@@ -2986,32 +2986,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000041\n+Vacc_SASA: Time elapsed: 0.000043\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.181500e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.743500e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.128000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.983000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.820600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.855600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.122724e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.903038e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.382442e-01\n Vprtstp: contraction number = 1.382442e-01\n Vprtstp: iteration = 2\n@@ -3031,32 +3031,32 @@\n Vprtstp: contraction number = 1.741425e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.778515e-06\n Vprtstp: contraction number = 1.810766e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.297938e-07\n Vprtstp: contraction number = 1.854322e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.320043e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.430859e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.867770e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.541890e-01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.171449807940E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.800000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.700000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.15\n Vpbe_ctor2:  solute dimensions = 2.3 x 2.3 x 2.3\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0.15\n Vpbe_ctor2:  xkappa = 0.128839\n@@ -3102,30 +3102,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.654498 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000245\n+Vacc_SASA: Time elapsed: 0.000042\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.973800e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.455800e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.367000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.195000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.125900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.031600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.271613e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.831455e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.297624e-01\n Vprtstp: contraction number = 1.297624e-01\n Vprtstp: iteration = 2\n@@ -3145,32 +3145,32 @@\n Vprtstp: contraction number = 1.701143e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.306208e-06\n Vprtstp: contraction number = 1.773242e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.371381e-07\n Vprtstp: contraction number = 1.815470e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.304039e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.421976e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.703800e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.402910e-01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.163593499843E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.100000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.700000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.15\n Vpbe_ctor2:  solute dimensions = 2.3 x 2.3 x 2.3\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -3191,28 +3191,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.580100e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.223500e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.857000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.700000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.930000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.903900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.415311e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.701790e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.118955e-01\n Vprtstp: contraction number = 1.118955e-01\n Vprtstp: iteration = 2\n@@ -3229,32 +3229,32 @@\n Vprtstp: contraction number = 1.069169e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.490424e-06\n Vprtstp: contraction number = 1.076150e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.611536e-07\n Vprtstp: contraction number = 1.081260e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.127467e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.243464e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.777210e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.545600e-01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.417301695136E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.700000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.15\n Vpbe_ctor2:  solute dimensions = 2.3 x 2.3 x 2.3\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -3298,28 +3298,28 @@\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n VPMG::extEnergy: extQmEnergy = 0 kT\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 27.9953 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.120100e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.333900e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.049000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.287000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.622800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.001800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.540341e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.475926e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.111894e-01\n Vprtstp: contraction number = 1.111894e-01\n Vprtstp: iteration = 2\n@@ -3336,16 +3336,16 @@\n Vprtstp: contraction number = 1.067651e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.469870e-06\n Vprtstp: contraction number = 1.074950e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.588283e-07\n Vprtstp: contraction number = 1.080560e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.134885e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.245790e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.835240e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.543410e-01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -3353,17 +3353,17 @@\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.406572492944E+03 kT\n Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.100000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.654100e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.016619e+01\n"}, {"source1": "./usr/share/apbs/examples/pka-lig/io.mc", "source2": "./usr/share/apbs/examples/pka-lig/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:35:39 2025\n+# Creation Date and Time:  Sun Jan  7 09:45:29 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path bx6_7_lig_apbs.pqr\n@@ -340,31 +340,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.008541\n+Vacc_SASA: Time elapsed: 0.020633\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.654200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.823500e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.958100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.383900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.981670e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.087600e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.126570e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.705470e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.561608e-01\n Vprtstp: contraction number = 1.561608e-01\n Vprtstp: iteration = 2\n@@ -390,30 +390,30 @@\n Vprtstp: contraction number = 2.750705e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.932473e-06\n Vprtstp: contraction number = 2.767817e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 5.373027e-07\n Vprtstp: contraction number = 2.780389e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.669242e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.918892e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.697777e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.941978e+00\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.795090079491E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.200000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.800000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 10.66\n Vpbe_ctor2:  solute dimensions = 17.188 x 12.75 x 15.33\n Vpbe_ctor2:  solute charge = 1.11022e-16\n@@ -461,29 +461,29 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.123733 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.007084\n+Vacc_SASA: Time elapsed: 0.018683\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.543500e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.177400e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.947400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.999200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.969570e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.056430e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.279472e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.358073e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.152775e-01\n Vprtstp: contraction number = 2.152775e-01\n Vprtstp: iteration = 2\n@@ -515,30 +515,30 @@\n Vprtstp: contraction number = 3.353090e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.328976e-06\n Vprtstp: contraction number = 3.371305e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 4.496116e-07\n Vprtstp: contraction number = 3.383143e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.228934e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.476799e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.297285e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.531900e+00\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.468794426258E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.800000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -561,31 +561,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.984543\n+Vacc_SASA: Time elapsed: 0.998448\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.052023e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.059318e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.003600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.959000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.106070e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.064430e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.826833e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.960147e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.188493e-01\n Vprtstp: contraction number = 1.188493e-01\n Vprtstp: iteration = 2\n@@ -638,30 +638,30 @@\n Vprtstp: contraction number = 6.152114e-01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.141886e-06\n Vprtstp: contraction number = 6.186689e-01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 7.101689e-07\n Vprtstp: contraction number = 6.219261e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.269353e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.532355e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.098957e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.341075e+00\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.467100888191E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.460000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.610000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -709,29 +709,29 @@\n VPMG::extEnergy: extQfEnergy = 119417 kT\n VPMG::extEnergy: extDiEnergy = 58605.1 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.961177\n+Vacc_SASA: Time elapsed: 0.970049\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.063748e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.104673e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.905700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.915300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.032260e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.069420e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.441664e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.440167e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.393577e-01\n Vprtstp: contraction number = 1.393577e-01\n Vprtstp: iteration = 2\n@@ -766,30 +766,30 @@\n Vprtstp: contraction number = 4.796270e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.074713e-06\n Vprtstp: contraction number = 4.999984e-01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 5.553244e-07\n Vprtstp: contraction number = 5.167187e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.695905e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.948890e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.526266e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.760379e+00\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.427017897319E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.280000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.750000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -812,31 +812,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.986482\n+Vacc_SASA: Time elapsed: 1.000613\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.068551e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.076001e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.804500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.719300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.092940e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.072500e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.944429e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.924075e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189544e-01\n Vprtstp: contraction number = 1.189544e-01\n Vprtstp: iteration = 2\n@@ -889,30 +889,30 @@\n Vprtstp: contraction number = 6.138674e-01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.173454e-06\n Vprtstp: contraction number = 6.173088e-01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 7.281097e-07\n Vprtstp: contraction number = 6.204841e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.621453e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.878775e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.170585e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.403829e+00\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.485227452845E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.570000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.590000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -960,29 +960,29 @@\n VPMG::extEnergy: extQfEnergy = 119415 kT\n VPMG::extEnergy: extDiEnergy = 58604.6 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.998952\n+Vacc_SASA: Time elapsed: 1.009459\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.103206e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.131963e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.037300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.922800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.163010e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.039390e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.643888e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.577811e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.423446e-01\n Vprtstp: contraction number = 1.423446e-01\n Vprtstp: iteration = 2\n@@ -1017,38 +1017,38 @@\n Vprtstp: contraction number = 4.820331e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.206020e-06\n Vprtstp: contraction number = 5.012326e-01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 6.232432e-07\n Vprtstp: contraction number = 5.167767e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.762409e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.027931e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.437028e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.667992e+00\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.511771058265E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.980000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.710000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.022916e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.923914e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:36:08 2025\n+# Creation Date and Time:  Sun Jan  7 09:45:43 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path bx6_7_lig_apbs.pqr\n@@ -1384,31 +1384,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.009510\n+Vacc_SASA: Time elapsed: 0.018928\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.634040e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.740210e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.001000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.990900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.050330e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.073430e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.552410e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.018410e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.452428e-01\n Vprtstp: contraction number = 1.452428e-01\n Vprtstp: iteration = 2\n@@ -1428,30 +1428,30 @@\n Vprtstp: contraction number = 1.683190e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.126022e-06\n Vprtstp: contraction number = 1.729184e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.755158e-07\n Vprtstp: contraction number = 1.766283e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.189416e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.444045e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.159104e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.401000e+00\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.796545857614E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.300000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.200000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 10.66\n Vpbe_ctor2:  solute dimensions = 17.188 x 12.75 x 15.33\n Vpbe_ctor2:  solute charge = 1.11022e-16\n@@ -1499,29 +1499,29 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.131443 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.006897\n+Vacc_SASA: Time elapsed: 0.018118\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.860100e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.852430e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.988100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.974500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.036070e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.049600e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.087982e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.082029e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.793309e-01\n Vprtstp: contraction number = 1.793309e-01\n Vprtstp: iteration = 2\n@@ -1541,30 +1541,30 @@\n Vprtstp: contraction number = 1.800338e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.360443e-06\n Vprtstp: contraction number = 1.860813e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.400789e-07\n Vprtstp: contraction number = 1.904746e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.162678e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.416558e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.161250e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.393710e+00\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.475324562943E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.200000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.900000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -1587,31 +1587,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.983082\n+Vacc_SASA: Time elapsed: 0.999382\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.204172e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.185382e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.190700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.953400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.252390e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.069580e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.734595e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.665178e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.027357e-02\n Vprtstp: contraction number = 9.027357e-02\n Vprtstp: iteration = 2\n@@ -1631,30 +1631,30 @@\n Vprtstp: contraction number = 1.817922e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.545186e-06\n Vprtstp: contraction number = 1.999061e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.371519e-07\n Vprtstp: contraction number = 2.181950e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.220008e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.496415e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.133116e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.366225e+00\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.474786197493E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.530000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.380000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -1702,29 +1702,29 @@\n VPMG::extEnergy: extQfEnergy = 120029 kT\n VPMG::extEnergy: extDiEnergy = 58911.7 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.964390\n+Vacc_SASA: Time elapsed: 0.968406\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.203586e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.226427e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.993800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.971800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.086440e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.064800e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.041979e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.026146e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.164650e-01\n Vprtstp: contraction number = 1.164650e-01\n Vprtstp: iteration = 2\n@@ -1744,32 +1744,32 @@\n Vprtstp: contraction number = 1.751675e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.167167e-06\n Vprtstp: contraction number = 1.847486e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.216013e-07\n Vprtstp: contraction number = 1.898626e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.266936e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.524038e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.157557e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.390482e+00\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.434258164340E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.800000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.720000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1790,31 +1790,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.989008\n+Vacc_SASA: Time elapsed: 1.004066\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.213336e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.201489e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.819900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.703500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.105910e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.040650e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.416232e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.385689e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.976616e-02\n Vprtstp: contraction number = 8.976616e-02\n Vprtstp: iteration = 2\n@@ -1834,30 +1834,30 @@\n Vprtstp: contraction number = 1.851080e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.610068e-06\n Vprtstp: contraction number = 2.038795e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.565510e-07\n Vprtstp: contraction number = 2.214509e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.208110e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.465600e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.132962e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.365869e+00\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.493215172512E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.130000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.570000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -1905,29 +1905,29 @@\n VPMG::extEnergy: extQfEnergy = 120027 kT\n VPMG::extEnergy: extDiEnergy = 58911 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.997469\n+Vacc_SASA: Time elapsed: 1.006971\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.222722e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.236363e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.942000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.860300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.044120e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.010810e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.784981e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.745627e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.180177e-01\n Vprtstp: contraction number = 1.180177e-01\n Vprtstp: iteration = 2\n@@ -1947,38 +1947,38 @@\n Vprtstp: contraction number = 1.739107e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.163103e-06\n Vprtstp: contraction number = 1.834388e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.205019e-07\n Vprtstp: contraction number = 1.895807e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.174294e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.427098e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.103444e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.329640e+00\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.519180536568E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.120000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.720000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.004978e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.958393e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:36:28 2025\n+# Creation Date and Time:  Sun Jan  7 09:45:53 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path bx6_7_lig_apbs.pqr\n@@ -2314,31 +2314,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.008357\n+Vacc_SASA: Time elapsed: 0.015162\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.939000e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.437800e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.971300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.009000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.002500e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.011830e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.250270e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.430670e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.599213e-01\n Vprtstp: contraction number = 1.599213e-01\n Vprtstp: iteration = 2\n@@ -2367,32 +2367,32 @@\n Vprtstp: contraction number = 2.963523e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.017970e-06\n Vprtstp: contraction number = 2.969958e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.027030e-07\n Vprtstp: contraction number = 2.973596e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.942629e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.191486e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.904769e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.135684e+00\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.810710599589E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.800000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.100000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 10.66\n Vpbe_ctor2:  solute dimensions = 17.188 x 12.75 x 15.33\n Vpbe_ctor2:  solute charge = 1.11022e-16\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -2438,29 +2438,29 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.127039 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.008245\n+Vacc_SASA: Time elapsed: 0.024575\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.930790e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.645050e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.979100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.052500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.024080e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.068950e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.716561e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.952309e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.128592e-01\n Vprtstp: contraction number = 2.128592e-01\n Vprtstp: iteration = 2\n@@ -2492,32 +2492,32 @@\n Vprtstp: contraction number = 3.367480e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.365284e-06\n Vprtstp: contraction number = 3.379196e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 4.626034e-07\n Vprtstp: contraction number = 3.388332e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.265818e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.517938e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.193713e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.430379e+00\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.488596110069E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.200000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -2538,31 +2538,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.660793\n+Vacc_SASA: Time elapsed: 0.695209\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.323710e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.264929e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.093000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.906400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.098810e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.045500e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.182330e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.646070e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.008467e-01\n Vprtstp: contraction number = 1.008467e-01\n Vprtstp: iteration = 2\n@@ -2591,32 +2591,32 @@\n Vprtstp: contraction number = 4.011046e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.434965e-06\n Vprtstp: contraction number = 4.261259e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.351498e-07\n Vprtstp: contraction number = 4.426237e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.022075e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.284231e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.881230e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.112990e+00\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.502732517701E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.900000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.480000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -2662,29 +2662,29 @@\n VPMG::extEnergy: extQfEnergy = 122258 kT\n VPMG::extEnergy: extDiEnergy = 60015.6 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.671317\n+Vacc_SASA: Time elapsed: 0.676903\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.053803e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.513355e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.903600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.994800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.016190e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.157180e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.251640e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.328822e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.444678e-01\n Vprtstp: contraction number = 1.444678e-01\n Vprtstp: iteration = 2\n@@ -2713,32 +2713,32 @@\n Vprtstp: contraction number = 3.502797e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.520619e-06\n Vprtstp: contraction number = 3.554465e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.554489e-07\n Vprtstp: contraction number = 3.652782e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.998127e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.251183e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.956116e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.199885e+00\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.462158714651E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.200000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.610000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -2759,31 +2759,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.679314\n+Vacc_SASA: Time elapsed: 0.721099\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.624630e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.294456e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.702900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.125400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.949320e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.077070e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.672607e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.777748e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.951095e-02\n Vprtstp: contraction number = 9.951095e-02\n Vprtstp: iteration = 2\n@@ -2812,30 +2812,30 @@\n Vprtstp: contraction number = 3.973081e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.298337e-06\n Vprtstp: contraction number = 4.223462e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.734047e-07\n Vprtstp: contraction number = 4.416455e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.026964e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.271047e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.042747e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.277788e+00\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.522103263384E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.900000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.410000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -2883,29 +2883,29 @@\n VPMG::extEnergy: extQfEnergy = 122254 kT\n VPMG::extEnergy: extDiEnergy = 60014.8 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.672517\n+Vacc_SASA: Time elapsed: 0.675589\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.005272e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.424133e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.202000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.055900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.207240e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.115750e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.103714e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.248883e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.413483e-01\n Vprtstp: contraction number = 1.413483e-01\n Vprtstp: iteration = 2\n@@ -2934,38 +2934,38 @@\n Vprtstp: contraction number = 3.543205e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.106047e-06\n Vprtstp: contraction number = 3.675340e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.216013e-07\n Vprtstp: contraction number = 3.811783e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.090636e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.365594e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.928461e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.169131e+00\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.548006855100E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.840000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.100000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.415105e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.544002e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:36:49 2025\n+# Creation Date and Time:  Sun Jan  7 09:46:04 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path bx6_7_lig_apbs.pqr\n@@ -3301,31 +3301,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.006983\n+Vacc_SASA: Time elapsed: 0.016218\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.760730e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.994800e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.017800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.993700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.023520e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.059720e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.637930e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.695160e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.452175e-01\n Vprtstp: contraction number = 1.452175e-01\n Vprtstp: iteration = 2\n@@ -3345,30 +3345,30 @@\n Vprtstp: contraction number = 1.752116e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.443360e-06\n Vprtstp: contraction number = 1.802654e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.491907e-07\n Vprtstp: contraction number = 1.838414e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.190093e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.441582e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.148697e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.381846e+00\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.816452194100E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.100000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 10.66\n Vpbe_ctor2:  solute dimensions = 17.188 x 12.75 x 15.33\n Vpbe_ctor2:  solute charge = 1.11022e-16\n@@ -3416,29 +3416,29 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.133537 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.008285\n+Vacc_SASA: Time elapsed: 0.026232\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.274150e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.974780e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.937700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.011800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.986120e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.089620e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.232466e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.455212e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.775500e-01\n Vprtstp: contraction number = 1.775500e-01\n Vprtstp: iteration = 2\n@@ -3458,32 +3458,32 @@\n Vprtstp: contraction number = 1.827663e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.496113e-06\n Vprtstp: contraction number = 1.891043e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.759954e-07\n Vprtstp: contraction number = 1.933563e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.148215e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.395885e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.149470e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.385659e+00\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.493961459749E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.200000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -3504,31 +3504,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.662685\n+Vacc_SASA: Time elapsed: 0.672262\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.057860e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.397884e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.975400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.954500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.031330e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.125730e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.693799e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.253176e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.789951e-02\n Vprtstp: contraction number = 8.789951e-02\n Vprtstp: iteration = 2\n@@ -3545,30 +3545,30 @@\n Vprtstp: contraction number = 1.398889e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 4.364929e-06\n Vprtstp: contraction number = 1.509054e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.472971e-07\n Vprtstp: contraction number = 1.941148e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.898237e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.150321e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.885675e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.132808e+00\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.503907197961E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.590000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.400000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -3616,29 +3616,29 @@\n VPMG::extEnergy: extQfEnergy = 122356 kT\n VPMG::extEnergy: extDiEnergy = 60065 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.666416\n+Vacc_SASA: Time elapsed: 0.675866\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.171658e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.646397e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.940200e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.935600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.048020e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.143580e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.002157e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.102917e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.361361e-01\n Vprtstp: contraction number = 1.361361e-01\n Vprtstp: iteration = 2\n@@ -3658,32 +3658,32 @@\n Vprtstp: contraction number = 1.780896e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.357861e-06\n Vprtstp: contraction number = 1.814853e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.460991e-07\n Vprtstp: contraction number = 1.812402e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.198768e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.453074e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.465020e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.705104e+00\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.463376211100E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.740000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.080000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -3704,31 +3704,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.681077\n+Vacc_SASA: Time elapsed: 0.690499\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.091871e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.419329e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.748600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.740800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.031740e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.087230e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.356571e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.514987e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.694592e-02\n Vprtstp: contraction number = 8.694592e-02\n Vprtstp: iteration = 2\n@@ -3745,30 +3745,30 @@\n Vprtstp: contraction number = 1.389852e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 4.160523e-06\n Vprtstp: contraction number = 1.496124e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.105844e-07\n Vprtstp: contraction number = 1.948275e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.958988e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.208572e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.930566e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.163368e+00\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.523234125638E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.105000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.320000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -3816,29 +3816,29 @@\n VPMG::extEnergy: extQfEnergy = 122353 kT\n VPMG::extEnergy: extDiEnergy = 60064.1 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.668833\n+Vacc_SASA: Time elapsed: 0.674262\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.126011e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.552117e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.950100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.807400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.033550e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.966120e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.690830e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.885721e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.348493e-01\n Vprtstp: contraction number = 1.348493e-01\n Vprtstp: iteration = 2\n@@ -3858,28 +3858,28 @@\n Vprtstp: contraction number = 1.735657e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.117086e-06\n Vprtstp: contraction number = 1.891826e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.184693e-07\n Vprtstp: contraction number = 1.955708e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.195546e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.447433e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.109122e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.329895e+00\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.549194232887E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.990000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.780000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.912466e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.099043e+01\n"}, {"source1": "./usr/share/apbs/examples/point-pmf/io.mc", "source2": "./usr/share/apbs/examples/point-pmf/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:37:06 2025\n+# Creation Date and Time:  Sun Jan  7 09:46:14 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol0.pqr\n@@ -184,28 +184,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.272800e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.631700e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.215000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.433100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.052100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.351600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.384690e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.347540e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.117158e-01\n Vprtstp: contraction number = 1.117158e-01\n Vprtstp: iteration = 2\n@@ -222,33 +222,33 @@\n Vprtstp: contraction number = 1.067217e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.472908e-06\n Vprtstp: contraction number = 1.074130e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.590269e-07\n Vprtstp: contraction number = 1.079680e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.140152e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.260635e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.719410e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.680570e-01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.887170085535E+01 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.473000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.486000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 0\n Vpbe_ctor2:  solute dimensions = 0 x 0 x 0\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -269,28 +269,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.492500e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.556000e-03\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.124000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.076000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.032100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.912000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.415680e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.253430e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.116487e-01\n Vprtstp: contraction number = 1.116487e-01\n Vprtstp: iteration = 2\n@@ -307,31 +307,31 @@\n Vprtstp: contraction number = 1.068390e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.476968e-06\n Vprtstp: contraction number = 1.075610e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.596976e-07\n Vprtstp: contraction number = 1.081253e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.132882e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.252218e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.500160e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.310940e-01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.241648379021E+01 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.454000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.500000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 0.5\n Vpbe_ctor2:  solute dimensions = 1 x 0 x 0\n Vpbe_ctor2:  solute charge = 2\n@@ -354,28 +354,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.551000e-03\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.759000e-03\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.999000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.959000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.855200e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.703600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.673690e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.678207e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.110273e-01\n Vprtstp: contraction number = 1.110273e-01\n Vprtstp: iteration = 2\n@@ -392,39 +392,39 @@\n Vprtstp: contraction number = 1.067630e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.464818e-06\n Vprtstp: contraction number = 1.074713e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.582462e-07\n Vprtstp: contraction number = 1.080314e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.131332e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.243061e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.459330e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.152810e-01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.660589930493E+02 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.464000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.506000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.809119e+00\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.344792e+00\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:37:10 2025\n+# Creation Date and Time:  Sun Jan  7 09:46:15 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol0.pqr\n@@ -604,28 +604,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.423400e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.379300e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.835000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.479600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.975700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.361100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.369150e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.322480e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.117158e-01\n Vprtstp: contraction number = 1.117158e-01\n Vprtstp: iteration = 2\n@@ -642,33 +642,33 @@\n Vprtstp: contraction number = 1.067217e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.472908e-06\n Vprtstp: contraction number = 1.074130e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.590269e-07\n Vprtstp: contraction number = 1.079680e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.156524e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.273666e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.743240e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.709440e-01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.887170085535E+01 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.475000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.522000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 0\n Vpbe_ctor2:  solute dimensions = 0 x 0 x 0\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -689,28 +689,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.355900e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.793000e-03\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.322000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.208000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.229600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.842000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.431586e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.169580e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.115116e-01\n Vprtstp: contraction number = 1.115116e-01\n Vprtstp: iteration = 2\n@@ -727,33 +727,33 @@\n Vprtstp: contraction number = 1.068563e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.477070e-06\n Vprtstp: contraction number = 1.075813e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.597562e-07\n Vprtstp: contraction number = 1.081575e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.167565e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.289651e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.453590e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.210280e-01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.209948502984E+01 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.489000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.499000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1\n Vpbe_ctor2:  solute dimensions = 2 x 0 x 0\n Vpbe_ctor2:  solute charge = 2\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -774,28 +774,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.826000e-03\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.892000e-03\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.794000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.086000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.852300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.653700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.726033e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.664396e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.112280e-01\n Vprtstp: contraction number = 1.112280e-01\n Vprtstp: iteration = 2\n@@ -812,39 +812,39 @@\n Vprtstp: contraction number = 1.067265e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.466596e-06\n Vprtstp: contraction number = 1.074314e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.583845e-07\n Vprtstp: contraction number = 1.079946e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.181123e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.295473e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.372290e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.271350e-01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.681569832028E+02 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.505000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.443000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.908859e+00\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.322851e+00\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:37:13 2025\n+# Creation Date and Time:  Sun Jan  7 09:46:16 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol0.pqr\n@@ -1024,28 +1024,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.391400e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.605500e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.556000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.341500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.873000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.883400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.367250e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.289850e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.117158e-01\n Vprtstp: contraction number = 1.117158e-01\n Vprtstp: iteration = 2\n@@ -1062,31 +1062,31 @@\n Vprtstp: contraction number = 1.067217e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.472908e-06\n Vprtstp: contraction number = 1.074130e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.590269e-07\n Vprtstp: contraction number = 1.079680e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.173253e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.290137e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.731050e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.637790e-01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.887170085535E+01 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.475000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.507000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 0\n Vpbe_ctor2:  solute dimensions = 0 x 0 x 0\n Vpbe_ctor2:  solute charge = 1\n@@ -1109,28 +1109,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.245900e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.387000e-03\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.897000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.888000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.896900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.829900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.445539e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.149330e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.122494e-01\n Vprtstp: contraction number = 1.122494e-01\n Vprtstp: iteration = 2\n@@ -1147,33 +1147,33 @@\n Vprtstp: contraction number = 1.068256e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.484900e-06\n Vprtstp: contraction number = 1.075504e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.605755e-07\n Vprtstp: contraction number = 1.081389e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.169703e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.290136e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.491560e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.245890e-01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.079207063662E+02 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.477000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.471000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.5\n Vpbe_ctor2:  solute dimensions = 3 x 0 x 0\n Vpbe_ctor2:  solute charge = 2\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1194,28 +1194,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.216200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.412000e-03\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.493000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.008000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.309100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.706500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.747095e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.667842e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.117126e-01\n Vprtstp: contraction number = 1.117126e-01\n Vprtstp: iteration = 2\n@@ -1232,39 +1232,39 @@\n Vprtstp: contraction number = 1.067223e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.472511e-06\n Vprtstp: contraction number = 1.074345e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.590395e-07\n Vprtstp: contraction number = 1.080057e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.150742e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.267738e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.375660e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.092410e-01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.915601904303E+02 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.700000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.495000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.899151e+00\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.325780e+00\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:37:17 2025\n+# Creation Date and Time:  Sun Jan  7 09:46:16 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol0.pqr\n@@ -1444,28 +1444,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.475500e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.738100e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.097000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.711000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.401000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.741700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.411770e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.097200e-02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.117158e-01\n Vprtstp: contraction number = 1.117158e-01\n Vprtstp: iteration = 2\n@@ -1482,31 +1482,31 @@\n Vprtstp: contraction number = 1.067217e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.472908e-06\n Vprtstp: contraction number = 1.074130e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.590269e-07\n Vprtstp: contraction number = 1.079680e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.166597e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.287203e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.448420e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.127960e-01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.887170085535E+01 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.493000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.485000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 0\n Vpbe_ctor2:  solute dimensions = 0 x 0 x 0\n Vpbe_ctor2:  solute charge = 1\n@@ -1529,28 +1529,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.433100e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.236000e-03\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.344000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.954000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.322800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.859800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.444942e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.482890e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.115116e-01\n Vprtstp: contraction number = 1.115116e-01\n Vprtstp: iteration = 2\n@@ -1567,33 +1567,33 @@\n Vprtstp: contraction number = 1.068563e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.477070e-06\n Vprtstp: contraction number = 1.075813e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.597562e-07\n Vprtstp: contraction number = 1.081575e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.170759e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.290921e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.610930e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.357030e-01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.209948502984E+01 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.450000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.481000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 2\n Vpbe_ctor2:  solute dimensions = 4 x 0 x 0\n Vpbe_ctor2:  solute charge = 2\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1614,28 +1614,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.276000e-03\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.415000e-03\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.200000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.998000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.078300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.625700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.741520e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.610609e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.113661e-01\n Vprtstp: contraction number = 1.113661e-01\n Vprtstp: iteration = 2\n@@ -1652,29 +1652,29 @@\n Vprtstp: contraction number = 1.067553e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.470482e-06\n Vprtstp: contraction number = 1.074604e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.588507e-07\n Vprtstp: contraction number = 1.080263e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.162932e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.276839e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.458890e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.175560e-01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.645453654146E+02 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.481000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.463000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.905491e+00\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.282196e+00\n"}, {"source1": "./usr/share/apbs/examples/protein-rna/io.mc", "source2": "./usr/share/apbs/examples/protein-rna/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:37:31 2025\n+# Creation Date and Time:  Sun Jan  7 09:46:19 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -274,151 +274,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.189225\n+Vacc_SASA: Time elapsed: 0.227247\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.342680e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.548750e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.793000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.770200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.699080e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.696940e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.461340e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.952430e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3489953.107213\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.874550e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.394630e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.541420e+05\n Vprtstp: contraction number = 4.541420e+05\n Vnewton: Attempting damping, relres = 0.152961\n Vnewton: Attempting damping, relres = 0.557868\n Vnewton: Damping accepted, relres = 0.152961\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.529613e-01\n Vprtstp: contraction number = 1.529613e-01\n Vnewton: Using errtol_s: 533827.862441\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.527639e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.454475e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.616204e+04\n Vprtstp: contraction number = 7.616204e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.889845e-02\n Vprtstp: contraction number = 1.889265e-01\n Vnewton: Using errtol_s: 100854.249053\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.373967e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.848977e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.621156e+04\n Vprtstp: contraction number = 1.621156e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.485254e-03\n Vprtstp: contraction number = 2.244153e-01\n Vnewton: Using errtol_s: 22633.233232\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.208068e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.267185e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.163481e+03\n Vprtstp: contraction number = 4.163481e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.448984e-03\n Vprtstp: contraction number = 2.234275e-01\n Vnewton: Using errtol_s: 5056.886378\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.009788e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.694683e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.135331e+03\n Vprtstp: contraction number = 1.135331e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.105204e-04\n Vprtstp: contraction number = 2.143021e-01\n Vnewton: Using errtol_s: 1083.701574\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.797357e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.122935e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.001303e+02\n Vprtstp: contraction number = 3.001303e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 7.746175e-05\n Vprtstp: contraction number = 2.494579e-01\n Vnewton: Using errtol_s: 270.337872\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.601203e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.509823e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.503484e+01\n Vprtstp: contraction number = 8.503484e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.192913e-05\n Vprtstp: contraction number = 2.830962e-01\n Vnewton: Using errtol_s: 76.531632\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.387388e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.936941e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.526272e+01\n Vprtstp: contraction number = 2.526272e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.514831e-06\n Vprtstp: contraction number = 2.970857e-01\n Vnewton: Using errtol_s: 22.736454\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.169353e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.356619e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.640103e+00\n Vprtstp: contraction number = 7.640103e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.970254e-06\n Vprtstp: contraction number = 3.024259e-01\n Vnewton: Using errtol_s: 6.876093\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.958777e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.751121e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.337433e+00\n Vprtstp: contraction number = 2.337433e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.027844e-07\n Vprtstp: contraction number = 3.059426e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.096289e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.293523e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.300713e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.503356e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -428,15 +428,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.965827433400E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.569434563500E+04 kT\n Vpmg_energy:  dielEnergy = 1.283478359962E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.828100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.815000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -485,160 +485,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.194992 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.179603\n+Vacc_SASA: Time elapsed: 0.204892\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.777210e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.935500e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.742700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.983000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.621080e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.663710e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.229811e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.912568e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3601925.484823\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.371619e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.075529e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.484865e+05\n Vprtstp: contraction number = 5.484865e+05\n Vnewton: Attempting damping, relres = 0.170948\n Vnewton: Attempting damping, relres = 0.567920\n Vnewton: Damping accepted, relres = 0.170948\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.709480e-01\n Vprtstp: contraction number = 1.709480e-01\n Vnewton: Using errtol_s: 615741.974888\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.025468e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.553272e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.034638e+05\n Vprtstp: contraction number = 1.034638e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.462084e-02\n Vprtstp: contraction number = 2.025226e-01\n Vnewton: Using errtol_s: 124701.671212\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.109915e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.012170e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.424561e+04\n Vprtstp: contraction number = 2.424561e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.233375e-03\n Vprtstp: contraction number = 2.378156e-01\n Vnewton: Using errtol_s: 29656.002425\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.196264e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.473133e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.562093e+03\n Vprtstp: contraction number = 6.562093e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.983416e-03\n Vprtstp: contraction number = 2.408995e-01\n Vnewton: Using errtol_s: 7144.117639\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.281004e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.885351e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.862413e+03\n Vprtstp: contraction number = 1.862413e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.794286e-04\n Vprtstp: contraction number = 2.417186e-01\n Vnewton: Using errtol_s: 1726.865972\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.363978e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.330863e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.263950e+02\n Vprtstp: contraction number = 5.263950e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.315588e-04\n Vprtstp: contraction number = 2.744075e-01\n Vnewton: Using errtol_s: 473.865007\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.446786e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.747832e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.568838e+02\n Vprtstp: contraction number = 1.568838e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.920007e-05\n Vprtstp: contraction number = 2.979661e-01\n Vnewton: Using errtol_s: 141.195715\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.530260e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.132485e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.889017e+01\n Vprtstp: contraction number = 4.889017e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.221601e-05\n Vprtstp: contraction number = 3.116325e-01\n Vnewton: Using errtol_s: 44.001172\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.612703e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.567344e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.562922e+01\n Vprtstp: contraction number = 1.562922e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.905217e-06\n Vprtstp: contraction number = 3.196802e-01\n Vnewton: Using errtol_s: 14.066301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.693138e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.955787e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.094993e+00\n Vprtstp: contraction number = 5.094993e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.273067e-06\n Vprtstp: contraction number = 3.259914e-01\n Vnewton: Using errtol_s: 4.585493\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.775169e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.039132e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.686155e+00\n Vprtstp: contraction number = 1.686155e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.213135e-07\n Vprtstp: contraction number = 3.309436e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.256986e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.445272e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.815584e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.017594e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -648,15 +648,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.946137752289E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.954048421546E+04 kT\n Vpmg_energy:  dielEnergy = 1.475783126623E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.794500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.793000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -685,151 +685,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.065196\n+Vacc_SASA: Time elapsed: 0.076478\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.483520e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.402050e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.794700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.737800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.698610e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.689530e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.967358e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.201494e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 990625.209730\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.981484e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.217245e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.350454e+05\n Vprtstp: contraction number = 1.350454e+05\n Vnewton: Attempting damping, relres = 0.127353\n Vnewton: Attempting damping, relres = 0.559577\n Vnewton: Damping accepted, relres = 0.127353\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.273531e-01\n Vprtstp: contraction number = 1.273531e-01\n Vnewton: Using errtol_s: 126159.215622\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.055021e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.267204e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.277893e+04\n Vprtstp: contraction number = 2.277893e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.085042e-02\n Vprtstp: contraction number = 1.637213e-01\n Vnewton: Using errtol_s: 20654.953727\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.119831e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.307638e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.649050e+03\n Vprtstp: contraction number = 4.649050e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.224159e-03\n Vprtstp: contraction number = 2.025935e-01\n Vnewton: Using errtol_s: 4184.558722\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.187184e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.348579e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.091881e+03\n Vprtstp: contraction number = 1.091881e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 9.919956e-04\n Vprtstp: contraction number = 2.348386e-01\n Vnewton: Using errtol_s: 982.695801\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.254157e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.388644e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.793836e+02\n Vprtstp: contraction number = 2.793836e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 2.538250e-04\n Vprtstp: contraction number = 2.558731e-01\n Vnewton: Using errtol_s: 251.445454\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.321157e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.427901e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.524959e+01\n Vprtstp: contraction number = 7.524959e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 6.836556e-05\n Vprtstp: contraction number = 2.693413e-01\n Vnewton: Using errtol_s: 67.724647\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.387062e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.472842e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.096668e+01\n Vprtstp: contraction number = 2.096668e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.904859e-05\n Vprtstp: contraction number = 2.786284e-01\n Vnewton: Using errtol_s: 18.870009\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.454162e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.512849e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.985543e+00\n Vprtstp: contraction number = 5.985543e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.437969e-06\n Vprtstp: contraction number = 2.854789e-01\n Vnewton: Using errtol_s: 5.386989\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.521156e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.552442e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.740420e+00\n Vprtstp: contraction number = 1.740420e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.581202e-06\n Vprtstp: contraction number = 2.907706e-01\n Vnewton: Using errtol_s: 1.566378\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.588977e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.592489e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.132173e-01\n Vprtstp: contraction number = 5.132173e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 4.662667e-07\n Vprtstp: contraction number = 2.948812e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.799340e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.995279e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.641398e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.841743e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -839,15 +839,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.196703875366E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.838438031793E+03 kT\n Vpmg_energy:  dielEnergy = 3.417360829181E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.876400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.982800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -896,149 +896,149 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.017697 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.062156\n+Vacc_SASA: Time elapsed: 0.077924\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.734090e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.722220e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.776900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.930100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.673690e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.343600e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.686345e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.722561e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1033125.204115\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.700502e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.749850e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.675387e+05\n Vprtstp: contraction number = 1.675387e+05\n Vnewton: Attempting damping, relres = 0.150147\n Vnewton: Attempting damping, relres = 0.571307\n Vnewton: Damping accepted, relres = 0.150147\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.501469e-01\n Vprtstp: contraction number = 1.501469e-01\n Vnewton: Using errtol_s: 155120.525305\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.776075e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.811193e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.209762e+04\n Vprtstp: contraction number = 3.209762e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.810624e-02\n Vprtstp: contraction number = 1.871917e-01\n Vnewton: Using errtol_s: 29037.270087\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.844001e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.882980e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.331420e+03\n Vprtstp: contraction number = 7.331420e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.387218e-03\n Vprtstp: contraction number = 2.272526e-01\n Vnewton: Using errtol_s: 6598.796330\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.911873e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.985799e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.824095e+03\n Vprtstp: contraction number = 1.824095e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.589055e-03\n Vprtstp: contraction number = 2.487867e-01\n Vnewton: Using errtol_s: 1641.692880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.980783e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.097026e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.792383e+02\n Vprtstp: contraction number = 4.792383e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.174858e-04\n Vprtstp: contraction number = 2.627258e-01\n Vnewton: Using errtol_s: 431.315051\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.048149e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.160791e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.310006e+02\n Vprtstp: contraction number = 1.310006e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.141203e-04\n Vprtstp: contraction number = 2.733515e-01\n Vnewton: Using errtol_s: 117.900599\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.117473e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.202639e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.696481e+01\n Vprtstp: contraction number = 3.696481e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.220165e-05\n Vprtstp: contraction number = 2.821727e-01\n Vnewton: Using errtol_s: 33.268335\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.187880e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.244902e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.072629e+01\n Vprtstp: contraction number = 1.072629e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.344133e-06\n Vprtstp: contraction number = 2.901756e-01\n Vnewton: Using errtol_s: 9.653659\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.257822e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.286949e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.196371e+00\n Vprtstp: contraction number = 3.196371e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.784497e-06\n Vprtstp: contraction number = 2.979941e-01\n Vnewton: Using errtol_s: 2.876734\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.326307e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.324935e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.745912e-01\n Vprtstp: contraction number = 9.745912e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.490085e-07\n Vprtstp: contraction number = 3.049056e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.004923e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.198030e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.373287e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.635726e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1048,15 +1048,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.190473517167E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.070936043953E+03 kT\n Vpmg_energy:  dielEnergy = 4.033615774534E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.867100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.844800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -1085,151 +1085,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.102615\n+Vacc_SASA: Time elapsed: 0.116287\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.249490e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.590640e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.840300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.693700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.726270e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.625630e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.511002e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.495773e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3098216.768197\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.524976e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.511262e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.288533e+05\n Vprtstp: contraction number = 4.288533e+05\n Vnewton: Attempting damping, relres = 0.287242\n Vnewton: Attempting damping, relres = 0.564665\n Vnewton: Damping accepted, relres = 0.287242\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.872423e-01\n Vprtstp: contraction number = 2.872423e-01\n Vnewton: Using errtol_s: 889939.028652\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.598546e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.559001e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.459682e+04\n Vprtstp: contraction number = 8.459682e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 7.479655e-02\n Vprtstp: contraction number = 2.603953e-01\n Vnewton: Using errtol_s: 231735.935287\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.684331e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.600480e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.140926e+04\n Vprtstp: contraction number = 2.140926e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.197950e-02\n Vprtstp: contraction number = 2.938571e-01\n Vnewton: Using errtol_s: 68097.244831\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.770665e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.643157e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.306461e+03\n Vprtstp: contraction number = 6.306461e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 6.113198e-03\n Vprtstp: contraction number = 2.781319e-01\n Vnewton: Using errtol_s: 18940.013709\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.847478e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.685545e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.039254e+03\n Vprtstp: contraction number = 2.039254e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.310252e-03\n Vprtstp: contraction number = 2.143317e-01\n Vnewton: Using errtol_s: 4059.444466\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.917062e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.723940e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.729156e+02\n Vprtstp: contraction number = 5.729156e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.010708e-04\n Vprtstp: contraction number = 1.534596e-01\n Vnewton: Using errtol_s: 622.960837\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.984110e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.766597e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.140542e+02\n Vprtstp: contraction number = 1.140542e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.330907e-05\n Vprtstp: contraction number = 1.656585e-01\n Vnewton: Using errtol_s: 103.198728\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.051623e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.808866e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.743226e+01\n Vprtstp: contraction number = 2.743226e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.968958e-06\n Vprtstp: contraction number = 2.392429e-01\n Vnewton: Using errtol_s: 24.689560\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.118757e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.846015e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.960222e+00\n Vprtstp: contraction number = 7.960222e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.312364e-06\n Vprtstp: contraction number = 2.901714e-01\n Vnewton: Using errtol_s: 7.164205\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.185951e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.888632e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.414518e+00\n Vprtstp: contraction number = 2.414518e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.013925e-07\n Vprtstp: contraction number = 3.033227e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.332914e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.531683e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.255337e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.450194e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1239,15 +1239,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.097220464694E+01 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.877310278267E+04 kT\n Vpmg_energy:  dielEnergy = 9.366275092847E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.841500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.834000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -1296,160 +1296,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.182726 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.102977\n+Vacc_SASA: Time elapsed: 0.120325\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.609160e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.195100e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.815200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.720400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.710660e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.619770e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.292201e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.984893e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3179322.196917\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.306606e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.999892e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157153e+05\n Vprtstp: contraction number = 5.157153e+05\n Vnewton: Attempting damping, relres = 0.300823\n Vnewton: Attempting damping, relres = 0.575285\n Vnewton: Damping accepted, relres = 0.300823\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.008234e-01\n Vprtstp: contraction number = 3.008234e-01\n Vnewton: Using errtol_s: 956414.609494\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.384617e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.050993e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.112831e+05\n Vprtstp: contraction number = 1.112831e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 7.919694e-02\n Vprtstp: contraction number = 2.632672e-01\n Vnewton: Using errtol_s: 251792.580740\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.471094e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.091987e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.912764e+04\n Vprtstp: contraction number = 2.912764e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.322957e-02\n Vprtstp: contraction number = 2.933140e-01\n Vnewton: Using errtol_s: 73854.286564\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.557346e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.133890e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.683374e+03\n Vprtstp: contraction number = 8.683374e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 6.478032e-03\n Vprtstp: contraction number = 2.788701e-01\n Vnewton: Using errtol_s: 20595.750772\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.638978e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.175785e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.778111e+03\n Vprtstp: contraction number = 2.778111e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.439717e-03\n Vprtstp: contraction number = 2.222460e-01\n Vnewton: Using errtol_s: 4577.322906\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.712220e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.216851e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.948966e+02\n Vprtstp: contraction number = 7.948966e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.541519e-04\n Vprtstp: contraction number = 1.765291e-01\n Vnewton: Using errtol_s: 808.030623\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.783507e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.259109e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.884080e+02\n Vprtstp: contraction number = 1.884080e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.345432e-05\n Vprtstp: contraction number = 2.103243e-01\n Vnewton: Using errtol_s: 169.948515\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.853700e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.297024e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.248467e+01\n Vprtstp: contraction number = 5.248467e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.485742e-05\n Vprtstp: contraction number = 2.779462e-01\n Vnewton: Using errtol_s: 47.236538\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.925096e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.338720e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.636645e+01\n Vprtstp: contraction number = 1.636645e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.633006e-06\n Vprtstp: contraction number = 3.118310e-01\n Vnewton: Using errtol_s: 14.729818\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.996137e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.379740e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.289991e+00\n Vprtstp: contraction number = 5.289991e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.497487e-06\n Vprtstp: contraction number = 3.232214e-01\n Vnewton: Using errtol_s: 4.760992\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.066622e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.421423e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.736329e+00\n Vprtstp: contraction number = 1.736329e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.915187e-07\n Vprtstp: contraction number = 3.282291e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.336620e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.533324e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.702174e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.897270e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1459,29 +1459,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.094905051954E+01 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.139048085008E+04 kT\n Vpmg_energy:  dielEnergy = 1.067494556843E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.832000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.808700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.210910e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.536798e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:38:17 2025\n+# Creation Date and Time:  Sun Jan  7 09:46:31 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -1751,151 +1751,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.185727\n+Vacc_SASA: Time elapsed: 0.226713\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.320260e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.767740e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.856000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.442500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.733040e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.687170e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.478960e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.244590e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2974958.994733\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.859270e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.867550e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.870275e+05\n Vprtstp: contraction number = 3.870275e+05\n Vnewton: Attempting damping, relres = 0.153059\n Vnewton: Attempting damping, relres = 0.557808\n Vnewton: Damping accepted, relres = 0.153059\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.530588e-01\n Vprtstp: contraction number = 1.530588e-01\n Vnewton: Using errtol_s: 455343.743026\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.541050e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.497194e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.695400e+04\n Vprtstp: contraction number = 6.695400e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.920739e-02\n Vprtstp: contraction number = 1.908246e-01\n Vnewton: Using errtol_s: 86890.793846\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.390672e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.918074e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.482146e+04\n Vprtstp: contraction number = 1.482146e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.545819e-03\n Vprtstp: contraction number = 2.241151e-01\n Vnewton: Using errtol_s: 19473.541826\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.249509e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.339202e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.884267e+03\n Vprtstp: contraction number = 3.884267e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.453691e-03\n Vprtstp: contraction number = 2.220793e-01\n Vnewton: Using errtol_s: 4324.671146\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.057485e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.750570e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.057768e+03\n Vprtstp: contraction number = 1.057768e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.284783e-04\n Vprtstp: contraction number = 2.259615e-01\n Vnewton: Using errtol_s: 977.209364\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.835546e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.163456e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.866048e+02\n Vprtstp: contraction number = 2.866048e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 8.672414e-05\n Vprtstp: contraction number = 2.640179e-01\n Vnewton: Using errtol_s: 258.000773\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.618264e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.598061e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.283684e+01\n Vprtstp: contraction number = 8.283684e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.506027e-05\n Vprtstp: contraction number = 2.889653e-01\n Vnewton: Using errtol_s: 74.553271\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.397173e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.065561e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.472736e+01\n Vprtstp: contraction number = 2.472736e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.480652e-06\n Vprtstp: contraction number = 2.985065e-01\n Vnewton: Using errtol_s: 22.254632\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.184702e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.477397e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.490971e+00\n Vprtstp: contraction number = 7.490971e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.266207e-06\n Vprtstp: contraction number = 3.029425e-01\n Vnewton: Using errtol_s: 6.741874\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.962034e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.909955e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.293363e+00\n Vprtstp: contraction number = 2.293363e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.938001e-07\n Vprtstp: contraction number = 3.061503e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.101827e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.302719e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.404014e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.613896e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1905,15 +1905,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.155593608884E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.568720386421E+04 kT\n Vpmg_energy:  dielEnergy = 1.283293314758E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.827300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.818800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -1962,160 +1962,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.103051 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.185760\n+Vacc_SASA: Time elapsed: 0.206024\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.788270e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.904950e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.737700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.762000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.652900e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.654630e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.242934e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.039862e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3077114.923847\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.380492e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.174355e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.742704e+05\n Vprtstp: contraction number = 4.742704e+05\n Vnewton: Attempting damping, relres = 0.172865\n Vnewton: Attempting damping, relres = 0.568730\n Vnewton: Damping accepted, relres = 0.172865\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.728651e-01\n Vprtstp: contraction number = 1.728651e-01\n Vnewton: Using errtol_s: 531925.831070\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.025909e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.708637e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.143761e+04\n Vprtstp: contraction number = 9.143761e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.526713e-02\n Vprtstp: contraction number = 2.040153e-01\n Vnewton: Using errtol_s: 108521.009470\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.110914e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.109574e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.196947e+04\n Vprtstp: contraction number = 2.196947e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.376912e-03\n Vprtstp: contraction number = 2.375275e-01\n Vnewton: Using errtol_s: 25776.719868\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.194563e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.507076e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.034692e+03\n Vprtstp: contraction number = 6.034692e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.018356e-03\n Vprtstp: contraction number = 2.409428e-01\n Vnewton: Using errtol_s: 6210.714220\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.278020e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.952751e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.718760e+03\n Vprtstp: contraction number = 1.718760e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.089360e-04\n Vprtstp: contraction number = 2.521537e-01\n Vnewton: Using errtol_s: 1566.054712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.359916e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.348579e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.951703e+02\n Vprtstp: contraction number = 4.951703e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.448376e-04\n Vprtstp: contraction number = 2.845889e-01\n Vnewton: Using errtol_s: 445.681818\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.440857e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.749169e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.503700e+02\n Vprtstp: contraction number = 1.503700e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.398054e-05\n Vprtstp: contraction number = 3.036542e-01\n Vnewton: Using errtol_s: 135.333176\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.523480e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.164801e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725124e+01\n Vprtstp: contraction number = 4.725124e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.382013e-05\n Vprtstp: contraction number = 3.142328e-01\n Vnewton: Using errtol_s: 42.526127\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.605865e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.592803e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.517823e+01\n Vprtstp: contraction number = 1.517823e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.439356e-06\n Vprtstp: contraction number = 3.212239e-01\n Vnewton: Using errtol_s: 13.660408\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.687390e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.978313e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.961627e+00\n Vprtstp: contraction number = 4.961627e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.451185e-06\n Vprtstp: contraction number = 3.268910e-01\n Vnewton: Using errtol_s: 4.465464\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.770088e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.039100e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.644451e+00\n Vprtstp: contraction number = 1.644451e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.809720e-07\n Vprtstp: contraction number = 3.314339e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.203353e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.394299e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.696567e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.896379e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2125,17 +2125,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.136719459534E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.953334472721E+04 kT\n Vpmg_energy:  dielEnergy = 1.475599755841E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.801300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.786800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -2162,151 +2162,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.064830\n+Vacc_SASA: Time elapsed: 0.073845\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.514470e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.352350e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.898500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.745200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.784300e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.634540e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.967828e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.200049e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 847635.298627\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.981837e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.213079e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.156652e+05\n Vprtstp: contraction number = 1.156652e+05\n Vnewton: Attempting damping, relres = 0.129563\n Vnewton: Attempting damping, relres = 0.559453\n Vnewton: Damping accepted, relres = 0.129563\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.295633e-01\n Vprtstp: contraction number = 1.295633e-01\n Vnewton: Using errtol_s: 109822.397033\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.055265e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.263605e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.025826e+04\n Vprtstp: contraction number = 2.025826e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.180592e-02\n Vprtstp: contraction number = 1.683033e-01\n Vnewton: Using errtol_s: 18483.468929\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.120936e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.304291e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.307643e+03\n Vprtstp: contraction number = 4.307643e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.574915e-03\n Vprtstp: contraction number = 2.098015e-01\n Vnewton: Using errtol_s: 3877.859579\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.186978e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.345224e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.042197e+03\n Vprtstp: contraction number = 1.042197e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.106587e-03\n Vprtstp: contraction number = 2.418813e-01\n Vnewton: Using errtol_s: 937.981802\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.251847e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.387570e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.719312e+02\n Vprtstp: contraction number = 2.719312e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 2.887307e-04\n Vprtstp: contraction number = 2.609201e-01\n Vnewton: Using errtol_s: 244.738306\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.317727e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.429341e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.411670e+01\n Vprtstp: contraction number = 7.411670e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 7.869545e-05\n Vprtstp: contraction number = 2.725566e-01\n Vnewton: Using errtol_s: 66.705044\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.382468e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.470376e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.079247e+01\n Vprtstp: contraction number = 2.079247e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.207697e-05\n Vprtstp: contraction number = 2.805368e-01\n Vnewton: Using errtol_s: 18.713222\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.447885e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.511366e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.958188e+00\n Vprtstp: contraction number = 5.958188e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.326270e-06\n Vprtstp: contraction number = 2.865551e-01\n Vnewton: Using errtol_s: 5.362370\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.512997e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.553132e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.735927e+00\n Vprtstp: contraction number = 1.735927e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.843168e-06\n Vprtstp: contraction number = 2.913515e-01\n Vnewton: Using errtol_s: 1.562335\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.578795e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.593198e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.124069e-01\n Vprtstp: contraction number = 5.124069e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 5.440621e-07\n Vprtstp: contraction number = 2.951777e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.672120e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.877461e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.251380e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.448670e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2316,15 +2316,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.454852948136E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.836680918650E+03 kT\n Vpmg_energy:  dielEnergy = 3.416367945808E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.883200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.860100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -2373,149 +2373,149 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0108218 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.062407\n+Vacc_SASA: Time elapsed: 0.075845\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.755800e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.713900e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.783000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.736900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.691740e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.615460e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.674555e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.673917e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 886073.910303\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.688735e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.689488e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.444647e+05\n Vprtstp: contraction number = 1.444647e+05\n Vnewton: Attempting damping, relres = 0.152834\n Vnewton: Attempting damping, relres = 0.571521\n Vnewton: Damping accepted, relres = 0.152834\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.528340e-01\n Vprtstp: contraction number = 1.528340e-01\n Vnewton: Using errtol_s: 135422.205259\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.763088e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.740035e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.834174e+04\n Vprtstp: contraction number = 2.834174e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.906007e-02\n Vprtstp: contraction number = 1.901414e-01\n Vnewton: Using errtol_s: 25749.370228\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.830947e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.783371e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.624232e+03\n Vprtstp: contraction number = 6.624232e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.729649e-03\n Vprtstp: contraction number = 2.315772e-01\n Vnewton: Using errtol_s: 5962.966787\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.897491e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.826982e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.678296e+03\n Vprtstp: contraction number = 1.678296e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.704684e-03\n Vprtstp: contraction number = 2.533095e-01\n Vnewton: Using errtol_s: 1510.476086\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.965824e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.870134e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.484576e+02\n Vprtstp: contraction number = 4.484576e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.555067e-04\n Vprtstp: contraction number = 2.672089e-01\n Vnewton: Using errtol_s: 403.612606\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.032539e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.911180e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.244400e+02\n Vprtstp: contraction number = 1.244400e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.263959e-04\n Vprtstp: contraction number = 2.774841e-01\n Vnewton: Using errtol_s: 111.996087\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.099222e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.951900e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.556127e+01\n Vprtstp: contraction number = 3.556127e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.612018e-05\n Vprtstp: contraction number = 2.857702e-01\n Vnewton: Using errtol_s: 32.005148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.166839e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.993126e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.042544e+01\n Vprtstp: contraction number = 1.042544e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.058929e-05\n Vprtstp: contraction number = 2.931684e-01\n Vnewton: Using errtol_s: 9.382897\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.234433e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.034264e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.131407e+00\n Vprtstp: contraction number = 3.131407e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.180622e-06\n Vprtstp: contraction number = 3.003620e-01\n Vnewton: Using errtol_s: 2.818266\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.301568e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.075477e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.605131e-01\n Vprtstp: contraction number = 9.605131e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 9.756091e-07\n Vprtstp: contraction number = 3.067353e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.848962e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.044328e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.365914e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.560305e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2525,17 +2525,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.447897988359E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.069186882543E+03 kT\n Vpmg_energy:  dielEnergy = 4.032629667471E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.853000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.858000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -2562,151 +2562,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.102154\n+Vacc_SASA: Time elapsed: 0.117715\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.218500e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.590730e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.746900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.761900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.607540e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.646540e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.481068e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.248432e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2425643.021917\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.494974e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.263487e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.395849e+05\n Vprtstp: contraction number = 3.395849e+05\n Vnewton: Attempting damping, relres = 0.271218\n Vnewton: Attempting damping, relres = 0.565917\n Vnewton: Damping accepted, relres = 0.271218\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.712177e-01\n Vprtstp: contraction number = 2.712177e-01\n Vnewton: Using errtol_s: 657877.293778\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.566563e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.313404e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.802706e+04\n Vprtstp: contraction number = 6.802706e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 6.815619e-02\n Vprtstp: contraction number = 2.512970e-01\n Vnewton: Using errtol_s: 165322.578504\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.651278e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.353633e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.706699e+04\n Vprtstp: contraction number = 1.706699e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.896759e-02\n Vprtstp: contraction number = 2.782960e-01\n Vnewton: Using errtol_s: 46008.609864\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.733456e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.397717e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.017255e+03\n Vprtstp: contraction number = 5.017255e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 4.765082e-03\n Vprtstp: contraction number = 2.512223e-01\n Vnewton: Using errtol_s: 11558.387363\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.805265e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.438623e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.518068e+03\n Vprtstp: contraction number = 1.518068e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 8.818480e-04\n Vprtstp: contraction number = 1.850646e-01\n Vnewton: Using errtol_s: 2139.048483\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.872467e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.478923e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.762132e+02\n Vprtstp: contraction number = 3.762132e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.458866e-04\n Vprtstp: contraction number = 1.654328e-01\n Vnewton: Using errtol_s: 353.868838\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.939713e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.519902e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.902937e+01\n Vprtstp: contraction number = 8.902937e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.304341e-05\n Vprtstp: contraction number = 2.265007e-01\n Vnewton: Using errtol_s: 80.151522\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.007385e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.560157e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.527505e+01\n Vprtstp: contraction number = 2.527505e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.377960e-06\n Vprtstp: contraction number = 2.838073e-01\n Vnewton: Using errtol_s: 22.747583\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.073287e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.600079e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.628220e+00\n Vprtstp: contraction number = 7.628220e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.830342e-06\n Vprtstp: contraction number = 3.018078e-01\n Vnewton: Using errtol_s: 6.865399\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.140026e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.641004e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.330827e+00\n Vprtstp: contraction number = 2.330827e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.648198e-07\n Vprtstp: contraction number = 3.055531e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.150100e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.336236e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.273318e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.463761e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2716,15 +2716,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.060833611390E+01 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.876241790075E+04 kT\n Vpmg_energy:  dielEnergy = 9.364173698262E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.839700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.827800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -2773,160 +2773,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0855205 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.104434\n+Vacc_SASA: Time elapsed: 0.120609\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.580170e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.239600e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.756500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.745400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.682040e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.623990e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.243448e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.739371e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2500270.754638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.257393e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.752954e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160810e+05\n Vprtstp: contraction number = 4.160810e+05\n Vnewton: Attempting damping, relres = 0.288431\n Vnewton: Attempting damping, relres = 0.577725\n Vnewton: Damping accepted, relres = 0.288431\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.884309e-01\n Vprtstp: contraction number = 2.884309e-01\n Vnewton: Using errtol_s: 721155.339967\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.334094e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.804675e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.034405e+04\n Vprtstp: contraction number = 9.034405e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 7.349134e-02\n Vprtstp: contraction number = 2.547970e-01\n Vnewton: Using errtol_s: 183748.247493\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.418455e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.846422e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.360950e+04\n Vprtstp: contraction number = 2.360950e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.053916e-02\n Vprtstp: contraction number = 2.794773e-01\n Vnewton: Using errtol_s: 51353.458771\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.502212e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.888088e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.072490e+03\n Vprtstp: contraction number = 7.072490e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 5.268603e-03\n Vprtstp: contraction number = 2.565150e-01\n Vnewton: Using errtol_s: 13172.933437\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.577456e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.928053e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.172100e+03\n Vprtstp: contraction number = 2.172100e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.067554e-03\n Vprtstp: contraction number = 2.026257e-01\n Vnewton: Using errtol_s: 2669.175106\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.648096e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.969620e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.851792e+02\n Vprtstp: contraction number = 5.851792e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.156116e-04\n Vprtstp: contraction number = 2.019677e-01\n Vnewton: Using errtol_s: 539.087280\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.717787e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.012242e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.590368e+02\n Vprtstp: contraction number = 1.590368e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.725368e-05\n Vprtstp: contraction number = 2.655409e-01\n Vnewton: Using errtol_s: 143.149712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.787307e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.051131e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.862838e+01\n Vprtstp: contraction number = 4.862838e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.750434e-05\n Vprtstp: contraction number = 3.057329e-01\n Vnewton: Using errtol_s: 43.765584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.857236e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.089469e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.560157e+01\n Vprtstp: contraction number = 1.560157e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.615959e-06\n Vprtstp: contraction number = 3.208324e-01\n Vnewton: Using errtol_s: 14.041419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.927901e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.133043e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.091636e+00\n Vprtstp: contraction number = 5.091636e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.832791e-06\n Vprtstp: contraction number = 3.263540e-01\n Vnewton: Using errtol_s: 4.582473\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.997981e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.171070e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.679382e+00\n Vprtstp: contraction number = 1.679382e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.045119e-07\n Vprtstp: contraction number = 3.298314e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.146462e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.340771e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.662614e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.854097e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2936,29 +2936,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.058843361489E+01 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.137979732190E+04 kT\n Vpmg_energy:  dielEnergy = 1.067286106944E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.832900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.797400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.141777e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.287686e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:39:09 2025\n+# Creation Date and Time:  Sun Jan  7 09:46:42 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -3228,151 +3228,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.184846\n+Vacc_SASA: Time elapsed: 0.234580\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.305280e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.682620e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.772800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.921600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.697630e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.589830e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.421510e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.995230e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2729151.378915\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.835900e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.443810e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.548080e+05\n Vprtstp: contraction number = 3.548080e+05\n Vnewton: Attempting damping, relres = 0.149964\n Vnewton: Attempting damping, relres = 0.557619\n Vnewton: Damping accepted, relres = 0.149964\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.499638e-01\n Vprtstp: contraction number = 1.499638e-01\n Vnewton: Using errtol_s: 409273.850655\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.527975e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.434927e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.220624e+04\n Vprtstp: contraction number = 6.220624e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.835999e-02\n Vprtstp: contraction number = 1.891123e-01\n Vnewton: Using errtol_s: 77398.710345\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.363264e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.872954e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.402989e+04\n Vprtstp: contraction number = 1.402989e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.278471e-03\n Vprtstp: contraction number = 2.213848e-01\n Vnewton: Using errtol_s: 17134.898633\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.217226e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.266528e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.695573e+03\n Vprtstp: contraction number = 3.695573e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.396538e-03\n Vprtstp: contraction number = 2.224328e-01\n Vnewton: Using errtol_s: 3811.362986\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.002905e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.659638e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.003191e+03\n Vprtstp: contraction number = 1.003191e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.340894e-04\n Vprtstp: contraction number = 2.392269e-01\n Vnewton: Using errtol_s: 911.780505\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.796970e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.095399e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.777519e+02\n Vprtstp: contraction number = 2.777519e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.159963e-05\n Vprtstp: contraction number = 2.741770e-01\n Vnewton: Using errtol_s: 249.989261\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.581203e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.490360e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.121282e+01\n Vprtstp: contraction number = 8.121282e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.678181e-05\n Vprtstp: contraction number = 2.923790e-01\n Vnewton: Using errtol_s: 73.091601\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.387819e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.925005e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.430204e+01\n Vprtstp: contraction number = 2.430204e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.014155e-06\n Vprtstp: contraction number = 2.992388e-01\n Vnewton: Using errtol_s: 21.871842\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.174195e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.351503e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.369042e+00\n Vprtstp: contraction number = 7.369042e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.430110e-06\n Vprtstp: contraction number = 3.032272e-01\n Vnewton: Using errtol_s: 6.632138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.956838e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.760632e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.256893e+00\n Vprtstp: contraction number = 2.256893e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.442621e-07\n Vprtstp: contraction number = 3.062668e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.113778e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.310956e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.304769e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.498128e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -3382,15 +3382,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.061471335398E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.568309380303E+04 kT\n Vpmg_energy:  dielEnergy = 1.283186160859E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.836700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.800100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -3439,160 +3439,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0651756 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.184183\n+Vacc_SASA: Time elapsed: 0.204484\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.845180e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.872650e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.892800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.672100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.768180e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.613150e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.267202e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.905500e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2820294.276955\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.411449e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.073478e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.376310e+05\n Vprtstp: contraction number = 4.376310e+05\n Vnewton: Attempting damping, relres = 0.171074\n Vnewton: Attempting damping, relres = 0.569073\n Vnewton: Damping accepted, relres = 0.171074\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.710740e-01\n Vprtstp: contraction number = 1.710740e-01\n Vnewton: Using errtol_s: 482478.932943\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.030615e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.550368e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.516733e+04\n Vprtstp: contraction number = 8.516733e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.468956e-02\n Vprtstp: contraction number = 2.027752e-01\n Vnewton: Using errtol_s: 97834.754534\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.115832e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.974717e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.072493e+04\n Vprtstp: contraction number = 2.072493e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.178682e-03\n Vprtstp: contraction number = 2.357678e-01\n Vnewton: Using errtol_s: 23066.288642\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.198913e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.394813e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.715545e+03\n Vprtstp: contraction number = 5.715545e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.982874e-03\n Vprtstp: contraction number = 2.424442e-01\n Vnewton: Using errtol_s: 5592.288694\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.282448e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.781018e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.627358e+03\n Vprtstp: contraction number = 1.627358e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.213861e-04\n Vprtstp: contraction number = 2.629446e-01\n Vnewton: Using errtol_s: 1470.462342\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.364793e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.210874e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.759299e+02\n Vprtstp: contraction number = 4.759299e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.518795e-04\n Vprtstp: contraction number = 2.912995e-01\n Vnewton: Using errtol_s: 428.344902\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.448495e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.594505e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.460718e+02\n Vprtstp: contraction number = 1.460718e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.661385e-05\n Vprtstp: contraction number = 3.069133e-01\n Vnewton: Using errtol_s: 131.464764\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.532713e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.019425e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.608450e+01\n Vprtstp: contraction number = 4.608450e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.470629e-05\n Vprtstp: contraction number = 3.154918e-01\n Vnewton: Using errtol_s: 41.476059\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.616380e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.413850e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.483594e+01\n Vprtstp: contraction number = 1.483594e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.734380e-06\n Vprtstp: contraction number = 3.219290e-01\n Vnewton: Using errtol_s: 13.352345\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.697433e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.849198e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.855098e+00\n Vprtstp: contraction number = 4.855098e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.549338e-06\n Vprtstp: contraction number = 3.272525e-01\n Vnewton: Using errtol_s: 4.369588\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.779563e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.026793e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.609852e+00\n Vprtstp: contraction number = 1.609852e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.137291e-07\n Vprtstp: contraction number = 3.315798e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.252958e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.458182e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.680083e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.873188e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -3602,17 +3602,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.043656925356E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.952923600964E+04 kT\n Vpmg_energy:  dielEnergy = 1.475493408028E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.783000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.779700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -3639,151 +3639,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.063336\n+Vacc_SASA: Time elapsed: 0.075972\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.482910e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.390060e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.679400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.713500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.549070e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.597810e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.967086e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.183796e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 782805.209515\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.980790e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.199244e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066964e+05\n Vprtstp: contraction number = 1.066964e+05\n Vnewton: Attempting damping, relres = 0.130466\n Vnewton: Attempting damping, relres = 0.559276\n Vnewton: Damping accepted, relres = 0.130466\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.304657e-01\n Vprtstp: contraction number = 1.304657e-01\n Vnewton: Using errtol_s: 102129.196068\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.052666e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.249768e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.906966e+04\n Vprtstp: contraction number = 1.906966e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.228836e-02\n Vprtstp: contraction number = 1.708370e-01\n Vnewton: Using errtol_s: 17447.447142\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.116955e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.285847e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.144180e+03\n Vprtstp: contraction number = 4.144180e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.766221e-03\n Vprtstp: contraction number = 2.138435e-01\n Vnewton: Using errtol_s: 3731.022666\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.180873e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.326424e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018149e+03\n Vprtstp: contraction number = 1.018149e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.170583e-03\n Vprtstp: contraction number = 2.455999e-01\n Vnewton: Using errtol_s: 916.338711\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.245289e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.367316e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.682787e+02\n Vprtstp: contraction number = 2.682787e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.084434e-04\n Vprtstp: contraction number = 2.634955e-01\n Vnewton: Using errtol_s: 241.451081\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.310891e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.407305e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.355327e+01\n Vprtstp: contraction number = 7.355327e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 8.456504e-05\n Vprtstp: contraction number = 2.741672e-01\n Vnewton: Using errtol_s: 66.197957\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.375433e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.447822e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.070399e+01\n Vprtstp: contraction number = 2.070399e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.380361e-05\n Vprtstp: contraction number = 2.814829e-01\n Vnewton: Using errtol_s: 18.633591\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.440811e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.487875e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.943814e+00\n Vprtstp: contraction number = 5.943814e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.833671e-06\n Vprtstp: contraction number = 2.870855e-01\n Vnewton: Using errtol_s: 5.349433\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.505099e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.528177e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.733432e+00\n Vprtstp: contraction number = 1.733432e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.992946e-06\n Vprtstp: contraction number = 2.916363e-01\n Vnewton: Using errtol_s: 1.560089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.568474e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.569629e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.119221e-01\n Vprtstp: contraction number = 5.119221e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 5.885626e-07\n Vprtstp: contraction number = 2.953228e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.554971e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.734320e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.192125e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.385513e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -3793,15 +3793,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.580382874271E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.835549724492E+03 kT\n Vpmg_energy:  dielEnergy = 3.415749841387E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.872800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.856700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -3850,160 +3850,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00827481 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.062339\n+Vacc_SASA: Time elapsed: 0.074860\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.706990e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.737860e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.736000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.650400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.722790e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.550180e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.661904e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.650564e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 817942.139336\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.676079e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.663994e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.333917e+05\n Vprtstp: contraction number = 1.333917e+05\n Vnewton: Attempting damping, relres = 0.153834\n Vnewton: Attempting damping, relres = 0.571434\n Vnewton: Damping accepted, relres = 0.153834\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.538338e-01\n Vprtstp: contraction number = 1.538338e-01\n Vnewton: Using errtol_s: 125827.150717\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.750857e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.713987e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.649228e+04\n Vprtstp: contraction number = 2.649228e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.948474e-02\n Vprtstp: contraction number = 1.916662e-01\n Vnewton: Using errtol_s: 24116.815003\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.816534e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.754649e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.270875e+03\n Vprtstp: contraction number = 6.270875e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.901762e-03\n Vprtstp: contraction number = 2.340791e-01\n Vnewton: Using errtol_s: 5645.242129\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.882371e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.795884e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.605106e+03\n Vprtstp: contraction number = 1.605106e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.766147e-03\n Vprtstp: contraction number = 2.558981e-01\n Vnewton: Using errtol_s: 1444.606457\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.949594e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.836831e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.329441e+02\n Vprtstp: contraction number = 4.329441e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.763791e-04\n Vprtstp: contraction number = 2.697278e-01\n Vnewton: Using errtol_s: 389.650539\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.016716e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.874264e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.211228e+02\n Vprtstp: contraction number = 1.211228e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.332742e-04\n Vprtstp: contraction number = 2.797649e-01\n Vnewton: Using errtol_s: 109.010550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.084022e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.915159e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.484891e+01\n Vprtstp: contraction number = 3.484891e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.834504e-05\n Vprtstp: contraction number = 2.877155e-01\n Vnewton: Using errtol_s: 31.364026\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.150790e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.955694e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.027201e+01\n Vprtstp: contraction number = 1.027201e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.130252e-05\n Vprtstp: contraction number = 2.947583e-01\n Vnewton: Using errtol_s: 9.244807\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.218152e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.997303e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.098070e+00\n Vprtstp: contraction number = 3.098070e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.408876e-06\n Vprtstp: contraction number = 3.016032e-01\n Vnewton: Using errtol_s: 2.788263\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.285933e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.034534e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.532281e-01\n Vprtstp: contraction number = 9.532281e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.048858e-06\n Vprtstp: contraction number = 3.076845e-01\n Vnewton: Using errtol_s: 0.857905\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.352869e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.075632e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.981595e-01\n Vprtstp: contraction number = 2.981595e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.280716e-07\n Vprtstp: contraction number = 3.127892e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.485580e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.684534e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.586368e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.765245e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -4013,15 +4013,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.573110826930E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.068060919052E+03 kT\n Vpmg_energy:  dielEnergy = 4.032015460715E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.860300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.842400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -4050,151 +4050,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.104283\n+Vacc_SASA: Time elapsed: 0.117002\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.207020e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.599520e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.703300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.726700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.566440e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.607300e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.530037e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.244354e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2117741.361264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.543864e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.259743e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.981667e+05\n Vprtstp: contraction number = 2.981667e+05\n Vnewton: Attempting damping, relres = 0.251946\n Vnewton: Attempting damping, relres = 0.566227\n Vnewton: Damping accepted, relres = 0.251946\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.519462e-01\n Vprtstp: contraction number = 2.519462e-01\n Vnewton: Using errtol_s: 533556.965989\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.614779e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.308861e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.927315e+04\n Vprtstp: contraction number = 5.927315e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 6.069562e-02\n Vprtstp: contraction number = 2.409070e-01\n Vnewton: Using errtol_s: 128537.620946\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.698421e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.352718e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.480174e+04\n Vprtstp: contraction number = 1.480174e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.600227e-02\n Vprtstp: contraction number = 2.636478e-01\n Vnewton: Using errtol_s: 33888.662126\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.774556e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.391622e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.318636e+03\n Vprtstp: contraction number = 4.318636e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.683613e-03\n Vprtstp: contraction number = 2.301932e-01\n Vnewton: Using errtol_s: 7800.938716\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.841940e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.434611e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.240563e+03\n Vprtstp: contraction number = 1.240563e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.541706e-04\n Vprtstp: contraction number = 1.775894e-01\n Vnewton: Using errtol_s: 1385.364119\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.907859e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.475364e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.070828e+02\n Vprtstp: contraction number = 3.070828e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.315622e-04\n Vprtstp: contraction number = 2.011130e-01\n Vnewton: Using errtol_s: 278.614703\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.974419e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.514448e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.245841e+01\n Vprtstp: contraction number = 8.245841e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.504428e-05\n Vprtstp: contraction number = 2.663704e-01\n Vnewton: Using errtol_s: 74.214712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.039216e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.554873e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.449789e+01\n Vprtstp: contraction number = 2.449789e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.041114e-05\n Vprtstp: contraction number = 2.970854e-01\n Vnewton: Using errtol_s: 22.048109\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.103832e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.596172e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.450269e+00\n Vprtstp: contraction number = 7.450269e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.166223e-06\n Vprtstp: contraction number = 3.041187e-01\n Vnewton: Using errtol_s: 6.705242\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.169097e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.637537e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.280137e+00\n Vprtstp: contraction number = 2.280137e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 9.690153e-07\n Vprtstp: contraction number = 3.060477e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.947746e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.128975e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.242844e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.436124e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -4204,15 +4204,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.019051099333E+01 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.875636108518E+04 kT\n Vpmg_energy:  dielEnergy = 9.362891956470E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.829200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.822200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -4261,160 +4261,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0483679 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.101365\n+Vacc_SASA: Time elapsed: 0.119425\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.606390e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.160420e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.592300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.695400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.750920e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.595670e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.274413e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.731646e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2182522.884057\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.288884e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.747861e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.686053e+05\n Vprtstp: contraction number = 3.686053e+05\n Vnewton: Attempting damping, relres = 0.272056\n Vnewton: Attempting damping, relres = 0.578831\n Vnewton: Damping accepted, relres = 0.272056\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.720560e-01\n Vprtstp: contraction number = 2.720560e-01\n Vnewton: Using errtol_s: 593768.373592\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.364724e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.797054e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.934239e+04\n Vprtstp: contraction number = 7.934239e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 6.680635e-02\n Vprtstp: contraction number = 2.455611e-01\n Vnewton: Using errtol_s: 145806.393631\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.447541e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.836844e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.075932e+04\n Vprtstp: contraction number = 2.075932e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.784022e-02\n Vprtstp: contraction number = 2.670438e-01\n Vnewton: Using errtol_s: 38936.692163\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.528063e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.877358e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.202423e+03\n Vprtstp: contraction number = 6.202423e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 4.287010e-03\n Vprtstp: contraction number = 2.403003e-01\n Vnewton: Using errtol_s: 9356.498262\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.600397e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.918311e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.844032e+03\n Vprtstp: contraction number = 1.844032e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 8.713644e-04\n Vprtstp: contraction number = 2.032569e-01\n Vnewton: Using errtol_s: 1901.772758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.669823e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.960261e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.035865e+02\n Vprtstp: contraction number = 5.035865e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.084187e-04\n Vprtstp: contraction number = 2.391867e-01\n Vnewton: Using errtol_s: 454.878668\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.738229e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.996773e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.482404e+02\n Vprtstp: contraction number = 1.482404e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 6.113004e-05\n Vprtstp: contraction number = 2.933039e-01\n Vnewton: Using errtol_s: 133.417702\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.806050e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.038012e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.685160e+01\n Vprtstp: contraction number = 4.685160e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.932006e-05\n Vprtstp: contraction number = 3.160485e-01\n Vnewton: Using errtol_s: 42.166463\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.874629e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.078980e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.516259e+01\n Vprtstp: contraction number = 1.516259e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 6.252549e-06\n Vprtstp: contraction number = 3.236300e-01\n Vnewton: Using errtol_s: 13.646331\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.943482e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.120710e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.968000e+00\n Vprtstp: contraction number = 4.968000e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.048639e-06\n Vprtstp: contraction number = 3.276485e-01\n Vnewton: Using errtol_s: 4.471200\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.011258e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.160114e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.642278e+00\n Vprtstp: contraction number = 1.642278e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.772208e-07\n Vprtstp: contraction number = 3.305711e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.959135e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.173236e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.611006e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.803995e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -4424,29 +4424,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.017305990862E+01 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.137374131733E+04 kT\n Vpmg_energy:  dielEnergy = 1.067158704261E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.826500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.794600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.153755e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.273110e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:39:57 2025\n+# Creation Date and Time:  Sun Jan  7 09:46:52 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -4716,151 +4716,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.185836\n+Vacc_SASA: Time elapsed: 0.221051\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.302020e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.470940e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.760000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.301700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.595340e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.616990e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.301380e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.877380e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2581577.235420\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.678010e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.573200e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.353899e+05\n Vprtstp: contraction number = 3.353899e+05\n Vnewton: Attempting damping, relres = 0.146634\n Vnewton: Attempting damping, relres = 0.557407\n Vnewton: Damping accepted, relres = 0.146634\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.466339e-01\n Vprtstp: contraction number = 1.466339e-01\n Vnewton: Using errtol_s: 378546.858038\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.498728e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.417446e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.923639e+04\n Vprtstp: contraction number = 5.923639e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.740677e-02\n Vprtstp: contraction number = 1.869061e-01\n Vnewton: Using errtol_s: 70752.704235\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.298435e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.845899e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.351296e+04\n Vprtstp: contraction number = 1.351296e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.004523e-03\n Vprtstp: contraction number = 2.190890e-01\n Vnewton: Using errtol_s: 15501.138648\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.113235e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.270448e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.562530e+03\n Vprtstp: contraction number = 3.562530e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.351206e-03\n Vprtstp: contraction number = 2.250314e-01\n Vnewton: Using errtol_s: 3488.243698\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.909848e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.670513e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.669348e+02\n Vprtstp: contraction number = 9.669348e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.383252e-04\n Vprtstp: contraction number = 2.503875e-01\n Vnewton: Using errtol_s: 873.412615\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.674307e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.111792e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.719290e+02\n Vprtstp: contraction number = 2.719290e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.480245e-05\n Vprtstp: contraction number = 2.802110e-01\n Vnewton: Using errtol_s: 244.739841\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.446457e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.519053e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.995844e+01\n Vprtstp: contraction number = 7.995844e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.787545e-05\n Vprtstp: contraction number = 2.940373e-01\n Vnewton: Using errtol_s: 71.962638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.231287e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.946177e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.395977e+01\n Vprtstp: contraction number = 2.395977e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.352954e-06\n Vprtstp: contraction number = 2.996527e-01\n Vnewton: Using errtol_s: 21.563797\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.024051e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.368878e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.269734e+00\n Vprtstp: contraction number = 7.269734e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.534405e-06\n Vprtstp: contraction number = 3.034141e-01\n Vnewton: Using errtol_s: 6.542761\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.800521e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.783202e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.227052e+00\n Vprtstp: contraction number = 2.227052e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.764038e-07\n Vprtstp: contraction number = 3.063457e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.956919e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.141947e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.359003e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.561795e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -4870,15 +4870,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.906130010440E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.568022982352E+04 kT\n Vpmg_energy:  dielEnergy = 1.283111172254E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.821400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.824700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -4927,160 +4927,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.046103 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.186661\n+Vacc_SASA: Time elapsed: 0.201475\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.817560e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.959720e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.772000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.851700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.692920e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.736030e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.087652e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.971922e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2663765.095172\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.230597e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.128847e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.151111e+05\n Vprtstp: contraction number = 4.151111e+05\n Vnewton: Attempting damping, relres = 0.168665\n Vnewton: Attempting damping, relres = 0.569219\n Vnewton: Damping accepted, relres = 0.168665\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.686646e-01\n Vprtstp: contraction number = 1.686646e-01\n Vnewton: Using errtol_s: 449282.900987\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.010688e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.619115e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.120110e+04\n Vprtstp: contraction number = 8.120110e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.393027e-02\n Vprtstp: contraction number = 2.011700e-01\n Vnewton: Using errtol_s: 90382.255629\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.094778e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.067503e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.991839e+04\n Vprtstp: contraction number = 1.991839e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.954387e-03\n Vprtstp: contraction number = 2.344334e-01\n Vnewton: Using errtol_s: 21188.618171\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.180812e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.483800e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.497898e+03\n Vprtstp: contraction number = 5.497898e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.952447e-03\n Vprtstp: contraction number = 2.454554e-01\n Vnewton: Using errtol_s: 5200.860154\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.265044e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.893879e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.566684e+03\n Vprtstp: contraction number = 1.566684e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.300165e-04\n Vprtstp: contraction number = 2.714627e-01\n Vnewton: Using errtol_s: 1411.839327\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.347258e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.298880e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.634720e+02\n Vprtstp: contraction number = 4.634720e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.565934e-04\n Vprtstp: contraction number = 2.954500e-01\n Vnewton: Using errtol_s: 417.127917\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.431956e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.752521e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.430369e+02\n Vprtstp: contraction number = 1.430369e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.832756e-05\n Vprtstp: contraction number = 3.086182e-01\n Vnewton: Using errtol_s: 128.733272\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.515153e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.166884e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.523062e+01\n Vprtstp: contraction number = 4.523062e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.528197e-05\n Vprtstp: contraction number = 3.162164e-01\n Vnewton: Using errtol_s: 40.707568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.598300e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.569045e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.458043e+01\n Vprtstp: contraction number = 1.458043e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.926255e-06\n Vprtstp: contraction number = 3.223574e-01\n Vnewton: Using errtol_s: 13.122387\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.681320e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.978802e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.774711e+00\n Vprtstp: contraction number = 4.774711e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.613220e-06\n Vprtstp: contraction number = 3.274740e-01\n Vnewton: Using errtol_s: 4.297240\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.763452e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.043022e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.583552e+00\n Vprtstp: contraction number = 1.583552e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.350309e-07\n Vprtstp: contraction number = 3.316539e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.282947e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.478318e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.785190e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.993190e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -5090,17 +5090,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.889253587078E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.952637303887E+04 kT\n Vpmg_energy:  dielEnergy = 1.475418891145E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.799400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.775400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -5127,151 +5127,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.063208\n+Vacc_SASA: Time elapsed: 0.076392\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.488370e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.395060e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.808000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.786900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.664930e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.697410e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.955984e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.205169e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 745120.170523\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.970194e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.219898e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.014015e+05\n Vprtstp: contraction number = 1.014015e+05\n Vnewton: Attempting damping, relres = 0.130811\n Vnewton: Attempting damping, relres = 0.559104\n Vnewton: Damping accepted, relres = 0.130811\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.308109e-01\n Vprtstp: contraction number = 1.308109e-01\n Vnewton: Using errtol_s: 97469.809951\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.042829e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.270849e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.835986e+04\n Vprtstp: contraction number = 1.835986e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.256558e-02\n Vprtstp: contraction number = 1.725054e-01\n Vnewton: Using errtol_s: 16814.071331\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.107704e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.313292e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.045264e+03\n Vprtstp: contraction number = 4.045264e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.887910e-03\n Vprtstp: contraction number = 2.166091e-01\n Vnewton: Using errtol_s: 3642.080543\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.172895e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.354212e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.003527e+03\n Vprtstp: contraction number = 1.003527e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.212126e-03\n Vprtstp: contraction number = 2.479845e-01\n Vnewton: Using errtol_s: 903.179662\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.234104e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.394680e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660395e+02\n Vprtstp: contraction number = 2.660395e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.213385e-04\n Vprtstp: contraction number = 2.651031e-01\n Vnewton: Using errtol_s: 239.435768\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.299604e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.436768e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.320387e+01\n Vprtstp: contraction number = 7.320387e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 8.841996e-05\n Vprtstp: contraction number = 2.751615e-01\n Vnewton: Using errtol_s: 65.883497\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.360635e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.478946e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.064818e+01\n Vprtstp: contraction number = 2.064818e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.494009e-05\n Vprtstp: contraction number = 2.820641e-01\n Vnewton: Using errtol_s: 18.583367\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.421468e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.518028e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.934502e+00\n Vprtstp: contraction number = 5.934502e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.168040e-06\n Vprtstp: contraction number = 2.874103e-01\n Vnewton: Using errtol_s: 5.341051\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.485807e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.560564e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.731750e+00\n Vprtstp: contraction number = 1.731750e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.091710e-06\n Vprtstp: contraction number = 2.918105e-01\n Vnewton: Using errtol_s: 1.558575\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.550252e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.603476e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.115793e-01\n Vprtstp: contraction number = 5.115793e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.179156e-07\n Vprtstp: contraction number = 2.954117e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.489924e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.683664e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.310149e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.513854e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -5281,15 +5281,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.655453691226E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.834706672328E+03 kT\n Vpmg_energy:  dielEnergy = 3.415300525959E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.867600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.869000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -5338,160 +5338,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00688905 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.062255\n+Vacc_SASA: Time elapsed: 0.076068\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.748540e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.758520e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.737900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.772800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.618400e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.646410e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.643669e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.685933e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 777935.905465\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.657907e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.701538e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.267239e+05\n Vprtstp: contraction number = 1.267239e+05\n Vnewton: Attempting damping, relres = 0.154165\n Vnewton: Attempting damping, relres = 0.571273\n Vnewton: Damping accepted, relres = 0.154165\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.541646e-01\n Vprtstp: contraction number = 1.541646e-01\n Vnewton: Using errtol_s: 119930.213668\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.731074e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.749068e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.535999e+04\n Vprtstp: contraction number = 2.535999e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.969700e-02\n Vprtstp: contraction number = 1.926317e-01\n Vnewton: Using errtol_s: 23102.366146\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.797191e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.791259e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.051917e+03\n Vprtstp: contraction number = 6.051917e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.003479e-03\n Vprtstp: contraction number = 2.358312e-01\n Vnewton: Using errtol_s: 5448.257890\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.864552e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.833539e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.559687e+03\n Vprtstp: contraction number = 1.559687e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.804429e-03\n Vprtstp: contraction number = 2.576475e-01\n Vnewton: Using errtol_s: 1403.729913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.932930e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.876061e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.232949e+02\n Vprtstp: contraction number = 4.232949e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.897143e-04\n Vprtstp: contraction number = 2.713957e-01\n Vnewton: Using errtol_s: 380.966319\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.000075e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.915391e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.190545e+02\n Vprtstp: contraction number = 1.190545e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.377351e-04\n Vprtstp: contraction number = 2.812561e-01\n Vnewton: Using errtol_s: 107.149093\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.066621e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.958762e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.440341e+01\n Vprtstp: contraction number = 3.440341e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.980158e-05\n Vprtstp: contraction number = 2.889719e-01\n Vnewton: Using errtol_s: 30.963075\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.133995e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.998055e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.017569e+01\n Vprtstp: contraction number = 1.017569e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.177234e-05\n Vprtstp: contraction number = 2.957757e-01\n Vnewton: Using errtol_s: 9.158125\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.202041e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.037342e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.077041e+00\n Vprtstp: contraction number = 3.077041e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.559852e-06\n Vprtstp: contraction number = 3.023913e-01\n Vnewton: Using errtol_s: 2.769337\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.269212e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.079922e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.486014e-01\n Vprtstp: contraction number = 9.486014e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.097444e-06\n Vprtstp: contraction number = 3.082837e-01\n Vnewton: Using errtol_s: 0.853741\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.337174e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.123393e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.971293e-01\n Vprtstp: contraction number = 2.971293e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.437512e-07\n Vprtstp: contraction number = 3.132288e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.511887e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.698966e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.699818e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.898144e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -5501,17 +5501,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.647978359783E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.067221403363E+03 kT\n Vpmg_energy:  dielEnergy = 4.031568484712E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.864000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.859500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -5538,162 +5538,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.102843\n+Vacc_SASA: Time elapsed: 0.119147\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.223270e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.623970e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.754700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.772600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.622750e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.622500e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.516381e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.292796e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1939359.308692\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.530353e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.310256e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.739516e+05\n Vprtstp: contraction number = 2.739516e+05\n Vnewton: Attempting damping, relres = 0.235690\n Vnewton: Attempting damping, relres = 0.566181\n Vnewton: Damping accepted, relres = 0.235690\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.356901e-01\n Vprtstp: contraction number = 2.356901e-01\n Vnewton: Using errtol_s: 457087.767732\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.602064e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.359927e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.385706e+04\n Vprtstp: contraction number = 5.385706e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.455782e-02\n Vprtstp: contraction number = 2.314812e-01\n Vnewton: Using errtol_s: 105807.213748\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.683088e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.400261e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.345524e+04\n Vprtstp: contraction number = 1.345524e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.370821e-02\n Vprtstp: contraction number = 2.512602e-01\n Vnewton: Using errtol_s: 26585.137711\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.757873e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.441751e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.888746e+03\n Vprtstp: contraction number = 3.888746e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.963355e-03\n Vprtstp: contraction number = 2.161738e-01\n Vnewton: Using errtol_s: 5747.009743\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.825908e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.483631e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.082322e+03\n Vprtstp: contraction number = 1.082322e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.510650e-04\n Vprtstp: contraction number = 1.859598e-01\n Vnewton: Using errtol_s: 1068.713018\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.891030e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.524677e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.783449e+02\n Vprtstp: contraction number = 2.783449e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.293604e-04\n Vprtstp: contraction number = 2.347461e-01\n Vnewton: Using errtol_s: 250.876218\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.956701e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.561514e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.935007e+01\n Vprtstp: contraction number = 7.935007e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.682419e-05\n Vprtstp: contraction number = 2.846636e-01\n Vnewton: Using errtol_s: 71.415338\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.023826e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.602686e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.391930e+01\n Vprtstp: contraction number = 2.391930e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.110025e-05\n Vprtstp: contraction number = 3.014391e-01\n Vnewton: Using errtol_s: 21.527377\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.090659e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.647065e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.292472e+00\n Vprtstp: contraction number = 7.292472e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.384223e-06\n Vprtstp: contraction number = 3.048781e-01\n Vnewton: Using errtol_s: 6.563225\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.156469e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.686901e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.233482e+00\n Vprtstp: contraction number = 2.233482e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.036494e-06\n Vprtstp: contraction number = 3.062723e-01\n Vnewton: Using errtol_s: 2.010134\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.223441e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.727089e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.858053e-01\n Vprtstp: contraction number = 6.858053e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.182622e-07\n Vprtstp: contraction number = 3.070566e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.645213e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.834711e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.676840e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.864718e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -5703,17 +5703,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.820035378221E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.875217906563E+04 kT\n Vpmg_energy:  dielEnergy = 9.361966912953E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.865800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.828600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n Vpbe_ctor2:  bulk ionic strength = 0.1\n Vpbe_ctor2:  xkappa = 0.102972\n@@ -5760,160 +5760,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0305183 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.106462\n+Vacc_SASA: Time elapsed: 0.110528\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.658720e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.203260e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.894900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.751300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.755400e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.632110e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.330119e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.823464e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1996023.779999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.344201e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.838150e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.403294e+05\n Vprtstp: contraction number = 3.403294e+05\n Vnewton: Attempting damping, relres = 0.257870\n Vnewton: Attempting damping, relres = 0.579346\n Vnewton: Damping accepted, relres = 0.257870\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.578703e-01\n Vprtstp: contraction number = 2.578703e-01\n Vnewton: Using errtol_s: 514715.207917\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.420409e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.887908e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.253173e+04\n Vprtstp: contraction number = 7.253173e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 6.121431e-02\n Vprtstp: contraction number = 2.373841e-01\n Vnewton: Using errtol_s: 122185.216313\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.504414e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.932636e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.904030e+04\n Vprtstp: contraction number = 1.904030e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.572892e-02\n Vprtstp: contraction number = 2.569484e-01\n Vnewton: Using errtol_s: 31395.299569\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.585097e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.972182e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.659593e+03\n Vprtstp: contraction number = 5.659593e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.629998e-03\n Vprtstp: contraction number = 2.307850e-01\n Vnewton: Using errtol_s: 7245.562904\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.656972e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.015259e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.651310e+03\n Vprtstp: contraction number = 1.651310e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.856291e-04\n Vprtstp: contraction number = 2.164268e-01\n Vnewton: Using errtol_s: 1568.134340\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.725990e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.053649e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.661219e+02\n Vprtstp: contraction number = 4.661219e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.102913e-04\n Vprtstp: contraction number = 2.676725e-01\n Vnewton: Using errtol_s: 419.746448\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.795752e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.097712e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.425822e+02\n Vprtstp: contraction number = 1.425822e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 6.428993e-05\n Vprtstp: contraction number = 3.057184e-01\n Vnewton: Using errtol_s: 128.324228\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.865992e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.137307e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.557507e+01\n Vprtstp: contraction number = 4.557507e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.054964e-05\n Vprtstp: contraction number = 3.196401e-01\n Vnewton: Using errtol_s: 41.017570\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.935267e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.177861e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.480670e+01\n Vprtstp: contraction number = 1.480670e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 6.676290e-06\n Vprtstp: contraction number = 3.248860e-01\n Vnewton: Using errtol_s: 13.326033\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.004177e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.222064e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.862220e+00\n Vprtstp: contraction number = 4.862220e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.192358e-06\n Vprtstp: contraction number = 3.283797e-01\n Vnewton: Using errtol_s: 4.375998\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.074108e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.262132e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.609470e+00\n Vprtstp: contraction number = 1.609470e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 7.257041e-07\n Vprtstp: contraction number = 3.310154e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.048485e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.253018e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.723133e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.911360e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -5923,29 +5923,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.804365657787E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.136955879048E+04 kT\n Vpmg_energy:  dielEnergy = 1.067066513912E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.812000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.796700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.216937e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.377484e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:40:45 2025\n+# Creation Date and Time:  Sun Jan  7 09:47:04 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -6215,151 +6215,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.189380\n+Vacc_SASA: Time elapsed: 0.223799\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.340680e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.617590e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.724800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.819100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.564160e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.657210e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.315060e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.997370e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2482316.849131\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.703150e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.686700e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.222887e+05\n Vprtstp: contraction number = 3.222887e+05\n Vnewton: Attempting damping, relres = 0.143642\n Vnewton: Attempting damping, relres = 0.557204\n Vnewton: Damping accepted, relres = 0.143642\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.436423e-01\n Vprtstp: contraction number = 1.436423e-01\n Vnewton: Using errtol_s: 356565.753990\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.469134e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.449634e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.719340e+04\n Vprtstp: contraction number = 5.719340e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.655317e-02\n Vprtstp: contraction number = 1.848561e-01\n Vnewton: Using errtol_s: 65913.370564\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.308712e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.877005e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.314754e+04\n Vprtstp: contraction number = 1.314754e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.777425e-03\n Vprtstp: contraction number = 2.175795e-01\n Vnewton: Using errtol_s: 14341.400512\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.124485e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.298009e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.464763e+03\n Vprtstp: contraction number = 3.464763e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.322569e-03\n Vprtstp: contraction number = 2.289202e-01\n Vnewton: Using errtol_s: 3283.035896\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.903134e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.722302e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.430238e+02\n Vprtstp: contraction number = 9.430238e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.423711e-04\n Vprtstp: contraction number = 2.588682e-01\n Vnewton: Using errtol_s: 849.873571\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.695470e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.108767e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.680844e+02\n Vprtstp: contraction number = 2.680844e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.719850e-05\n Vprtstp: contraction number = 2.838981e-01\n Vnewton: Using errtol_s: 241.277472\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.493590e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.510572e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.904724e+01\n Vprtstp: contraction number = 7.904724e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.865974e-05\n Vprtstp: contraction number = 2.948578e-01\n Vnewton: Using errtol_s: 71.142545\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.287008e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.932658e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.370878e+01\n Vprtstp: contraction number = 2.370878e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.595964e-06\n Vprtstp: contraction number = 2.999317e-01\n Vnewton: Using errtol_s: 21.337905\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.084833e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.362001e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.196546e+00\n Vprtstp: contraction number = 7.196546e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.609212e-06\n Vprtstp: contraction number = 3.035392e-01\n Vnewton: Using errtol_s: 6.476891\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.881359e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.785039e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.205063e+00\n Vprtstp: contraction number = 2.205063e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.994776e-07\n Vprtstp: contraction number = 3.064057e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.048608e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.231536e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.337571e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.536953e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -6369,17 +6369,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.741026947406E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.567804611788E+04 kT\n Vpmg_energy:  dielEnergy = 1.283053686435E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.819000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.818200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.125\n Vpbe_ctor2:  xkappa = 0.115127\n@@ -6426,160 +6426,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0353875 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.182742\n+Vacc_SASA: Time elapsed: 0.200275\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.750050e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.949680e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.772500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.756700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.664270e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.699280e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.170709e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.957577e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2557475.753383\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.311015e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.120442e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.996924e+05\n Vprtstp: contraction number = 3.996924e+05\n Vnewton: Attempting damping, relres = 0.166335\n Vnewton: Attempting damping, relres = 0.569269\n Vnewton: Damping accepted, relres = 0.166335\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.663353e-01\n Vprtstp: contraction number = 1.663353e-01\n Vnewton: Using errtol_s: 425398.550037\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.018722e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.631037e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.844641e+04\n Vprtstp: contraction number = 7.844641e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.321581e-02\n Vprtstp: contraction number = 1.996918e-01\n Vnewton: Using errtol_s: 84948.619306\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.102893e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.042755e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.934802e+04\n Vprtstp: contraction number = 1.934802e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.763061e-03\n Vprtstp: contraction number = 2.337159e-01\n Vnewton: Using errtol_s: 19853.840744\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.186569e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.449318e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.339655e+03\n Vprtstp: contraction number = 5.339655e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.934926e-03\n Vprtstp: contraction number = 2.492478e-01\n Vnewton: Using errtol_s: 4948.526141\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.267952e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.897847e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.525404e+03\n Vprtstp: contraction number = 1.525404e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.370526e-04\n Vprtstp: contraction number = 2.775572e-01\n Vnewton: Using errtol_s: 1373.498967\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.350080e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.299188e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.551328e+02\n Vprtstp: contraction number = 4.551328e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.601661e-04\n Vprtstp: contraction number = 2.982316e-01\n Vnewton: Using errtol_s: 409.620859\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.433700e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.737849e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.409185e+02\n Vprtstp: contraction number = 1.409185e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.959057e-05\n Vprtstp: contraction number = 3.096197e-01\n Vnewton: Using errtol_s: 126.826691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.516928e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.146386e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.462999e+01\n Vprtstp: contraction number = 4.462999e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.570572e-05\n Vprtstp: contraction number = 3.167077e-01\n Vnewton: Using errtol_s: 40.166995\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.600175e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.560841e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.440051e+01\n Vprtstp: contraction number = 1.440051e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.067675e-06\n Vprtstp: contraction number = 3.226643e-01\n Vnewton: Using errtol_s: 12.960456\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.683054e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.002769e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.718013e+00\n Vprtstp: contraction number = 4.718013e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.660314e-06\n Vprtstp: contraction number = 3.276283e-01\n Vnewton: Using errtol_s: 4.246212\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.766031e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.044020e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.564985e+00\n Vprtstp: contraction number = 1.564985e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.507330e-07\n Vprtstp: contraction number = 3.317042e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.226049e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.420476e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.829912e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.034003e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -6589,15 +6589,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.724934425703E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.952419017164E+04 kT\n Vpmg_energy:  dielEnergy = 1.475361712291E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.785900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.794900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -6626,151 +6626,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.062709\n+Vacc_SASA: Time elapsed: 0.076640\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.482330e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.397070e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.809300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.808600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.644580e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.718120e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.958863e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.207804e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 720364.541598\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.972711e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.223292e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.787737e+04\n Vprtstp: contraction number = 9.787737e+04\n Vnewton: Attempting damping, relres = 0.130881\n Vnewton: Attempting damping, relres = 0.558946\n Vnewton: Damping accepted, relres = 0.130881\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.308815e-01\n Vprtstp: contraction number = 1.308815e-01\n Vnewton: Using errtol_s: 94282.387082\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.043114e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.272279e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.788353e+04\n Vprtstp: contraction number = 1.788353e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.273611e-02\n Vprtstp: contraction number = 1.737152e-01\n Vnewton: Using errtol_s: 16378.286782\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.105940e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.318453e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.978150e+03\n Vprtstp: contraction number = 3.978150e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.972005e-03\n Vprtstp: contraction number = 2.186832e-01\n Vnewton: Using errtol_s: 3581.655852\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.168840e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.358988e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.935846e+02\n Vprtstp: contraction number = 9.935846e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.241360e-03\n Vprtstp: contraction number = 2.496698e-01\n Vnewton: Using errtol_s: 894.231472\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.231663e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.399125e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.645071e+02\n Vprtstp: contraction number = 2.645071e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.304670e-04\n Vprtstp: contraction number = 2.662137e-01\n Vnewton: Using errtol_s: 238.056677\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.295389e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.442522e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.296267e+01\n Vprtstp: contraction number = 7.296267e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.115721e-05\n Vprtstp: contraction number = 2.758437e-01\n Vnewton: Using errtol_s: 65.666425\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.358140e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.484237e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.060915e+01\n Vprtstp: contraction number = 2.060915e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.574840e-05\n Vprtstp: contraction number = 2.824615e-01\n Vnewton: Using errtol_s: 18.548236\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.420876e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.527114e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.927860e+00\n Vprtstp: contraction number = 5.927860e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.406076e-06\n Vprtstp: contraction number = 2.876324e-01\n Vnewton: Using errtol_s: 5.335074\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.484528e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.570399e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.730517e+00\n Vprtstp: contraction number = 1.730517e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.162052e-06\n Vprtstp: contraction number = 2.919295e-01\n Vnewton: Using errtol_s: 1.557466\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.547271e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.612787e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.113205e-01\n Vprtstp: contraction number = 5.113205e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.388271e-07\n Vprtstp: contraction number = 2.954726e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.425461e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.616001e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.404368e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.610545e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -6780,15 +6780,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.705203011942E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.834032014754E+03 kT\n Vpmg_energy:  dielEnergy = 3.414947804784E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.868800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.877500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -6837,160 +6837,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0059523 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.063536\n+Vacc_SASA: Time elapsed: 0.077058\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.718920e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.780750e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.784400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.809800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.689490e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.722680e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.640649e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.698253e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 751497.765770\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.654511e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.714781e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.222283e+05\n Vprtstp: contraction number = 1.222283e+05\n Vnewton: Attempting damping, relres = 0.154183\n Vnewton: Attempting damping, relres = 0.571098\n Vnewton: Damping accepted, relres = 0.154183\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.541833e-01\n Vprtstp: contraction number = 1.541833e-01\n Vnewton: Using errtol_s: 115868.383651\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.727906e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.763462e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.458734e+04\n Vprtstp: contraction number = 2.458734e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.980652e-02\n Vprtstp: contraction number = 1.933188e-01\n Vnewton: Using errtol_s: 22399.536309\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.795030e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.807034e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.900997e+03\n Vprtstp: contraction number = 5.900997e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.069086e-03\n Vprtstp: contraction number = 2.371657e-01\n Vnewton: Using errtol_s: 5312.402554\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.861516e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.850442e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.528364e+03\n Vprtstp: contraction number = 1.528364e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.830398e-03\n Vprtstp: contraction number = 2.589300e-01\n Vnewton: Using errtol_s: 1375.540379\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.927308e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.893415e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.166306e+02\n Vprtstp: contraction number = 4.166306e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.989616e-04\n Vprtstp: contraction number = 2.725973e-01\n Vnewton: Using errtol_s: 374.968546\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.994049e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.937392e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.176231e+02\n Vprtstp: contraction number = 1.176231e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.408665e-04\n Vprtstp: contraction number = 2.823194e-01\n Vnewton: Using errtol_s: 105.860894\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.059563e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.980663e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.409436e+01\n Vprtstp: contraction number = 3.409436e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.083170e-05\n Vprtstp: contraction number = 2.898609e-01\n Vnewton: Using errtol_s: 30.684933\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.126062e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.020572e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.010867e+01\n Vprtstp: contraction number = 1.010867e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.210623e-05\n Vprtstp: contraction number = 2.964909e-01\n Vnewton: Using errtol_s: 9.097804\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.192728e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.064230e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.062356e+00\n Vprtstp: contraction number = 3.062356e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.667504e-06\n Vprtstp: contraction number = 3.029435e-01\n Vnewton: Using errtol_s: 2.756121\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.259161e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.106178e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.453520e-01\n Vprtstp: contraction number = 9.453520e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.132162e-06\n Vprtstp: contraction number = 3.087009e-01\n Vnewton: Using errtol_s: 0.850817\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.325923e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.149570e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.964013e-01\n Vprtstp: contraction number = 2.964013e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.549727e-07\n Vprtstp: contraction number = 3.135354e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.429729e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.626507e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.849248e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.047855e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -7000,15 +7000,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.697571697895E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.066549555181E+03 kT\n Vpmg_energy:  dielEnergy = 4.031217527268E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.881900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.862100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -7037,162 +7037,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.102972\n+Vacc_SASA: Time elapsed: 0.121378\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.253670e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.660590e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.790600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.838800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.676700e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.779050e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.508626e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.323838e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1823063.193603\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.522752e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.338167e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.580519e+05\n Vprtstp: contraction number = 2.580519e+05\n Vnewton: Attempting damping, relres = 0.222567\n Vnewton: Attempting damping, relres = 0.565989\n Vnewton: Damping accepted, relres = 0.222567\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.225671e-01\n Vprtstp: contraction number = 2.225671e-01\n Vnewton: Using errtol_s: 405753.919509\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.595194e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.392035e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.022631e+04\n Vprtstp: contraction number = 5.022631e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.970113e-02\n Vprtstp: contraction number = 2.233085e-01\n Vnewton: Using errtol_s: 90608.292404\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.678838e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.434216e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.257885e+04\n Vprtstp: contraction number = 1.257885e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.198700e-02\n Vprtstp: contraction number = 2.411816e-01\n Vnewton: Using errtol_s: 21853.051254\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.751368e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.477426e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.600602e+03\n Vprtstp: contraction number = 3.600602e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.500944e-03\n Vprtstp: contraction number = 2.086381e-01\n Vnewton: Using errtol_s: 4559.378536\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.819575e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.520068e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.867332e+02\n Vprtstp: contraction number = 9.867332e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.056164e-04\n Vprtstp: contraction number = 2.021702e-01\n Vnewton: Using errtol_s: 921.770690\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.885170e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.561619e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.646218e+02\n Vprtstp: contraction number = 2.646218e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.306754e-04\n Vprtstp: contraction number = 2.584478e-01\n Vnewton: Using errtol_s: 238.229561\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.949511e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.604609e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.765679e+01\n Vprtstp: contraction number = 7.765679e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.833723e-05\n Vprtstp: contraction number = 2.933775e-01\n Vnewton: Using errtol_s: 69.891187\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.015772e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.646667e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.351839e+01\n Vprtstp: contraction number = 2.351839e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.161043e-05\n Vprtstp: contraction number = 3.028501e-01\n Vnewton: Using errtol_s: 21.166555\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.081534e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.689768e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.178418e+00\n Vprtstp: contraction number = 7.178418e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.543803e-06\n Vprtstp: contraction number = 3.052257e-01\n Vnewton: Using errtol_s: 6.460576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.147060e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.731742e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.199458e+00\n Vprtstp: contraction number = 2.199458e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.085817e-06\n Vprtstp: contraction number = 3.063988e-01\n Vnewton: Using errtol_s: 1.979513\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.212590e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.773931e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.755609e-01\n Vprtstp: contraction number = 6.755609e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.335073e-07\n Vprtstp: contraction number = 3.071488e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.601303e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.795929e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.863661e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.075679e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -7202,17 +7202,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.498944659129E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.874900883074E+04 kT\n Vpmg_energy:  dielEnergy = 9.361242882871E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.856300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.846500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n Vpbe_ctor2:  bulk ionic strength = 0.125\n Vpbe_ctor2:  xkappa = 0.115127\n@@ -7259,160 +7259,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0207746 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.104289\n+Vacc_SASA: Time elapsed: 0.120952\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.620990e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.254880e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.790800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.852600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.712890e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.715890e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.316819e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.875558e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1873431.596335\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.330637e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.888692e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.215071e+05\n Vprtstp: contraction number = 3.215071e+05\n Vnewton: Attempting damping, relres = 0.246235\n Vnewton: Attempting damping, relres = 0.579562\n Vnewton: Damping accepted, relres = 0.246235\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.462348e-01\n Vprtstp: contraction number = 2.462348e-01\n Vnewton: Using errtol_s: 461304.132219\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.405007e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.942383e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.793925e+04\n Vprtstp: contraction number = 6.793925e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.674078e-02\n Vprtstp: contraction number = 2.304336e-01\n Vnewton: Using errtol_s: 106299.974305\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.489298e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.983234e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.790128e+04\n Vprtstp: contraction number = 1.790128e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.413343e-02\n Vprtstp: contraction number = 2.490877e-01\n Vnewton: Using errtol_s: 26478.015957\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.567267e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.027959e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.289572e+03\n Vprtstp: contraction number = 5.289572e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.207748e-03\n Vprtstp: contraction number = 2.269618e-01\n Vnewton: Using errtol_s: 6009.496862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.639860e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.070919e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.531645e+03\n Vprtstp: contraction number = 1.531645e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.505521e-04\n Vprtstp: contraction number = 2.339810e-01\n Vnewton: Using errtol_s: 1406.107935\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.709834e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.110526e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.459814e+02\n Vprtstp: contraction number = 4.459814e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.142740e-04\n Vprtstp: contraction number = 2.854885e-01\n Vnewton: Using errtol_s: 401.427706\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.779221e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.153953e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.392761e+02\n Vprtstp: contraction number = 1.392761e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 6.690856e-05\n Vprtstp: contraction number = 3.122570e-01\n Vnewton: Using errtol_s: 125.348607\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.848193e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.194830e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.474617e+01\n Vprtstp: contraction number = 4.474617e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.149615e-05\n Vprtstp: contraction number = 3.212765e-01\n Vnewton: Using errtol_s: 40.271562\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.917506e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.239310e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.457086e+01\n Vprtstp: contraction number = 1.457086e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 6.999869e-06\n Vprtstp: contraction number = 3.256337e-01\n Vnewton: Using errtol_s: 13.113776\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.987664e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.282166e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.791596e+00\n Vprtstp: contraction number = 4.791596e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.301892e-06\n Vprtstp: contraction number = 3.288478e-01\n Vnewton: Using errtol_s: 4.312437\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.056968e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.326322e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.587543e+00\n Vprtstp: contraction number = 1.587543e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 7.626585e-07\n Vprtstp: contraction number = 3.313182e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.998518e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.195473e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.835996e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.042463e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -7422,29 +7422,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.484583962910E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.136638905481E+04 kT\n Vpmg_energy:  dielEnergy = 1.066994369938E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.804600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.816100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.199885e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.442217e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:41:35 2025\n+# Creation Date and Time:  Sun Jan  7 09:47:15 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -7714,151 +7714,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.187356\n+Vacc_SASA: Time elapsed: 0.209890\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.339850e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.145540e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.759900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.921500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.613150e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.726590e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.361470e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.371790e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2410732.356899\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.759000e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.962100e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.128143e+05\n Vprtstp: contraction number = 3.128143e+05\n Vnewton: Attempting damping, relres = 0.141068\n Vnewton: Attempting damping, relres = 0.557017\n Vnewton: Damping accepted, relres = 0.141068\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.410683e-01\n Vprtstp: contraction number = 1.410683e-01\n Vnewton: Using errtol_s: 340078.014247\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.520720e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.385127e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.570013e+04\n Vprtstp: contraction number = 5.570013e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.582927e-02\n Vprtstp: contraction number = 1.830975e-01\n Vnewton: Using errtol_s: 62267.446259\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.361506e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.814117e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.287475e+04\n Vprtstp: contraction number = 1.287475e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.599207e-03\n Vprtstp: contraction number = 2.167776e-01\n Vnewton: Using errtol_s: 13498.190114\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.175479e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.235942e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.390785e+03\n Vprtstp: contraction number = 3.390785e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.306467e-03\n Vprtstp: contraction number = 2.333308e-01\n Vnewton: Using errtol_s: 3149.543372\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.953008e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.664408e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.269338e+02\n Vprtstp: contraction number = 9.269338e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.462424e-04\n Vprtstp: contraction number = 2.650218e-01\n Vnewton: Using errtol_s: 834.697770\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.741594e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.091752e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.654672e+02\n Vprtstp: contraction number = 2.654672e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.910734e-05\n Vprtstp: contraction number = 2.862369e-01\n Vnewton: Using errtol_s: 238.921266\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.521440e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.506410e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.840492e+01\n Vprtstp: contraction number = 7.840492e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.927096e-05\n Vprtstp: contraction number = 2.953460e-01\n Vnewton: Using errtol_s: 70.564451\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.313786e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.947383e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.353183e+01\n Vprtstp: contraction number = 2.353183e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.785152e-06\n Vprtstp: contraction number = 3.001320e-01\n Vnewton: Using errtol_s: 21.178651\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.119546e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.370368e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.144902e+00\n Vprtstp: contraction number = 7.144902e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.667410e-06\n Vprtstp: contraction number = 3.036271e-01\n Vnewton: Using errtol_s: 6.430412\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.909860e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.792037e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.189586e+00\n Vprtstp: contraction number = 2.189586e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.174393e-07\n Vprtstp: contraction number = 3.064543e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.085606e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.273326e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.411377e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.619129e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -7868,17 +7868,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.581693957245E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.567629004923E+04 kT\n Vpmg_energy:  dielEnergy = 1.283007133277E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.827000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.826300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.15\n Vpbe_ctor2:  xkappa = 0.126115\n@@ -7925,160 +7925,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0289035 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.183079\n+Vacc_SASA: Time elapsed: 0.209204\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.791270e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.950530e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.815800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.834400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.716570e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.713850e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.221163e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.970741e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2480363.897694\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.365755e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.134978e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.884147e+05\n Vprtstp: contraction number = 3.884147e+05\n Vnewton: Attempting damping, relres = 0.164249\n Vnewton: Attempting damping, relres = 0.569268\n Vnewton: Damping accepted, relres = 0.164249\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.642495e-01\n Vprtstp: contraction number = 1.642495e-01\n Vnewton: Using errtol_s: 407398.416424\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.024985e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.616326e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.641742e+04\n Vprtstp: contraction number = 7.641742e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.259356e-02\n Vprtstp: contraction number = 1.984394e-01\n Vnewton: Using errtol_s: 80843.885291\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.109765e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.052171e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.892121e+04\n Vprtstp: contraction number = 1.892121e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.611596e-03\n Vprtstp: contraction number = 2.335307e-01\n Vnewton: Using errtol_s: 18879.528241\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.192490e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.487585e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.219825e+03\n Vprtstp: contraction number = 5.219825e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.927310e-03\n Vprtstp: contraction number = 2.532071e-01\n Vnewton: Using errtol_s: 4780.429766\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.275374e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.905942e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.496544e+03\n Vprtstp: contraction number = 1.496544e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.431250e-04\n Vprtstp: contraction number = 2.818047e-01\n Vnewton: Using errtol_s: 1347.147545\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.356659e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.317939e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.492633e+02\n Vprtstp: contraction number = 4.492633e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.630155e-04\n Vprtstp: contraction number = 3.001437e-01\n Vnewton: Using errtol_s: 404.337796\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.439158e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.758180e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.394005e+02\n Vprtstp: contraction number = 1.394005e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.058149e-05\n Vprtstp: contraction number = 3.102863e-01\n Vnewton: Using errtol_s: 125.460496\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.523163e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.200651e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.420063e+01\n Vprtstp: contraction number = 4.420063e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.603820e-05\n Vprtstp: contraction number = 3.170765e-01\n Vnewton: Using errtol_s: 39.780577\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.606818e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.601157e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.427219e+01\n Vprtstp: contraction number = 1.427219e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.178663e-06\n Vprtstp: contraction number = 3.228955e-01\n Vnewton: Using errtol_s: 12.844969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.691267e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.003432e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.677701e+00\n Vprtstp: contraction number = 4.677701e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.697304e-06\n Vprtstp: contraction number = 3.277495e-01\n Vnewton: Using errtol_s: 4.209931\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.773566e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.045074e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.551790e+00\n Vprtstp: contraction number = 1.551790e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.630670e-07\n Vprtstp: contraction number = 3.317420e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.237496e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.436543e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.835096e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.040854e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8088,17 +8088,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.566249593084E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.952243483734E+04 kT\n Vpmg_energy:  dielEnergy = 1.475315373786E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.791700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.814800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -8125,151 +8125,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.065498\n+Vacc_SASA: Time elapsed: 0.076040\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.488920e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.385310e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.750500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.826300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.662210e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.714300e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.964370e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.209793e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 702833.844391\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.978289e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.226517e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.535199e+04\n Vprtstp: contraction number = 9.535199e+04\n Vnewton: Attempting damping, relres = 0.130807\n Vnewton: Attempting damping, relres = 0.558803\n Vnewton: Damping accepted, relres = 0.130807\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.308068e-01\n Vprtstp: contraction number = 1.308068e-01\n Vnewton: Using errtol_s: 91935.456218\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.049258e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.275511e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.754021e+04\n Vprtstp: contraction number = 1.754021e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.284568e-02\n Vprtstp: contraction number = 1.746521e-01\n Vnewton: Using errtol_s: 16056.717423\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.113350e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.316077e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.929316e+03\n Vprtstp: contraction number = 3.929316e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.033389e-03\n Vprtstp: contraction number = 2.203212e-01\n Vnewton: Using errtol_s: 3537.635824\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.177216e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.361428e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.863417e+02\n Vprtstp: contraction number = 9.863417e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.263048e-03\n Vprtstp: contraction number = 2.509340e-01\n Vnewton: Using errtol_s: 887.712932\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.241450e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.402640e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.633855e+02\n Vprtstp: contraction number = 2.633855e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.372735e-04\n Vprtstp: contraction number = 2.670314e-01\n Vnewton: Using errtol_s: 237.047224\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.305315e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.440939e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.278494e+01\n Vprtstp: contraction number = 7.278494e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.320334e-05\n Vprtstp: contraction number = 2.763435e-01\n Vnewton: Using errtol_s: 65.506461\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.369415e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.483258e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.058009e+01\n Vprtstp: contraction number = 2.058009e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.635343e-05\n Vprtstp: contraction number = 2.827520e-01\n Vnewton: Using errtol_s: 18.522083\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.433214e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.525839e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.922842e+00\n Vprtstp: contraction number = 5.922842e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.584378e-06\n Vprtstp: contraction number = 2.877947e-01\n Vnewton: Using errtol_s: 5.330558\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.497830e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.568407e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.729569e+00\n Vprtstp: contraction number = 1.729569e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.214765e-06\n Vprtstp: contraction number = 2.920167e-01\n Vnewton: Using errtol_s: 1.556612\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.561808e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.606543e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.111172e-01\n Vprtstp: contraction number = 5.111172e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.545011e-07\n Vprtstp: contraction number = 2.955171e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.515716e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.707755e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.312705e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.510226e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8336,160 +8336,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00524143 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.063265\n+Vacc_SASA: Time elapsed: 0.077676\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.743900e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.770330e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.782100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.779700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.683510e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.673750e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.655337e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.690394e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 732702.640135\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.669488e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.704647e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189776e+05\n Vprtstp: contraction number = 1.189776e+05\n Vnewton: Attempting damping, relres = 0.154045\n Vnewton: Attempting damping, relres = 0.570927\n Vnewton: Damping accepted, relres = 0.154045\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.540451e-01\n Vprtstp: contraction number = 1.540451e-01\n Vnewton: Using errtol_s: 112869.287383\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.742732e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.755598e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402351e+04\n Vprtstp: contraction number = 2.402351e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.986126e-02\n Vprtstp: contraction number = 1.938474e-01\n Vnewton: Using errtol_s: 21879.422460\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.809861e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.799744e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.789967e+03\n Vprtstp: contraction number = 5.789967e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.113936e-03\n Vprtstp: contraction number = 2.382330e-01\n Vnewton: Using errtol_s: 5212.399665\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.878181e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.839949e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.505316e+03\n Vprtstp: contraction number = 1.505316e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.849041e-03\n Vprtstp: contraction number = 2.599182e-01\n Vnewton: Using errtol_s: 1354.797457\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.946033e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.878489e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.117226e+02\n Vprtstp: contraction number = 4.117226e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.057322e-04\n Vprtstp: contraction number = 2.735105e-01\n Vnewton: Using errtol_s: 370.551343\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.012368e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.919058e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.165670e+02\n Vprtstp: contraction number = 1.165670e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.431828e-04\n Vprtstp: contraction number = 2.831198e-01\n Vnewton: Using errtol_s: 104.910419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.078855e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.962356e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.386584e+01\n Vprtstp: contraction number = 3.386584e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.159841e-05\n Vprtstp: contraction number = 2.905266e-01\n Vnewton: Using errtol_s: 30.479265\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.144138e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.001900e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.005899e+01\n Vprtstp: contraction number = 1.005899e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.235575e-05\n Vprtstp: contraction number = 2.970246e-01\n Vnewton: Using errtol_s: 9.053091\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.211415e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.041221e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.051439e+00\n Vprtstp: contraction number = 3.051439e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.748171e-06\n Vprtstp: contraction number = 3.033544e-01\n Vnewton: Using errtol_s: 2.746295\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.278151e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.086039e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.429257e-01\n Vprtstp: contraction number = 9.429257e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.158223e-06\n Vprtstp: contraction number = 3.090102e-01\n Vnewton: Using errtol_s: 0.848633\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.345751e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.125807e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.958550e-01\n Vprtstp: contraction number = 2.958550e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.634073e-07\n Vprtstp: contraction number = 3.137628e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.491944e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.688933e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.681901e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.874913e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8499,15 +8499,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.732432041867E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.065988471810E+03 kT\n Vpmg_energy:  dielEnergy = 4.030928944477E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.864000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.851800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -8536,162 +8536,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.102900\n+Vacc_SASA: Time elapsed: 0.120379\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.267860e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.631940e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.846700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.830500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.743700e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.736010e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.529370e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.298126e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1741500.081736\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.543626e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.311964e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.468341e+05\n Vprtstp: contraction number = 2.468341e+05\n Vnewton: Attempting damping, relres = 0.211968\n Vnewton: Attempting damping, relres = 0.565739\n Vnewton: Damping accepted, relres = 0.211968\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.119682e-01\n Vprtstp: contraction number = 2.119682e-01\n Vnewton: Using errtol_s: 369142.647388\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.616943e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.364053e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.765545e+04\n Vprtstp: contraction number = 4.765545e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.585316e-02\n Vprtstp: contraction number = 2.163209e-01\n Vnewton: Using errtol_s: 79853.288161\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.698639e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.407822e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.196657e+04\n Vprtstp: contraction number = 1.196657e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.069307e-02\n Vprtstp: contraction number = 2.332024e-01\n Vnewton: Using errtol_s: 18621.978068\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.769834e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.449340e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.396204e+03\n Vprtstp: contraction number = 3.396204e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.206422e-03\n Vprtstp: contraction number = 2.063414e-01\n Vnewton: Using errtol_s: 3842.484890\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.833067e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.489439e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.262198e+02\n Vprtstp: contraction number = 9.262198e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.857523e-04\n Vprtstp: contraction number = 2.201538e-01\n Vnewton: Using errtol_s: 845.937714\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.900394e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.533029e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.568315e+02\n Vprtstp: contraction number = 2.568315e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.327389e-04\n Vprtstp: contraction number = 2.732646e-01\n Vnewton: Using errtol_s: 231.164809\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.967923e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.572668e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.648381e+01\n Vprtstp: contraction number = 7.648381e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.952654e-05\n Vprtstp: contraction number = 2.977766e-01\n Vnewton: Using errtol_s: 68.835472\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.031085e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.616749e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.321302e+01\n Vprtstp: contraction number = 2.321302e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.199639e-05\n Vprtstp: contraction number = 3.035022e-01\n Vnewton: Using errtol_s: 20.891720\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.097183e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.657023e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.089761e+00\n Vprtstp: contraction number = 7.089761e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.663959e-06\n Vprtstp: contraction number = 3.054217e-01\n Vnewton: Using errtol_s: 6.380785\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.162262e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.696300e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.172932e+00\n Vprtstp: contraction number = 2.172932e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.122962e-06\n Vprtstp: contraction number = 3.064887e-01\n Vnewton: Using errtol_s: 1.955639\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.227906e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.739051e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.675659e-01\n Vprtstp: contraction number = 6.675659e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.449953e-07\n Vprtstp: contraction number = 3.072190e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.533189e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.734253e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.766994e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.974852e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8701,15 +8701,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.219214525491E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.874647090507E+04 kT\n Vpmg_energy:  dielEnergy = 9.360649736533E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.841100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.844700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -8758,160 +8758,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0149776 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.102520\n+Vacc_SASA: Time elapsed: 0.122774\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.587900e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.271080e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.785200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.833400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.683020e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.740890e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.330263e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.840511e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1787000.080841\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.344175e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.856428e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.080871e+05\n Vprtstp: contraction number = 3.080871e+05\n Vnewton: Attempting damping, relres = 0.236727\n Vnewton: Attempting damping, relres = 0.579616\n Vnewton: Damping accepted, relres = 0.236727\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.367272e-01\n Vprtstp: contraction number = 2.367272e-01\n Vnewton: Using errtol_s: 423031.456074\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.418954e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.906470e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.466075e+04\n Vprtstp: contraction number = 6.466075e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.316615e-02\n Vprtstp: contraction number = 2.245883e-01\n Vnewton: Using errtol_s: 95007.918174\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.503861e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.948889e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.709590e+04\n Vprtstp: contraction number = 1.709590e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.292750e-02\n Vprtstp: contraction number = 2.431528e-01\n Vnewton: Using errtol_s: 23101.438026\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.583138e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.993155e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.023315e+03\n Vprtstp: contraction number = 5.023315e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.939979e-03\n Vprtstp: contraction number = 2.274206e-01\n Vnewton: Using errtol_s: 5253.742566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.655750e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.035600e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.453031e+03\n Vprtstp: contraction number = 1.453031e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.371716e-04\n Vprtstp: contraction number = 2.507404e-01\n Vnewton: Using errtol_s: 1317.325709\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.725319e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.080461e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.332970e+02\n Vprtstp: contraction number = 4.332970e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.182303e-04\n Vprtstp: contraction number = 2.960373e-01\n Vnewton: Using errtol_s: 389.977573\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.794258e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.127245e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.367395e+02\n Vprtstp: contraction number = 1.367395e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 6.886719e-05\n Vprtstp: contraction number = 3.155711e-01\n Vnewton: Using errtol_s: 123.065671\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.864098e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.172952e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.406045e+01\n Vprtstp: contraction number = 4.406045e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.219049e-05\n Vprtstp: contraction number = 3.222216e-01\n Vnewton: Using errtol_s: 39.654416\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.934830e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.220088e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.437042e+01\n Vprtstp: contraction number = 1.437042e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.237482e-06\n Vprtstp: contraction number = 3.261524e-01\n Vnewton: Using errtol_s: 12.933382\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.005740e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.265256e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.730536e+00\n Vprtstp: contraction number = 4.730536e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.382475e-06\n Vprtstp: contraction number = 3.291856e-01\n Vnewton: Using errtol_s: 4.257482\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.076890e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.309490e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.568402e+00\n Vprtstp: contraction number = 1.568402e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 7.899057e-07\n Vprtstp: contraction number = 3.315484e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.089997e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.285308e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.042925e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.251036e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8921,29 +8921,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.205829898099E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.136385155975E+04 kT\n Vpmg_energy:  dielEnergy = 1.066935223116E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.810000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.823600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.222102e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.430060e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:42:21 2025\n+# Creation Date and Time:  Sun Jan  7 09:47:27 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -9213,151 +9213,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.186303\n+Vacc_SASA: Time elapsed: 0.204918\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.333630e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.160880e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.720800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.920800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.620540e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.771680e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.371160e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.435980e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2356583.284651\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.820440e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.880760e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.056288e+05\n Vprtstp: contraction number = 3.056288e+05\n Vnewton: Attempting damping, relres = 0.138875\n Vnewton: Attempting damping, relres = 0.556850\n Vnewton: Damping accepted, relres = 0.138875\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.388745e-01\n Vprtstp: contraction number = 1.388745e-01\n Vnewton: Using errtol_s: 327269.333015\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.525718e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.433057e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.456208e+04\n Vprtstp: contraction number = 5.456208e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.522390e-02\n Vprtstp: contraction number = 1.816309e-01\n Vnewton: Using errtol_s: 59442.210907\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.383225e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.840234e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.266310e+04\n Vprtstp: contraction number = 1.266310e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.461794e-03\n Vprtstp: contraction number = 2.165325e-01\n Vnewton: Using errtol_s: 12871.173067\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.184370e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.294729e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.333848e+03\n Vprtstp: contraction number = 3.333848e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.298357e-03\n Vprtstp: contraction number = 2.377162e-01\n Vnewton: Using errtol_s: 3059.685767\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.977995e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.721485e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.158069e+02\n Vprtstp: contraction number = 9.158069e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.498387e-04\n Vprtstp: contraction number = 2.694473e-01\n Vnewton: Using errtol_s: 824.424114\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.758370e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.118620e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.635874e+02\n Vprtstp: contraction number = 2.635874e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.006665e-04\n Vprtstp: contraction number = 2.877513e-01\n Vnewton: Using errtol_s: 237.229108\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.538750e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.551618e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.793651e+01\n Vprtstp: contraction number = 7.793651e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.976465e-05\n Vprtstp: contraction number = 2.956757e-01\n Vnewton: Using errtol_s: 70.142875\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.325139e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.973896e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.340231e+01\n Vprtstp: contraction number = 2.340231e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.937548e-06\n Vprtstp: contraction number = 3.002739e-01\n Vnewton: Using errtol_s: 21.062077\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.120511e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.390668e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.107171e+00\n Vprtstp: contraction number = 7.107171e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.714292e-06\n Vprtstp: contraction number = 3.036953e-01\n Vnewton: Using errtol_s: 6.396454\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.925138e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.790574e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.178301e+00\n Vprtstp: contraction number = 2.178301e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.319126e-07\n Vprtstp: contraction number = 3.064934e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.096859e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.285776e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.400108e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.612787e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -9367,15 +9367,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.432923079366E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.567482695315E+04 kT\n Vpmg_energy:  dielEnergy = 1.282968021669E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.826400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.808700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -9424,160 +9424,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.024752 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.182535\n+Vacc_SASA: Time elapsed: 0.209420\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.776580e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.961910e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.751600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.829900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.668550e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.697880e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.226743e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.965602e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2421825.168549\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.366349e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.138313e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.797843e+05\n Vprtstp: contraction number = 3.797843e+05\n Vnewton: Attempting damping, relres = 0.162423\n Vnewton: Attempting damping, relres = 0.569239\n Vnewton: Damping accepted, relres = 0.162423\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.624227e-01\n Vprtstp: contraction number = 1.624227e-01\n Vnewton: Using errtol_s: 393359.388162\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.019294e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.629880e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.485976e+04\n Vprtstp: contraction number = 7.485976e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.206345e-02\n Vprtstp: contraction number = 1.974075e-01\n Vnewton: Using errtol_s: 77652.078067\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.103862e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.081577e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.858810e+04\n Vprtstp: contraction number = 1.858810e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.494162e-03\n Vprtstp: contraction number = 2.337291e-01\n Vnewton: Using errtol_s: 18149.549466\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.187681e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.502836e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.126907e+03\n Vprtstp: contraction number = 5.126907e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.925418e-03\n Vprtstp: contraction number = 2.569223e-01\n Vnewton: Using errtol_s: 4663.024844\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.271047e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.928732e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.475836e+03\n Vprtstp: contraction number = 1.475836e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.485012e-04\n Vprtstp: contraction number = 2.848739e-01\n Vnewton: Using errtol_s: 1328.373956\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.354082e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.371524e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.449115e+02\n Vprtstp: contraction number = 4.449115e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.653385e-04\n Vprtstp: contraction number = 3.014369e-01\n Vnewton: Using errtol_s: 400.420960\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.439533e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.765548e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.382677e+02\n Vprtstp: contraction number = 1.382677e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.138313e-05\n Vprtstp: contraction number = 3.107753e-01\n Vnewton: Using errtol_s: 124.440953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.523843e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.189319e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.388153e+01\n Vprtstp: contraction number = 4.388153e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.630728e-05\n Vprtstp: contraction number = 3.173665e-01\n Vnewton: Using errtol_s: 39.493386\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.609526e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.600833e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.417721e+01\n Vprtstp: contraction number = 1.417721e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.268543e-06\n Vprtstp: contraction number = 3.230792e-01\n Vnewton: Using errtol_s: 12.759491\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.693084e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.001914e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.647969e+00\n Vprtstp: contraction number = 4.647969e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.727281e-06\n Vprtstp: contraction number = 3.278479e-01\n Vnewton: Using errtol_s: 4.183172\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.766968e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.046861e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.542077e+00\n Vprtstp: contraction number = 1.542077e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.730676e-07\n Vprtstp: contraction number = 3.317744e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.198385e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.391681e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.824623e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.029243e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -9587,15 +9587,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.418015826462E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.952097240352E+04 kT\n Vpmg_energy:  dielEnergy = 1.475276420502E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.811600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.791700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -9624,151 +9624,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.064303\n+Vacc_SASA: Time elapsed: 0.076452\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.507210e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.389850e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.772400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.778600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.697850e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.643710e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.963106e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.206325e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 689766.139707\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.977310e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.219272e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.344903e+04\n Vprtstp: contraction number = 9.344903e+04\n Vnewton: Attempting damping, relres = 0.130653\n Vnewton: Attempting damping, relres = 0.558674\n Vnewton: Damping accepted, relres = 0.130653\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.306530e-01\n Vprtstp: contraction number = 1.306530e-01\n Vnewton: Using errtol_s: 90120.018484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.049139e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.270194e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.728022e+04\n Vprtstp: contraction number = 1.728022e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.291797e-02\n Vprtstp: contraction number = 1.754110e-01\n Vnewton: Using errtol_s: 15808.042794\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.113566e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.313207e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.892059e+03\n Vprtstp: contraction number = 3.892059e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.080008e-03\n Vprtstp: contraction number = 2.216604e-01\n Vnewton: Using errtol_s: 3504.017199\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.178063e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.352015e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.808109e+02\n Vprtstp: contraction number = 9.808109e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.279760e-03\n Vprtstp: contraction number = 2.519209e-01\n Vnewton: Using errtol_s: 882.735296\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.243679e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.394293e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.625258e+02\n Vprtstp: contraction number = 2.625258e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.425414e-04\n Vprtstp: contraction number = 2.676606e-01\n Vnewton: Using errtol_s: 236.273473\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.308424e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.433044e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.264793e+01\n Vprtstp: contraction number = 7.264793e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.479032e-05\n Vprtstp: contraction number = 2.767266e-01\n Vnewton: Using errtol_s: 65.383155\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.374537e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.476465e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.055752e+01\n Vprtstp: contraction number = 2.055752e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.682325e-05\n Vprtstp: contraction number = 2.829746e-01\n Vnewton: Using errtol_s: 18.501770\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.435708e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.516422e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.918897e+00\n Vprtstp: contraction number = 5.918897e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.722918e-06\n Vprtstp: contraction number = 2.879188e-01\n Vnewton: Using errtol_s: 5.327008\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.501700e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.554026e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.728813e+00\n Vprtstp: contraction number = 1.728813e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.255738e-06\n Vprtstp: contraction number = 2.920837e-01\n Vnewton: Using errtol_s: 1.555932\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.566715e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.595607e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.109531e-01\n Vprtstp: contraction number = 5.109531e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.666866e-07\n Vprtstp: contraction number = 2.955514e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.590464e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.787556e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.227549e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.425598e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -9778,15 +9778,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.765725415923E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.832984433292E+03 kT\n Vpmg_energy:  dielEnergy = 3.414411854652E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.880900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.864000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -9835,160 +9835,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00466833 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.061740\n+Vacc_SASA: Time elapsed: 0.076377\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.694240e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.764320e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.776200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.853300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.717340e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.675550e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.661470e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.679319e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 718654.980128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.675375e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.692075e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.165117e+05\n Vprtstp: contraction number = 1.165117e+05\n Vnewton: Attempting damping, relres = 0.153827\n Vnewton: Attempting damping, relres = 0.570766\n Vnewton: Damping accepted, relres = 0.153827\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.538266e-01\n Vprtstp: contraction number = 1.538266e-01\n Vnewton: Using errtol_s: 110548.228061\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.748728e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.742173e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.359273e+04\n Vprtstp: contraction number = 2.359273e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.988514e-02\n Vprtstp: contraction number = 1.942782e-01\n Vnewton: Using errtol_s: 21477.106835\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.815493e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.784724e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.704562e+03\n Vprtstp: contraction number = 5.704562e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.145907e-03\n Vprtstp: contraction number = 2.391124e-01\n Vnewton: Using errtol_s: 5135.441496\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.882055e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.825515e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.487585e+03\n Vprtstp: contraction number = 1.487585e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.862980e-03\n Vprtstp: contraction number = 2.607059e-01\n Vnewton: Using errtol_s: 1338.839679\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.948936e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.869900e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.079440e+02\n Vprtstp: contraction number = 4.079440e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.108858e-04\n Vprtstp: contraction number = 2.742305e-01\n Vnewton: Using errtol_s: 367.150629\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.016578e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.910364e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.157528e+02\n Vprtstp: contraction number = 1.157528e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.449619e-04\n Vprtstp: contraction number = 2.837461e-01\n Vnewton: Using errtol_s: 104.177567\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.084372e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.954363e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.368933e+01\n Vprtstp: contraction number = 3.368933e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.219048e-05\n Vprtstp: contraction number = 2.910454e-01\n Vnewton: Using errtol_s: 30.320401\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.151573e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.994240e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.002053e+01\n Vprtstp: contraction number = 1.002053e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.254910e-05\n Vprtstp: contraction number = 2.974392e-01\n Vnewton: Using errtol_s: 9.018476\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.219214e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.035010e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.042966e+00\n Vprtstp: contraction number = 3.042966e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.810826e-06\n Vprtstp: contraction number = 3.036732e-01\n Vnewton: Using errtol_s: 2.738669\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.285430e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.078258e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.410367e-01\n Vprtstp: contraction number = 9.410367e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.178497e-06\n Vprtstp: contraction number = 3.092499e-01\n Vnewton: Using errtol_s: 0.846933\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.351505e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.120219e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.954277e-01\n Vprtstp: contraction number = 2.954277e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.699758e-07\n Vprtstp: contraction number = 3.139386e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.480233e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.679688e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.757868e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.960699e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -9998,15 +9998,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.757851015992E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.065506328732E+03 kT\n Vpmg_energy:  dielEnergy = 4.030684199537E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.851800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.859200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -10035,162 +10035,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.102561\n+Vacc_SASA: Time elapsed: 0.118110\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.209410e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.630770e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.773900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.768000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.671920e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.639630e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.531928e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.291626e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1681345.800904\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.545950e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.306003e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.385175e+05\n Vprtstp: contraction number = 2.385175e+05\n Vnewton: Attempting damping, relres = 0.203314\n Vnewton: Attempting damping, relres = 0.565471\n Vnewton: Damping accepted, relres = 0.203314\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.033139e-01\n Vprtstp: contraction number = 2.033139e-01\n Vnewton: Using errtol_s: 341841.011255\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.619040e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.356264e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.575913e+04\n Vprtstp: contraction number = 4.575913e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.277261e-02\n Vprtstp: contraction number = 2.103772e-01\n Vnewton: Using errtol_s: 71915.546235\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.698461e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.398891e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.151626e+04\n Vprtstp: contraction number = 1.151626e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.711565e-03\n Vprtstp: contraction number = 2.270510e-01\n Vnewton: Using errtol_s: 16328.498943\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.768825e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.439099e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.244716e+03\n Vprtstp: contraction number = 3.244716e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.018619e-03\n Vprtstp: contraction number = 2.078572e-01\n Vnewton: Using errtol_s: 3393.995992\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.835621e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.479142e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.861858e+02\n Vprtstp: contraction number = 8.861858e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.771677e-04\n Vprtstp: contraction number = 2.363833e-01\n Vnewton: Using errtol_s: 802.283944\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.901352e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.519771e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.516488e+02\n Vprtstp: contraction number = 2.516488e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.347069e-04\n Vprtstp: contraction number = 2.823051e-01\n Vnewton: Using errtol_s: 226.488825\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.967087e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.559082e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.546930e+01\n Vprtstp: contraction number = 7.546930e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.039764e-05\n Vprtstp: contraction number = 2.998929e-01\n Vnewton: Using errtol_s: 67.922396\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.032964e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.602385e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.293241e+01\n Vprtstp: contraction number = 2.293241e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.227539e-05\n Vprtstp: contraction number = 3.038640e-01\n Vnewton: Using errtol_s: 20.639168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.099366e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.641108e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.006994e+00\n Vprtstp: contraction number = 7.006994e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.750742e-06\n Vprtstp: contraction number = 3.055499e-01\n Vnewton: Using errtol_s: 6.306295\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.166126e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.683562e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.148054e+00\n Vprtstp: contraction number = 2.148054e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.149822e-06\n Vprtstp: contraction number = 3.065586e-01\n Vnewton: Using errtol_s: 1.933249\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.232560e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.724215e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.600422e-01\n Vprtstp: contraction number = 6.600422e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.533110e-07\n Vprtstp: contraction number = 3.072745e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.568729e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.762388e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.658970e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.848379e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -10200,15 +10200,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.973061479643E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.874436395142E+04 kT\n Vpmg_energy:  dielEnergy = 9.360148310218E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.845500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.823800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -10257,160 +10257,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.011302 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.100941\n+Vacc_SASA: Time elapsed: 0.121828\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.601810e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.211470e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.781200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.789400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.697390e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.633870e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.336577e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.820716e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1723046.376364\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.350640e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.835524e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.980547e+05\n Vprtstp: contraction number = 2.980547e+05\n Vnewton: Attempting damping, relres = 0.228891\n Vnewton: Attempting damping, relres = 0.579579\n Vnewton: Damping accepted, relres = 0.228891\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.288909e-01\n Vprtstp: contraction number = 2.288909e-01\n Vnewton: Using errtol_s: 394389.718028\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.426505e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.883893e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.222537e+04\n Vprtstp: contraction number = 6.222537e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.028364e-02\n Vprtstp: contraction number = 2.196838e-01\n Vnewton: Using errtol_s: 86641.047132\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.510553e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.926536e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.649630e+04\n Vprtstp: contraction number = 1.649630e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.200939e-02\n Vprtstp: contraction number = 2.388330e-01\n Vnewton: Using errtol_s: 20692.741964\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.584952e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.969001e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.824465e+03\n Vprtstp: contraction number = 4.824465e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.771121e-03\n Vprtstp: contraction number = 2.307461e-01\n Vnewton: Using errtol_s: 4774.769213\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.652390e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.009946e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.399802e+03\n Vprtstp: contraction number = 1.399802e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.332377e-04\n Vprtstp: contraction number = 2.645997e-01\n Vnewton: Using errtol_s: 1263.402543\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.719636e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.057340e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.245121e+02\n Vprtstp: contraction number = 4.245121e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.217376e-04\n Vprtstp: contraction number = 3.024089e-01\n Vnewton: Using errtol_s: 382.064121\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.786640e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.098167e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.346888e+02\n Vprtstp: contraction number = 1.346888e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.035216e-05\n Vprtstp: contraction number = 3.172767e-01\n Vnewton: Using errtol_s: 121.220033\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.854497e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.137809e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.348380e+01\n Vprtstp: contraction number = 4.348380e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.271293e-05\n Vprtstp: contraction number = 3.228462e-01\n Vnewton: Using errtol_s: 39.135424\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.925097e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.181595e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.419901e+01\n Vprtstp: contraction number = 1.419901e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.416577e-06\n Vprtstp: contraction number = 3.265355e-01\n Vnewton: Using errtol_s: 12.779106\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.995166e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.221064e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.677787e+00\n Vprtstp: contraction number = 4.677787e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.443352e-06\n Vprtstp: contraction number = 3.294447e-01\n Vnewton: Using errtol_s: 4.210009\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.065684e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.263419e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.551755e+00\n Vprtstp: contraction number = 1.551755e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.105291e-07\n Vprtstp: contraction number = 3.317283e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.886469e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.082590e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.757546e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.947092e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -10420,29 +10420,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.960413626041E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.136174499148E+04 kT\n Vpmg_energy:  dielEnergy = 1.066885194167E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.812600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.798700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.205319e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.378743e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:43:05 2025\n+# Creation Date and Time:  Sun Jan  7 09:47:39 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -10712,151 +10712,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.189854\n+Vacc_SASA: Time elapsed: 0.208622\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.443180e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.131930e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.784800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.881800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.875690e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.669930e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.893070e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.225130e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2314164.846818\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.162640e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.724700e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.999858e+05\n Vprtstp: contraction number = 2.999858e+05\n Vnewton: Attempting damping, relres = 0.137001\n Vnewton: Attempting damping, relres = 0.556699\n Vnewton: Damping accepted, relres = 0.137001\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.370010e-01\n Vprtstp: contraction number = 1.370010e-01\n Vnewton: Using errtol_s: 317042.938668\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.855236e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.382626e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.366653e+04\n Vprtstp: contraction number = 5.366653e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.471777e-02\n Vprtstp: contraction number = 1.804203e-01\n Vnewton: Using errtol_s: 57200.987288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.661318e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.832677e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.249422e+04\n Vprtstp: contraction number = 1.249422e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.356401e-03\n Vprtstp: contraction number = 2.167025e-01\n Vnewton: Using errtol_s: 12395.595920\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.472782e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.233460e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.289496e+03\n Vprtstp: contraction number = 3.289496e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.295127e-03\n Vprtstp: contraction number = 2.417905e-01\n Vnewton: Using errtol_s: 2997.137107\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.217130e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.680451e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.079428e+02\n Vprtstp: contraction number = 9.079428e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.531481e-04\n Vprtstp: contraction number = 2.726745e-01\n Vnewton: Using errtol_s: 817.243005\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.965808e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.080207e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.621817e+02\n Vprtstp: contraction number = 2.621817e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.019650e-04\n Vprtstp: contraction number = 2.887315e-01\n Vnewton: Using errtol_s: 235.963838\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.673724e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.501279e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.758363e+01\n Vprtstp: contraction number = 7.758363e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.017299e-05\n Vprtstp: contraction number = 2.959152e-01\n Vnewton: Using errtol_s: 69.825280\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.416096e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.968376e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.330457e+01\n Vprtstp: contraction number = 2.330457e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.063361e-06\n Vprtstp: contraction number = 3.003799e-01\n Vnewton: Using errtol_s: 20.974111\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.201854e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.397121e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.078759e+00\n Vprtstp: contraction number = 7.078759e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.752995e-06\n Vprtstp: contraction number = 3.037499e-01\n Vnewton: Using errtol_s: 6.370884\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.056564e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.819630e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.169820e+00\n Vprtstp: contraction number = 2.169820e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.438628e-07\n Vprtstp: contraction number = 3.065254e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.205302e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.422572e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.436654e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.631032e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -10866,15 +10866,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.295748470746E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.567357663948E+04 kT\n Vpmg_energy:  dielEnergy = 1.282934286498E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.765500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.821700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -10923,160 +10923,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0219675 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.185879\n+Vacc_SASA: Time elapsed: 0.195262\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.336650e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.972560e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.733100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.873100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.194920e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.828000e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.712952e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.995056e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2375881.010490\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.996185e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.163905e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.729565e+05\n Vprtstp: contraction number = 3.729565e+05\n Vnewton: Attempting damping, relres = 0.160831\n Vnewton: Attempting damping, relres = 0.569195\n Vnewton: Damping accepted, relres = 0.160831\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.608306e-01\n Vprtstp: contraction number = 1.608306e-01\n Vnewton: Using errtol_s: 382114.425441\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.143192e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.668881e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.362534e+04\n Vprtstp: contraction number = 7.362534e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.161380e-02\n Vprtstp: contraction number = 1.965658e-01\n Vnewton: Using errtol_s: 75110.631839\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.268670e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.102174e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.832017e+04\n Vprtstp: contraction number = 1.832017e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.403849e-03\n Vprtstp: contraction number = 2.341967e-01\n Vnewton: Using errtol_s: 17590.663892\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.387800e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.527123e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.053669e+03\n Vprtstp: contraction number = 5.053669e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.926673e-03\n Vprtstp: contraction number = 2.602258e-01\n Vnewton: Using errtol_s: 4577.545268\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.521550e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.954350e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.460468e+03\n Vprtstp: contraction number = 1.460468e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.532624e-04\n Vprtstp: contraction number = 2.871595e-01\n Vnewton: Using errtol_s: 1314.485731\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.653660e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.376566e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.415879e+02\n Vprtstp: contraction number = 4.415879e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.672767e-04\n Vprtstp: contraction number = 3.023461e-01\n Vnewton: Using errtol_s: 397.429641\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.770567e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.809939e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.374012e+02\n Vprtstp: contraction number = 1.374012e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.204853e-05\n Vprtstp: contraction number = 3.111522e-01\n Vnewton: Using errtol_s: 123.661104\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.887152e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.237857e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.363894e+01\n Vprtstp: contraction number = 4.363894e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.653073e-05\n Vprtstp: contraction number = 3.176023e-01\n Vnewton: Using errtol_s: 39.275049\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.013301e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.663114e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.410540e+01\n Vprtstp: contraction number = 1.410540e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.343223e-06\n Vprtstp: contraction number = 3.232297e-01\n Vnewton: Using errtol_s: 12.694863\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.141721e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.011875e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.625592e+00\n Vprtstp: contraction number = 4.625592e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.752206e-06\n Vprtstp: contraction number = 3.279305e-01\n Vnewton: Using errtol_s: 4.163033\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.263411e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.054069e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.534788e+00\n Vprtstp: contraction number = 1.534788e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.813881e-07\n Vprtstp: contraction number = 3.318035e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.394582e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.419759e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.904951e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.122328e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -11086,17 +11086,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.281289332707E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951972269789E+04 kT\n Vpmg_energy:  dielEnergy = 1.475242807069E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.937700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.784300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -11123,151 +11123,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.069945\n+Vacc_SASA: Time elapsed: 0.076985\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.437680e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.392970e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.796500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.774800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.162010e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.727340e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.498596e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.220159e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 679651.374556\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.529303e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.236927e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.196081e+04\n Vprtstp: contraction number = 9.196081e+04\n Vnewton: Attempting damping, relres = 0.130456\n Vnewton: Attempting damping, relres = 0.558557\n Vnewton: Damping accepted, relres = 0.130456\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.304558e-01\n Vprtstp: contraction number = 1.304558e-01\n Vnewton: Using errtol_s: 88664.431621\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.619981e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.287772e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.707604e+04\n Vprtstp: contraction number = 1.707604e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.296641e-02\n Vprtstp: contraction number = 1.760475e-01\n Vnewton: Using errtol_s: 15609.155466\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.717394e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.328451e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.862634e+03\n Vprtstp: contraction number = 3.862634e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.116511e-03\n Vprtstp: contraction number = 2.227823e-01\n Vnewton: Using errtol_s: 3477.443419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.819002e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.371796e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.764405e+02\n Vprtstp: contraction number = 9.764405e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.293019e-03\n Vprtstp: contraction number = 2.527150e-01\n Vnewton: Using errtol_s: 878.801976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.925023e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.416155e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.618442e+02\n Vprtstp: contraction number = 2.618442e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.467366e-04\n Vprtstp: contraction number = 2.681606e-01\n Vnewton: Using errtol_s: 235.660041\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.027439e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.486392e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.253883e+01\n Vprtstp: contraction number = 7.253883e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.605654e-05\n Vprtstp: contraction number = 2.770303e-01\n Vnewton: Using errtol_s: 65.284962\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.133785e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.531304e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.053942e+01\n Vprtstp: contraction number = 2.053942e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.719848e-05\n Vprtstp: contraction number = 2.831507e-01\n Vnewton: Using errtol_s: 18.485484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.240628e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.579805e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.915703e+00\n Vprtstp: contraction number = 5.915703e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.833623e-06\n Vprtstp: contraction number = 2.880170e-01\n Vnewton: Using errtol_s: 5.324133\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.340563e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.628129e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.728194e+00\n Vprtstp: contraction number = 1.728194e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.288489e-06\n Vprtstp: contraction number = 2.921367e-01\n Vnewton: Using errtol_s: 1.555375\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.439678e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.673539e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.108177e-01\n Vprtstp: contraction number = 5.108177e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.764290e-07\n Vprtstp: contraction number = 2.955789e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.022633e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.046862e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.970134e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.168478e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -11277,15 +11277,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.784786682149E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.832559781230E+03 kT\n Vpmg_energy:  dielEnergy = 3.414198595280E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.576000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.791800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -11334,160 +11334,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00419075 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.077950\n+Vacc_SASA: Time elapsed: 0.076489\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.959750e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.841830e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.843700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.842400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.693310e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.680030e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.563507e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.769165e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 707760.874892\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.578306e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.782952e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.145732e+05\n Vprtstp: contraction number = 1.145732e+05\n Vnewton: Attempting damping, relres = 0.153567\n Vnewton: Attempting damping, relres = 0.570617\n Vnewton: Damping accepted, relres = 0.153567\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.535669e-01\n Vprtstp: contraction number = 1.535669e-01\n Vnewton: Using errtol_s: 108688.631756\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.652030e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.857659e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.325223e+04\n Vprtstp: contraction number = 2.325223e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.989096e-02\n Vprtstp: contraction number = 1.946446e-01\n Vnewton: Using errtol_s: 21155.653880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.720015e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.900478e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.636674e+03\n Vprtstp: contraction number = 5.636674e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.169438e-03\n Vprtstp: contraction number = 2.398530e-01\n Vnewton: Using errtol_s: 5074.248008\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.783455e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.953356e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.473491e+03\n Vprtstp: contraction number = 1.473491e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.873734e-03\n Vprtstp: contraction number = 2.613502e-01\n Vnewton: Using errtol_s: 1326.155494\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.851076e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.047754e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.049387e+02\n Vprtstp: contraction number = 4.049387e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.149280e-04\n Vprtstp: contraction number = 2.748139e-01\n Vnewton: Using errtol_s: 364.445920\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.917456e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.181264e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.151043e+02\n Vprtstp: contraction number = 1.151043e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.463685e-04\n Vprtstp: contraction number = 2.842504e-01\n Vnewton: Using errtol_s: 103.593915\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.983272e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.303810e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.354853e+01\n Vprtstp: contraction number = 3.354853e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.266085e-05\n Vprtstp: contraction number = 2.914619e-01\n Vnewton: Using errtol_s: 30.193683\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.050085e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.421981e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.989786e+00\n Vprtstp: contraction number = 9.989786e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.270317e-05\n Vprtstp: contraction number = 2.977712e-01\n Vnewton: Using errtol_s: 8.990808\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.116392e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.540812e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.036177e+00\n Vprtstp: contraction number = 3.036177e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.860851e-06\n Vprtstp: contraction number = 3.039281e-01\n Vnewton: Using errtol_s: 2.732559\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.184554e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.675249e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.395196e-01\n Vprtstp: contraction number = 9.395196e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.194708e-06\n Vprtstp: contraction number = 3.094416e-01\n Vnewton: Using errtol_s: 0.845568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.252604e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.806200e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.950830e-01\n Vprtstp: contraction number = 2.950830e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.752323e-07\n Vprtstp: contraction number = 3.140786e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.472930e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.669423e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.130330e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.150516e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -11497,15 +11497,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.776812399064E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.065083445518E+03 kT\n Vpmg_energy:  dielEnergy = 4.030471976313E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.864300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.645000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -11534,162 +11534,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.100459\n+Vacc_SASA: Time elapsed: 0.158621\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.226950e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.038520e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.756000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.938800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.650600e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.204710e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.434196e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.051350e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1635307.042590\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.448888e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.078900e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.321219e+05\n Vprtstp: contraction number = 2.321219e+05\n Vnewton: Attempting damping, relres = 0.196154\n Vnewton: Attempting damping, relres = 0.565205\n Vnewton: Damping accepted, relres = 0.196154\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.961538e-01\n Vprtstp: contraction number = 1.961538e-01\n Vnewton: Using errtol_s: 320771.668801\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.521944e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.196724e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.431372e+04\n Vprtstp: contraction number = 4.431372e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.027511e-02\n Vprtstp: contraction number = 2.053242e-01\n Vnewton: Using errtol_s: 65862.177446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.602116e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.332260e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.117167e+04\n Vprtstp: contraction number = 1.117167e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.959711e-03\n Vprtstp: contraction number = 2.224627e-01\n Vnewton: Using errtol_s: 14651.878140\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.672278e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.443604e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.129072e+03\n Vprtstp: contraction number = 3.129072e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.898262e-03\n Vprtstp: contraction number = 2.118664e-01\n Vnewton: Using errtol_s: 3104.240662\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.741000e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.551595e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.589092e+02\n Vprtstp: contraction number = 8.589092e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.739068e-04\n Vprtstp: contraction number = 2.496530e-01\n Vnewton: Using errtol_s: 774.983094\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.808174e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.638845e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.479971e+02\n Vprtstp: contraction number = 2.479971e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.364875e-04\n Vprtstp: contraction number = 2.880050e-01\n Vnewton: Using errtol_s: 223.198993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.875084e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.745182e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.463517e+01\n Vprtstp: contraction number = 7.463517e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.107588e-05\n Vprtstp: contraction number = 3.009497e-01\n Vnewton: Using errtol_s: 67.171671\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.941707e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.876588e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.269594e+01\n Vprtstp: contraction number = 2.269594e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.249083e-05\n Vprtstp: contraction number = 3.040916e-01\n Vnewton: Using errtol_s: 20.426343\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.008469e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.979298e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.936769e+00\n Vprtstp: contraction number = 6.936769e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.817688e-06\n Vprtstp: contraction number = 3.056392e-01\n Vnewton: Using errtol_s: 6.243092\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.075976e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.096238e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.126909e+00\n Vprtstp: contraction number = 2.126909e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.170556e-06\n Vprtstp: contraction number = 3.066138e-01\n Vnewton: Using errtol_s: 1.914218\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.142208e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.218793e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.536389e-01\n Vprtstp: contraction number = 6.536389e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.597337e-07\n Vprtstp: contraction number = 3.073187e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.650196e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.841563e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.271345e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.298153e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -11699,17 +11699,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.754232717219E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.874256879798E+04 kT\n Vpmg_energy:  dielEnergy = 9.359714713535E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.836600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.341700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n Vpbe_ctor2:  bulk ionic strength = 0.2\n Vpbe_ctor2:  xkappa = 0.145625\n@@ -11756,160 +11756,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00885234 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.100632\n+Vacc_SASA: Time elapsed: 0.111206\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.575820e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.334010e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.814600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.845100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.677620e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.294090e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.246708e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.399768e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1674007.100681\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.261159e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.427414e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.902880e+05\n Vprtstp: contraction number = 2.902880e+05\n Vnewton: Attempting damping, relres = 0.222356\n Vnewton: Attempting damping, relres = 0.579491\n Vnewton: Damping accepted, relres = 0.222356\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.223561e-01\n Vprtstp: contraction number = 2.223561e-01\n Vnewton: Using errtol_s: 372225.695633\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.335523e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.537978e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.035839e+04\n Vprtstp: contraction number = 6.035839e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.793121e-02\n Vprtstp: contraction number = 2.155606e-01\n Vnewton: Using errtol_s: 80237.189117\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.421236e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.672056e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.603151e+04\n Vprtstp: contraction number = 1.603151e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.130393e-02\n Vprtstp: contraction number = 2.358364e-01\n Vnewton: Using errtol_s: 18922.853010\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.497081e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.796237e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.671524e+03\n Vprtstp: contraction number = 4.671524e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.665747e-03\n Vprtstp: contraction number = 2.358248e-01\n Vnewton: Using errtol_s: 4462.478601\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.568082e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.903299e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.362565e+03\n Vprtstp: contraction number = 1.362565e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.334180e-04\n Vprtstp: contraction number = 2.751267e-01\n Vnewton: Using errtol_s: 1227.746995\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.638060e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.004344e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.182590e+02\n Vprtstp: contraction number = 4.182590e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.248702e-04\n Vprtstp: contraction number = 3.066058e-01\n Vnewton: Using errtol_s: 376.434346\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.709065e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.105129e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.331321e+02\n Vprtstp: contraction number = 1.331321e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.157615e-05\n Vprtstp: contraction number = 3.182998e-01\n Vnewton: Using errtol_s: 119.818985\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.780739e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.210490e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.304104e+01\n Vprtstp: contraction number = 4.304104e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.314025e-05\n Vprtstp: contraction number = 3.232955e-01\n Vnewton: Using errtol_s: 38.736937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.852317e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.341948e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.406731e+01\n Vprtstp: contraction number = 1.406731e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.563038e-06\n Vprtstp: contraction number = 3.268348e-01\n Vnewton: Using errtol_s: 12.660580\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.922787e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.436119e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.637253e+00\n Vprtstp: contraction number = 4.637253e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.493136e-06\n Vprtstp: contraction number = 3.296474e-01\n Vnewton: Using errtol_s: 4.173527\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.992488e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.521975e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.538961e+00\n Vprtstp: contraction number = 1.538961e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.273947e-07\n Vprtstp: contraction number = 3.318691e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.065167e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.259613e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.172119e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.200763e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -11919,29 +11919,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.742146487539E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.135995019180E+04 kT\n Vpmg_energy:  dielEnergy = 1.066841914089E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.822600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.208700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 6.134646e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.661053e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:43:38 2025\n+# Creation Date and Time:  Sun Jan  7 09:47:54 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -12211,151 +12211,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.188309\n+Vacc_SASA: Time elapsed: 0.238957\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.331230e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.597420e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.755800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.861500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.690870e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.102070e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.437300e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.457620e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2280031.151733\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.825970e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.147679e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.954329e+05\n Vprtstp: contraction number = 2.954329e+05\n Vnewton: Attempting damping, relres = 0.135391\n Vnewton: Attempting damping, relres = 0.556564\n Vnewton: Damping accepted, relres = 0.135391\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.353914e-01\n Vprtstp: contraction number = 1.353914e-01\n Vnewton: Using errtol_s: 308696.705205\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.544473e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.506187e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.294410e+04\n Vprtstp: contraction number = 5.294410e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.429290e-02\n Vprtstp: contraction number = 1.794272e-01\n Vnewton: Using errtol_s: 55388.580044\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.389618e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.023305e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.235644e+04\n Vprtstp: contraction number = 1.235644e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.275732e-03\n Vprtstp: contraction number = 2.171717e-01\n Vnewton: Using errtol_s: 12028.832542\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.201356e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.260389e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.254639e+03\n Vprtstp: contraction number = 3.254639e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.294905e-03\n Vprtstp: contraction number = 2.454457e-01\n Vnewton: Using errtol_s: 2952.424699\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.998460e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.488707e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.022338e+02\n Vprtstp: contraction number = 9.022338e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.561621e-04\n Vprtstp: contraction number = 2.750487e-01\n Vnewton: Using errtol_s: 812.060580\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.795166e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.822550e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.611146e+02\n Vprtstp: contraction number = 2.611146e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.030702e-04\n Vprtstp: contraction number = 2.893914e-01\n Vnewton: Using errtol_s: 235.003369\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.580844e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.313239e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.731468e+01\n Vprtstp: contraction number = 7.731468e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.051854e-05\n Vprtstp: contraction number = 2.960946e-01\n Vnewton: Using errtol_s: 69.583224\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.391862e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.078557e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.323028e+01\n Vprtstp: contraction number = 2.323028e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.169724e-06\n Vprtstp: contraction number = 3.004640e-01\n Vnewton: Using errtol_s: 20.907256\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.175226e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.230350e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.057246e+00\n Vprtstp: contraction number = 7.057246e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.785717e-06\n Vprtstp: contraction number = 3.037951e-01\n Vnewton: Using errtol_s: 6.351522\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.976183e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.366687e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.163411e+00\n Vprtstp: contraction number = 2.163411e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.539662e-07\n Vprtstp: contraction number = 3.065517e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.123472e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.319452e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.383677e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.408510e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -12365,17 +12365,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.169811385763E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.567248755988E+04 kT\n Vpmg_energy:  dielEnergy = 1.282904610946E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.818500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.210500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.225\n Vpbe_ctor2:  xkappa = 0.154458\n@@ -12422,160 +12422,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0200222 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.184362\n+Vacc_SASA: Time elapsed: 0.192241\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.859780e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.905630e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.801700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.823300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.686360e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.124580e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.272753e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.556681e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2338884.582029\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.413425e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.585271e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.674153e+05\n Vprtstp: contraction number = 3.674153e+05\n Vnewton: Attempting damping, relres = 0.159441\n Vnewton: Attempting damping, relres = 0.569142\n Vnewton: Damping accepted, relres = 0.159441\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.594406e-01\n Vprtstp: contraction number = 1.594406e-01\n Vnewton: Using errtol_s: 372913.066228\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.026139e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.732375e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.262273e+04\n Vprtstp: contraction number = 7.262273e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.123186e-02\n Vprtstp: contraction number = 1.958841e-01\n Vnewton: Using errtol_s: 73047.725996\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.110055e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.855063e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.810013e+04\n Vprtstp: contraction number = 1.810013e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.334559e-03\n Vprtstp: contraction number = 2.348422e-01\n Vnewton: Using errtol_s: 17154.687500\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.191262e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.921833e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.995290e+03\n Vprtstp: contraction number = 4.995290e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.929832e-03\n Vprtstp: contraction number = 2.631149e-01\n Vnewton: Using errtol_s: 4513.654553\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.271083e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.055524e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.448761e+03\n Vprtstp: contraction number = 1.448761e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.574979e-04\n Vprtstp: contraction number = 2.888841e-01\n Vnewton: Using errtol_s: 1303.923175\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.352792e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.180836e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.389996e+02\n Vprtstp: contraction number = 4.389996e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.689267e-04\n Vprtstp: contraction number = 3.030087e-01\n Vnewton: Using errtol_s: 395.100089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.431608e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.289686e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.367279e+02\n Vprtstp: contraction number = 1.367279e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.261275e-05\n Vprtstp: contraction number = 3.114531e-01\n Vnewton: Using errtol_s: 123.055159\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.516226e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.428083e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.345198e+01\n Vprtstp: contraction number = 4.345198e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.672027e-05\n Vprtstp: contraction number = 3.177988e-01\n Vnewton: Using errtol_s: 39.106785\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.597919e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.562014e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.405050e+01\n Vprtstp: contraction number = 1.405050e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.406615e-06\n Vprtstp: contraction number = 3.233569e-01\n Vnewton: Using errtol_s: 12.645449\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.673971e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.693114e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.608577e+00\n Vprtstp: contraction number = 4.608577e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.773375e-06\n Vprtstp: contraction number = 3.280010e-01\n Vnewton: Using errtol_s: 4.147720\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.755958e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.810732e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.529264e+00\n Vprtstp: contraction number = 1.529264e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.884589e-07\n Vprtstp: contraction number = 3.318299e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.018444e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.215801e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.386211e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.410630e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -12585,15 +12585,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.155729316700E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951863418321E+04 kT\n Vpmg_energy:  dielEnergy = 1.475213228301E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.784200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.007300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -12622,151 +12622,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.063459\n+Vacc_SASA: Time elapsed: 0.075074\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.494480e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.312300e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.789700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.836300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.665900e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.279190e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.947540e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.082344e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 671593.797102\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.961820e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.112182e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.076362e+04\n Vprtstp: contraction number = 9.076362e+04\n Vnewton: Attempting damping, relres = 0.130235\n Vnewton: Attempting damping, relres = 0.558450\n Vnewton: Damping accepted, relres = 0.130235\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.302353e-01\n Vprtstp: contraction number = 1.302353e-01\n Vnewton: Using errtol_s: 87465.248573\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.034072e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.219805e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.691112e+04\n Vprtstp: contraction number = 1.691112e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.299894e-02\n Vprtstp: contraction number = 1.765952e-01\n Vnewton: Using errtol_s: 15445.947049\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.098064e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.313118e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.838772e+03\n Vprtstp: contraction number = 3.838772e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.145781e-03\n Vprtstp: contraction number = 2.237399e-01\n Vnewton: Using errtol_s: 3455.874833\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.162689e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.410135e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.728949e+02\n Vprtstp: contraction number = 9.728949e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.303780e-03\n Vprtstp: contraction number = 2.533688e-01\n Vnewton: Using errtol_s: 875.610893\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.224290e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.475236e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.612895e+02\n Vprtstp: contraction number = 2.612895e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.501534e-04\n Vprtstp: contraction number = 2.685677e-01\n Vnewton: Using errtol_s: 235.160844\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.287875e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.598078e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.244969e+01\n Vprtstp: contraction number = 7.244969e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.708955e-05\n Vprtstp: contraction number = 2.772772e-01\n Vnewton: Using errtol_s: 65.204742\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.351296e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.691302e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052456e+01\n Vprtstp: contraction number = 2.052456e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.750488e-05\n Vprtstp: contraction number = 2.832939e-01\n Vnewton: Using errtol_s: 18.472107\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.416742e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.806864e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.913055e+00\n Vprtstp: contraction number = 5.913055e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.924060e-06\n Vprtstp: contraction number = 2.880965e-01\n Vnewton: Using errtol_s: 5.321750\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.480148e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.930784e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.727677e+00\n Vprtstp: contraction number = 1.727677e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.315252e-06\n Vprtstp: contraction number = 2.921800e-01\n Vnewton: Using errtol_s: 1.554909\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.544610e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.032319e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.107037e-01\n Vprtstp: contraction number = 5.107037e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.843918e-07\n Vprtstp: contraction number = 2.956014e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.504335e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.698305e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.049681e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.075694e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -12776,15 +12776,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.799206762060E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.832181524092E+03 kT\n Vpmg_energy:  dielEnergy = 3.414010557344E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.881300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.552300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -12833,160 +12833,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00378487 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.061404\n+Vacc_SASA: Time elapsed: 0.076475\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.713280e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.803040e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.768700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.812900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.660340e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.060180e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.636685e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.187861e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 699069.872719\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.650954e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.211394e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.130075e+05\n Vprtstp: contraction number = 1.130075e+05\n Vnewton: Attempting damping, relres = 0.153289\n Vnewton: Attempting damping, relres = 0.570479\n Vnewton: Damping accepted, relres = 0.153289\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.532887e-01\n Vprtstp: contraction number = 1.532887e-01\n Vnewton: Using errtol_s: 107159.480370\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.725982e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.327558e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.297596e+04\n Vprtstp: contraction number = 2.297596e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.988594e-02\n Vprtstp: contraction number = 1.949651e-01\n Vnewton: Using errtol_s: 20892.361484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.794723e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.418956e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.581341e+03\n Vprtstp: contraction number = 5.581341e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.187204e-03\n Vprtstp: contraction number = 2.404878e-01\n Vnewton: Using errtol_s: 5024.357995\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.862294e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.499779e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.462004e+03\n Vprtstp: contraction number = 1.462004e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.882240e-03\n Vprtstp: contraction number = 2.618876e-01\n Vnewton: Using errtol_s: 1315.817196\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.929816e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.598562e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.024878e+02\n Vprtstp: contraction number = 4.024878e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.181744e-04\n Vprtstp: contraction number = 2.752967e-01\n Vnewton: Using errtol_s: 362.240101\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.997445e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.698017e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.145747e+02\n Vprtstp: contraction number = 1.145747e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.475065e-04\n Vprtstp: contraction number = 2.846658e-01\n Vnewton: Using errtol_s: 103.117357\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.064384e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.764526e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.343339e+01\n Vprtstp: contraction number = 3.343339e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.304299e-05\n Vprtstp: contraction number = 2.918040e-01\n Vnewton: Using errtol_s: 30.090059\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.130651e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.852703e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.964601e+00\n Vprtstp: contraction number = 9.964601e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.282868e-05\n Vprtstp: contraction number = 2.980433e-01\n Vnewton: Using errtol_s: 8.968142\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.198171e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.922241e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.030606e+00\n Vprtstp: contraction number = 3.030606e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.901677e-06\n Vprtstp: contraction number = 3.041372e-01\n Vnewton: Using errtol_s: 2.727545\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.264628e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.032233e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.382714e-01\n Vprtstp: contraction number = 9.382714e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.207954e-06\n Vprtstp: contraction number = 3.095986e-01\n Vnewton: Using errtol_s: 0.844444\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.331946e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.125134e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.947982e-01\n Vprtstp: contraction number = 2.947982e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.795306e-07\n Vprtstp: contraction number = 3.141929e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.530060e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.724026e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.032427e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.055623e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -12996,15 +12996,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.791143336195E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.064706767372E+03 kT\n Vpmg_energy:  dielEnergy = 4.030284850929E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.857200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.239200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -13033,162 +13033,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.100157\n+Vacc_SASA: Time elapsed: 0.109319\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.201940e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.327280e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.817800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.775700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.697390e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.282050e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.511581e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.364371e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1599051.147684\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.525687e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.395804e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.270628e+05\n Vprtstp: contraction number = 2.270628e+05\n Vnewton: Attempting damping, relres = 0.190153\n Vnewton: Attempting damping, relres = 0.564950\n Vnewton: Damping accepted, relres = 0.190153\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.901527e-01\n Vprtstp: contraction number = 1.901527e-01\n Vnewton: Using errtol_s: 304063.886192\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.598949e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.536242e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.318204e+04\n Vprtstp: contraction number = 4.318204e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.822370e-02\n Vprtstp: contraction number = 2.010158e-01\n Vnewton: Using errtol_s: 61121.655411\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.677300e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.671851e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.090069e+04\n Vprtstp: contraction number = 1.090069e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.378283e-03\n Vprtstp: contraction number = 2.191908e-01\n Vnewton: Using errtol_s: 13397.302580\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.747948e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.772397e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.039014e+03\n Vprtstp: contraction number = 3.039014e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.821126e-03\n Vprtstp: contraction number = 2.173626e-01\n Vnewton: Using errtol_s: 2912.073157\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.812901e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.873839e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.399695e+02\n Vprtstp: contraction number = 8.399695e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.733052e-04\n Vprtstp: contraction number = 2.598970e-01\n Vnewton: Using errtol_s: 756.839199\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.877974e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.969665e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.453869e+02\n Vprtstp: contraction number = 2.453869e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.381125e-04\n Vprtstp: contraction number = 2.918043e-01\n Vnewton: Using errtol_s: 220.848913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.969185e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.085747e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.399321e+01\n Vprtstp: contraction number = 7.399321e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.164589e-05\n Vprtstp: contraction number = 3.015360e-01\n Vnewton: Using errtol_s: 66.593908\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.068631e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.207711e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.251212e+01\n Vprtstp: contraction number = 2.251212e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.267058e-05\n Vprtstp: contraction number = 3.042457e-01\n Vnewton: Using errtol_s: 20.260912\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.178495e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.316772e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.882100e+00\n Vprtstp: contraction number = 6.882100e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.873479e-06\n Vprtstp: contraction number = 3.057064e-01\n Vnewton: Using errtol_s: 6.193891\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.287174e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.422350e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.110443e+00\n Vprtstp: contraction number = 2.110443e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.187828e-06\n Vprtstp: contraction number = 3.066568e-01\n Vnewton: Using errtol_s: 1.899398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.387755e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.541501e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.486511e-01\n Vprtstp: contraction number = 6.486511e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.650828e-07\n Vprtstp: contraction number = 3.073531e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.685750e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.881197e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.275143e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.301156e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -13198,17 +13198,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.557875288956E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.874100920803E+04 kT\n Vpmg_energy:  dielEnergy = 9.359333289528E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.870400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.999900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n Vpbe_ctor2:  bulk ionic strength = 0.225\n Vpbe_ctor2:  xkappa = 0.154458\n@@ -13255,160 +13255,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00715191 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.111355\n+Vacc_SASA: Time elapsed: 0.109600\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.171700e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.220980e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.795400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.823700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.082460e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.122210e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.547842e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.710986e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1635353.597903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.576173e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.739334e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.841111e+05\n Vprtstp: contraction number = 2.841111e+05\n Vnewton: Attempting damping, relres = 0.216841\n Vnewton: Attempting damping, relres = 0.579374\n Vnewton: Damping accepted, relres = 0.216841\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.168415e-01\n Vprtstp: contraction number = 2.168415e-01\n Vnewton: Using errtol_s: 354612.472828\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.699296e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.844468e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.888895e+04\n Vprtstp: contraction number = 5.888895e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.598888e-02\n Vprtstp: contraction number = 2.120853e-01\n Vnewton: Using errtol_s: 75208.075023\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.823779e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.963710e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.566082e+04\n Vprtstp: contraction number = 1.566082e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.075687e-02\n Vprtstp: contraction number = 2.339015e-01\n Vnewton: Using errtol_s: 17591.280350\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.897431e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.058995e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.551176e+03\n Vprtstp: contraction number = 4.551176e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.599859e-03\n Vprtstp: contraction number = 2.416930e-01\n Vnewton: Using errtol_s: 4251.688603\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.992723e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.169695e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.335913e+03\n Vprtstp: contraction number = 1.335913e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.355871e-04\n Vprtstp: contraction number = 2.829335e-01\n Vnewton: Using errtol_s: 1202.945014\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.095373e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.260664e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.136155e+02\n Vprtstp: contraction number = 4.136155e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.276295e-04\n Vprtstp: contraction number = 3.094528e-01\n Vnewton: Using errtol_s: 372.254692\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.204444e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.365623e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.319427e+02\n Vprtstp: contraction number = 1.319427e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.261334e-05\n Vprtstp: contraction number = 3.189980e-01\n Vnewton: Using errtol_s: 118.748486\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.313638e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.463699e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.270247e+01\n Vprtstp: contraction number = 4.270247e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.350087e-05\n Vprtstp: contraction number = 3.236440e-01\n Vnewton: Using errtol_s: 38.432230\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.423401e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.589834e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.396688e+01\n Vprtstp: contraction number = 1.396688e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.686528e-06\n Vprtstp: contraction number = 3.270742e-01\n Vnewton: Using errtol_s: 12.570191\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.535398e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.691403e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.606421e+00\n Vprtstp: contraction number = 4.606421e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.535096e-06\n Vprtstp: contraction number = 3.298104e-01\n Vnewton: Using errtol_s: 4.145779\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.644467e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.790263e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.529247e+00\n Vprtstp: contraction number = 1.529247e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.416053e-07\n Vprtstp: contraction number = 3.319816e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.191905e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.215712e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.189863e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.214376e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -13418,29 +13418,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.546220466896E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.135839093340E+04 kT\n Vpmg_energy:  dielEnergy = 1.066803828890E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.616700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.813200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.823964e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.984782e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:44:15 2025\n+# Creation Date and Time:  Sun Jan  7 09:48:12 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -13710,151 +13710,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.210484\n+Vacc_SASA: Time elapsed: 0.210164\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.415160e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.961290e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.855100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.853800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.952930e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.096750e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.056420e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.532880e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2251971.697064\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.088990e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.061498e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.916802e+05\n Vprtstp: contraction number = 2.916802e+05\n Vnewton: Attempting damping, relres = 0.133998\n Vnewton: Attempting damping, relres = 0.556443\n Vnewton: Damping accepted, relres = 0.133998\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.339981e-01\n Vprtstp: contraction number = 1.339981e-01\n Vnewton: Using errtol_s: 301759.930673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.484253e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.612192e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.235007e+04\n Vprtstp: contraction number = 5.235007e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.393476e-02\n Vprtstp: contraction number = 1.786201e-01\n Vnewton: Using errtol_s: 53900.402880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.547499e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.892261e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.224190e+04\n Vprtstp: contraction number = 1.224190e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.213784e-03\n Vprtstp: contraction number = 2.178331e-01\n Vnewton: Using errtol_s: 11741.294295\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.369285e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.075935e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.226956e+03\n Vprtstp: contraction number = 3.226956e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.296373e-03\n Vprtstp: contraction number = 2.486433e-01\n Vnewton: Using errtol_s: 2919.394410\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.166656e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.156856e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.979745e+02\n Vprtstp: contraction number = 8.979745e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.588880e-04\n Vprtstp: contraction number = 2.768402e-01\n Vnewton: Using errtol_s: 808.205614\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.961762e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.280725e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.602996e+02\n Vprtstp: contraction number = 2.602996e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.040288e-04\n Vprtstp: contraction number = 2.898642e-01\n Vnewton: Using errtol_s: 234.269873\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.759321e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.383382e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.710898e+01\n Vprtstp: contraction number = 7.710898e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.081659e-05\n Vprtstp: contraction number = 2.962314e-01\n Vnewton: Using errtol_s: 69.398097\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.556133e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.528023e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.317379e+01\n Vprtstp: contraction number = 2.317379e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.261402e-06\n Vprtstp: contraction number = 3.005329e-01\n Vnewton: Using errtol_s: 20.856415\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.350882e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.074227e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.040959e+00\n Vprtstp: contraction number = 7.040959e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.813918e-06\n Vprtstp: contraction number = 3.038328e-01\n Vnewton: Using errtol_s: 6.336864\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.142153e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.182973e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.158573e+00\n Vprtstp: contraction number = 2.158573e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.626731e-07\n Vprtstp: contraction number = 3.065736e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.038646e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.265762e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.198088e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.222326e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -13864,15 +13864,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.054258370854E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.567152466024E+04 kT\n Vpmg_energy:  dielEnergy = 1.282878106932E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.795800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.421500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -13921,160 +13921,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0186115 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.180519\n+Vacc_SASA: Time elapsed: 0.189107\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.728450e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.531190e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.842000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.836800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.678140e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.126000e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.043458e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.359819e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2308477.613734\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.057544e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.390747e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.628256e+05\n Vprtstp: contraction number = 3.628256e+05\n Vnewton: Attempting damping, relres = 0.158221\n Vnewton: Attempting damping, relres = 0.569085\n Vnewton: Damping accepted, relres = 0.158221\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.582211e-01\n Vprtstp: contraction number = 1.582211e-01\n Vnewton: Using errtol_s: 365249.935342\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.143746e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.540367e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.179371e+04\n Vprtstp: contraction number = 7.179371e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.090684e-02\n Vprtstp: contraction number = 1.953395e-01\n Vnewton: Using errtol_s: 71347.745828\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.227958e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.686916e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.791601e+04\n Vprtstp: contraction number = 1.791601e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.281434e-03\n Vprtstp: contraction number = 2.355930e-01\n Vnewton: Using errtol_s: 16809.026903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.312496e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.788508e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.947991e+03\n Vprtstp: contraction number = 4.947991e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.933961e-03\n Vprtstp: contraction number = 2.656017e-01\n Vnewton: Using errtol_s: 4464.506758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.395055e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.897355e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.439628e+03\n Vprtstp: contraction number = 1.439628e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.612744e-04\n Vprtstp: contraction number = 2.902201e-01\n Vnewton: Using errtol_s: 1295.689464\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.477704e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.026313e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.369472e+02\n Vprtstp: contraction number = 4.369472e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.703516e-04\n Vprtstp: contraction number = 3.035087e-01\n Vnewton: Using errtol_s: 393.252962\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.562266e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.151713e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.361967e+02\n Vprtstp: contraction number = 1.361967e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.309866e-05\n Vprtstp: contraction number = 3.117003e-01\n Vnewton: Using errtol_s: 122.577063\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.643736e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.261766e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.330599e+01\n Vprtstp: contraction number = 4.330599e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.688359e-05\n Vprtstp: contraction number = 3.179665e-01\n Vnewton: Using errtol_s: 38.975398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.721305e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.386597e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.400799e+01\n Vprtstp: contraction number = 1.400799e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.461259e-06\n Vprtstp: contraction number = 3.234655e-01\n Vnewton: Using errtol_s: 12.607195\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.804620e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.520035e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.595493e+00\n Vprtstp: contraction number = 4.595493e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.791632e-06\n Vprtstp: contraction number = 3.280621e-01\n Vnewton: Using errtol_s: 4.135943\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.888548e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.635757e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.525032e+00\n Vprtstp: contraction number = 1.525032e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.945603e-07\n Vprtstp: contraction number = 3.318539e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.197944e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.394552e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.373835e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.400871e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -14084,15 +14084,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.040496519362E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951767181280E+04 kT\n Vpmg_energy:  dielEnergy = 1.475186803356E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.796500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.523400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -14121,151 +14121,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.063345\n+Vacc_SASA: Time elapsed: 0.075323\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.491020e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.325720e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.779200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.818100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.663890e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.197250e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.081290e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.868387e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 665026.668065\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.095004e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.892655e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.977874e+04\n Vprtstp: contraction number = 8.977874e+04\n Vnewton: Attempting damping, relres = 0.130004\n Vnewton: Attempting damping, relres = 0.558352\n Vnewton: Damping accepted, relres = 0.130004\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.300040e-01\n Vprtstp: contraction number = 1.300040e-01\n Vnewton: Using errtol_s: 86456.120106\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.165522e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.998115e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.677494e+04\n Vprtstp: contraction number = 1.677494e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.302058e-02\n Vprtstp: contraction number = 1.770760e-01\n Vnewton: Using errtol_s: 15309.299757\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.229580e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.090522e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.819009e+03\n Vprtstp: contraction number = 3.819009e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.169720e-03\n Vprtstp: contraction number = 2.245695e-01\n Vnewton: Using errtol_s: 3438.001701\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.293177e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.206524e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.699577e+02\n Vprtstp: contraction number = 9.699577e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.312680e-03\n Vprtstp: contraction number = 2.539171e-01\n Vnewton: Using errtol_s: 872.967407\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.356213e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.322326e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.608286e+02\n Vprtstp: contraction number = 2.608286e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.529874e-04\n Vprtstp: contraction number = 2.689059e-01\n Vnewton: Using errtol_s: 234.746058\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.419395e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.424986e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.237536e+01\n Vprtstp: contraction number = 7.237536e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.794772e-05\n Vprtstp: contraction number = 2.774822e-01\n Vnewton: Using errtol_s: 65.137847\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.483585e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.513162e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.051211e+01\n Vprtstp: contraction number = 2.051211e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.775964e-05\n Vprtstp: contraction number = 2.834128e-01\n Vnewton: Using errtol_s: 18.460901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.547655e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.613746e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.910817e+00\n Vprtstp: contraction number = 5.910817e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.999282e-06\n Vprtstp: contraction number = 2.881623e-01\n Vnewton: Using errtol_s: 5.319736\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.611445e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.728192e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.727236e+00\n Vprtstp: contraction number = 1.727236e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.337519e-06\n Vprtstp: contraction number = 2.922161e-01\n Vnewton: Using errtol_s: 1.554512\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.674405e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.839885e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.106059e-01\n Vprtstp: contraction number = 5.106059e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.910179e-07\n Vprtstp: contraction number = 2.956203e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.465978e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.657672e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.049066e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.074156e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -14275,17 +14275,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.810176987891E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.831840502654E+03 kT\n Vpmg_energy:  dielEnergy = 3.413842577574E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.867200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.706500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n Vpbe_ctor2:  bulk ionic strength = 0.25\n Vpbe_ctor2:  xkappa = 0.162813\n@@ -14332,160 +14332,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00343543 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.061609\n+Vacc_SASA: Time elapsed: 0.069310\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.721180e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.663280e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.690900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.826700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.604250e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.283810e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.766179e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.973764e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 691979.805773\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.779708e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.006130e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.117154e+05\n Vprtstp: contraction number = 1.117154e+05\n Vnewton: Attempting damping, relres = 0.153004\n Vnewton: Attempting damping, relres = 0.570353\n Vnewton: Damping accepted, relres = 0.153004\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.530041e-01\n Vprtstp: contraction number = 1.530041e-01\n Vnewton: Using errtol_s: 105875.763511\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.849721e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.129965e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.274708e+04\n Vprtstp: contraction number = 2.274708e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.987439e-02\n Vprtstp: contraction number = 1.952522e-01\n Vnewton: Using errtol_s: 20672.472417\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.914963e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.230339e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.535330e+03\n Vprtstp: contraction number = 5.535330e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.200880e-03\n Vprtstp: contraction number = 2.410386e-01\n Vnewton: Using errtol_s: 4982.863785\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.981505e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.345885e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.452451e+03\n Vprtstp: contraction number = 1.452451e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.889102e-03\n Vprtstp: contraction number = 2.623432e-01\n Vnewton: Using errtol_s: 1307.220185\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.047260e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.445294e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.004485e+02\n Vprtstp: contraction number = 4.004485e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.208313e-04\n Vprtstp: contraction number = 2.757032e-01\n Vnewton: Using errtol_s: 360.404730\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.112035e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.536837e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.141337e+02\n Vprtstp: contraction number = 1.141337e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.484443e-04\n Vprtstp: contraction number = 2.850142e-01\n Vnewton: Using errtol_s: 102.720463\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.178112e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.631409e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.333734e+01\n Vprtstp: contraction number = 3.333734e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.335909e-05\n Vprtstp: contraction number = 2.920899e-01\n Vnewton: Using errtol_s: 30.003614\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.240431e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.746476e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.943557e+00\n Vprtstp: contraction number = 9.943557e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.293275e-05\n Vprtstp: contraction number = 2.982708e-01\n Vnewton: Using errtol_s: 8.949202\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.300765e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.849112e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.025944e+00\n Vprtstp: contraction number = 3.025944e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.935591e-06\n Vprtstp: contraction number = 3.043120e-01\n Vnewton: Using errtol_s: 2.723350\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.367306e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.938542e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.372238e-01\n Vprtstp: contraction number = 9.372238e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.218968e-06\n Vprtstp: contraction number = 3.097294e-01\n Vnewton: Using errtol_s: 0.843501\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.433757e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.040433e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.945582e-01\n Vprtstp: contraction number = 2.945582e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.831071e-07\n Vprtstp: contraction number = 3.142880e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.248847e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.433688e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.142891e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.169154e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -14495,15 +14495,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.802033666464E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.064367172760E+03 kT\n Vpmg_energy:  dielEnergy = 4.030117685645E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.850600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.300600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -14532,162 +14532,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.101079\n+Vacc_SASA: Time elapsed: 0.118133\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.191410e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.435430e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.696500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.944100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.573680e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.041920e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.609793e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.263815e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1569842.241791\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.623877e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.293042e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.229696e+05\n Vprtstp: contraction number = 2.229696e+05\n Vnewton: Attempting damping, relres = 0.185061\n Vnewton: Attempting damping, relres = 0.564709\n Vnewton: Damping accepted, relres = 0.185061\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.850613e-01\n Vprtstp: contraction number = 1.850613e-01\n Vnewton: Using errtol_s: 290517.094461\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.695436e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.414275e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.227646e+04\n Vprtstp: contraction number = 4.227646e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.651895e-02\n Vprtstp: contraction number = 1.973343e-01\n Vnewton: Using errtol_s: 57328.986523\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.770875e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.486601e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.068153e+04\n Vprtstp: contraction number = 1.068153e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.924548e-03\n Vprtstp: contraction number = 2.169982e-01\n Vnewton: Using errtol_s: 12440.289572\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.838825e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.600016e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.967582e+03\n Vprtstp: contraction number = 2.967582e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.771235e-03\n Vprtstp: contraction number = 2.235125e-01\n Vnewton: Using errtol_s: 2780.560196\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.900006e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.706334e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.265098e+02\n Vprtstp: contraction number = 8.265098e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.740960e-04\n Vprtstp: contraction number = 2.676640e-01\n Vnewton: Using errtol_s: 744.255948\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.966943e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.806334e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.434115e+02\n Vprtstp: contraction number = 2.434115e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.395496e-04\n Vprtstp: contraction number = 2.943487e-01\n Vnewton: Using errtol_s: 219.070780\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.034585e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.926441e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.348771e+01\n Vprtstp: contraction number = 7.348771e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.213095e-05\n Vprtstp: contraction number = 3.019068e-01\n Vnewton: Using errtol_s: 66.138952\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.101167e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.048069e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.236672e+01\n Vprtstp: contraction number = 2.236672e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.282298e-05\n Vprtstp: contraction number = 3.043600e-01\n Vnewton: Using errtol_s: 20.130053\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.167668e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.169403e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.838847e+00\n Vprtstp: contraction number = 6.838847e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.920752e-06\n Vprtstp: contraction number = 3.057599e-01\n Vnewton: Using errtol_s: 6.154962\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.233417e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.284980e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.097413e+00\n Vprtstp: contraction number = 2.097413e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.202459e-06\n Vprtstp: contraction number = 3.066910e-01\n Vnewton: Using errtol_s: 1.887672\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.299843e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.378255e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.447028e-01\n Vprtstp: contraction number = 6.447028e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.696120e-07\n Vprtstp: contraction number = 3.073800e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.467190e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.648940e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.194783e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.219147e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -14697,15 +14697,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.380223605804E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.873963354108E+04 kT\n Vpmg_energy:  dielEnergy = 9.358993220617E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.833700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.231400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -14754,160 +14754,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00593059 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.105398\n+Vacc_SASA: Time elapsed: 0.136167\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.603830e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.325270e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.752300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.768800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.672650e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.887930e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.404079e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.529455e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1604207.937715\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.418041e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.559622e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.790911e+05\n Vprtstp: contraction number = 2.790911e+05\n Vnewton: Attempting damping, relres = 0.212135\n Vnewton: Attempting damping, relres = 0.579242\n Vnewton: Damping accepted, relres = 0.212135\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.121354e-01\n Vprtstp: contraction number = 2.121354e-01\n Vnewton: Using errtol_s: 340309.311873\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.493102e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.644301e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.770596e+04\n Vprtstp: contraction number = 5.770596e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.436697e-02\n Vprtstp: contraction number = 2.091445e-01\n Vnewton: Using errtol_s: 71173.837804\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.575667e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.780934e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.535772e+04\n Vprtstp: contraction number = 1.535772e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.032915e-02\n Vprtstp: contraction number = 2.328117e-01\n Vnewton: Using errtol_s: 16570.101449\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.648944e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.852632e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.454547e+03\n Vprtstp: contraction number = 4.454547e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.558458e-03\n Vprtstp: contraction number = 2.476930e-01\n Vnewton: Using errtol_s: 4104.298326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.718495e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.928700e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.316329e+03\n Vprtstp: contraction number = 1.316329e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.386763e-04\n Vprtstp: contraction number = 2.887193e-01\n Vnewton: Using errtol_s: 1184.990339\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.788565e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.023184e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.099732e+02\n Vprtstp: contraction number = 4.099732e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.300054e-04\n Vprtstp: contraction number = 3.113751e-01\n Vnewton: Using errtol_s: 368.976439\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.858400e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.101687e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.309902e+02\n Vprtstp: contraction number = 1.309902e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.348872e-05\n Vprtstp: contraction number = 3.195087e-01\n Vnewton: Using errtol_s: 117.891195\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.929227e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.213050e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.243118e+01\n Vprtstp: contraction number = 4.243118e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.380494e-05\n Vprtstp: contraction number = 3.239264e-01\n Vnewton: Using errtol_s: 38.188070\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.000149e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.340001e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.388647e+01\n Vprtstp: contraction number = 1.388647e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.790652e-06\n Vprtstp: contraction number = 3.272704e-01\n Vnewton: Using errtol_s: 12.497826\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.070378e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.445577e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.581763e+00\n Vprtstp: contraction number = 4.581763e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.570482e-06\n Vprtstp: contraction number = 3.299443e-01\n Vnewton: Using errtol_s: 4.123587\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.140179e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.550970e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.521483e+00\n Vprtstp: contraction number = 1.521483e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.535894e-07\n Vprtstp: contraction number = 3.320737e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.975588e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.169562e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.128489e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.151119e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -14917,29 +14917,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.368902130517E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.135701558187E+04 kT\n Vpmg_energy:  dielEnergy = 1.066769863960E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.824900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.340700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.283785e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.743466e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:44:59 2025\n+# Creation Date and Time:  Sun Jan  7 09:48:31 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -15209,151 +15209,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.183652\n+Vacc_SASA: Time elapsed: 0.219024\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.279720e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.601650e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.733400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.735300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.612590e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.252910e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.301370e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.548270e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2228500.711111\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.744330e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.186960e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.885324e+05\n Vprtstp: contraction number = 2.885324e+05\n Vnewton: Attempting damping, relres = 0.132783\n Vnewton: Attempting damping, relres = 0.556333\n Vnewton: Damping accepted, relres = 0.132783\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.327828e-01\n Vprtstp: contraction number = 1.327828e-01\n Vnewton: Using errtol_s: 295906.495800\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.529539e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.889091e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.185298e+04\n Vprtstp: contraction number = 5.185298e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.363031e-02\n Vprtstp: contraction number = 1.779622e-01\n Vnewton: Using errtol_s: 52660.160944\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.367290e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.351225e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214543e+04\n Vprtstp: contraction number = 1.214543e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.166063e-03\n Vprtstp: contraction number = 2.186202e-01\n Vnewton: Using errtol_s: 11512.574293\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.188864e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.048375e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.204841e+03\n Vprtstp: contraction number = 3.204841e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.298834e-03\n Vprtstp: contraction number = 2.514166e-01\n Vnewton: Using errtol_s: 2894.452376\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.972300e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.993636e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.947420e+02\n Vprtstp: contraction number = 8.947420e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.613575e-04\n Vprtstp: contraction number = 2.782168e-01\n Vnewton: Using errtol_s: 805.285400\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.759120e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.764222e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.596666e+02\n Vprtstp: contraction number = 2.596666e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.048688e-04\n Vprtstp: contraction number = 2.902078e-01\n Vnewton: Using errtol_s: 233.700117\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.556259e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.240194e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.695052e+01\n Vprtstp: contraction number = 7.695052e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.107716e-05\n Vprtstp: contraction number = 2.963434e-01\n Vnewton: Using errtol_s: 69.255484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.356329e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.348461e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.313064e+01\n Vprtstp: contraction number = 2.313064e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.341518e-06\n Vprtstp: contraction number = 3.005911e-01\n Vnewton: Using errtol_s: 20.817580\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.157751e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.035706e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.028571e+00\n Vprtstp: contraction number = 7.028571e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.838551e-06\n Vprtstp: contraction number = 3.038640e-01\n Vnewton: Using errtol_s: 6.325714\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.963818e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.165664e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.154905e+00\n Vprtstp: contraction number = 2.154905e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.702776e-07\n Vprtstp: contraction number = 3.065922e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.141984e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.329478e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.196269e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.221979e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -15363,17 +15363,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.948103828558E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.567066305004E+04 kT\n Vpmg_energy:  dielEnergy = 1.282854148760E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.808000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.538500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.275\n Vpbe_ctor2:  xkappa = 0.17076\n@@ -15420,160 +15420,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0175518 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.180404\n+Vacc_SASA: Time elapsed: 0.202393\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.746920e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.982270e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.759400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.066900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.637440e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.280190e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.258933e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.372320e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2283064.573073\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.404808e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.406230e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.589605e+05\n Vprtstp: contraction number = 3.589605e+05\n Vnewton: Attempting damping, relres = 0.157146\n Vnewton: Attempting damping, relres = 0.569027\n Vnewton: Damping accepted, relres = 0.157146\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.571455e-01\n Vprtstp: contraction number = 1.571455e-01\n Vnewton: Using errtol_s: 358773.390898\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.028902e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.561298e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.109555e+04\n Vprtstp: contraction number = 7.109555e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.062803e-02\n Vprtstp: contraction number = 1.949023e-01\n Vnewton: Using errtol_s: 69925.774403\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.114145e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.704850e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.775956e+04\n Vprtstp: contraction number = 1.775956e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.240527e-03\n Vprtstp: contraction number = 2.364020e-01\n Vnewton: Using errtol_s: 16530.590965\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.198157e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.813153e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.909187e+03\n Vprtstp: contraction number = 4.909187e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.938451e-03\n Vprtstp: contraction number = 2.677224e-01\n Vnewton: Using errtol_s: 4425.608962\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.279863e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.930987e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.432328e+03\n Vprtstp: contraction number = 1.432328e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.646405e-04\n Vprtstp: contraction number = 2.912844e-01\n Vnewton: Using errtol_s: 1289.110788\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.363875e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.023294e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.352860e+02\n Vprtstp: contraction number = 4.352860e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.715930e-04\n Vprtstp: contraction number = 3.038977e-01\n Vnewton: Using errtol_s: 391.757810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.440410e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.187834e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.357704e+02\n Vprtstp: contraction number = 1.357704e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.352166e-05\n Vprtstp: contraction number = 3.119106e-01\n Vnewton: Using errtol_s: 122.193412\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.525972e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.280625e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.319013e+01\n Vprtstp: contraction number = 4.319013e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.702585e-05\n Vprtstp: contraction number = 3.181115e-01\n Vnewton: Using errtol_s: 38.871124\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.600838e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.411181e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.397456e+01\n Vprtstp: contraction number = 1.397456e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.508868e-06\n Vprtstp: contraction number = 3.235590e-01\n Vnewton: Using errtol_s: 12.577101\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.684603e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.523055e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.585274e+00\n Vprtstp: contraction number = 4.585274e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.807547e-06\n Vprtstp: contraction number = 3.281159e-01\n Vnewton: Using errtol_s: 4.126746\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.769324e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.639676e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.521742e+00\n Vprtstp: contraction number = 1.521742e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.998813e-07\n Vprtstp: contraction number = 3.318759e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.184346e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.375441e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.399877e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.426308e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -15583,17 +15583,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.934616474565E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951681070136E+04 kT\n Vpmg_energy:  dielEnergy = 1.475162911234E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.786500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.888400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -15620,151 +15620,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.063219\n+Vacc_SASA: Time elapsed: 0.074902\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.475170e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.379800e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.766400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.800200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.660440e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.935430e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.963003e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.902629e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 659573.848020\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.977419e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.931845e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.895379e+04\n Vprtstp: contraction number = 8.895379e+04\n Vnewton: Attempting damping, relres = 0.129769\n Vnewton: Attempting damping, relres = 0.558262\n Vnewton: Damping accepted, relres = 0.129769\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.297694e-01\n Vprtstp: contraction number = 1.297694e-01\n Vnewton: Using errtol_s: 85592.483355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.048127e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.061254e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.666045e+04\n Vprtstp: contraction number = 1.666045e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.303462e-02\n Vprtstp: contraction number = 1.775043e-01\n Vnewton: Using errtol_s: 15193.035895\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.110005e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.150009e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.802357e+03\n Vprtstp: contraction number = 3.802357e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.189623e-03\n Vprtstp: contraction number = 2.252966e-01\n Vnewton: Using errtol_s: 3422.939434\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.174700e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.256808e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.674822e+02\n Vprtstp: contraction number = 9.674822e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.320155e-03\n Vprtstp: contraction number = 2.543835e-01\n Vnewton: Using errtol_s: 870.739405\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.238352e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.377228e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.604392e+02\n Vprtstp: contraction number = 2.604392e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.553742e-04\n Vprtstp: contraction number = 2.691914e-01\n Vnewton: Using errtol_s: 234.395549\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.302659e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.497747e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.231232e+01\n Vprtstp: contraction number = 7.231232e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.867144e-05\n Vprtstp: contraction number = 2.776550e-01\n Vnewton: Using errtol_s: 65.081104\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.365369e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.598866e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.050149e+01\n Vprtstp: contraction number = 2.050149e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.797465e-05\n Vprtstp: contraction number = 2.835131e-01\n Vnewton: Using errtol_s: 18.451347\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.427642e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.706315e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.908895e+00\n Vprtstp: contraction number = 5.908895e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.062791e-06\n Vprtstp: contraction number = 2.882178e-01\n Vnewton: Using errtol_s: 5.318006\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.490879e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.831160e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.726854e+00\n Vprtstp: contraction number = 1.726854e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.356322e-06\n Vprtstp: contraction number = 2.922465e-01\n Vnewton: Using errtol_s: 1.554169\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.554912e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.933898e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.105208e-01\n Vprtstp: contraction number = 5.105208e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.966145e-07\n Vprtstp: contraction number = 2.956364e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.465876e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.657613e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.112765e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.135947e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -15774,17 +15774,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.818510917310E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.831530055588E+03 kT\n Vpmg_energy:  dielEnergy = 3.413690932719E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.884600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.216600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n Vpbe_ctor2:  bulk ionic strength = 0.275\n Vpbe_ctor2:  xkappa = 0.17076\n@@ -15831,160 +15831,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00313173 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.061910\n+Vacc_SASA: Time elapsed: 0.068919\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.737950e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.858800e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.778600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.872600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.664690e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.102020e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.648599e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.072293e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 686089.077180\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.663216e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.101704e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.106303e+05\n Vprtstp: contraction number = 1.106303e+05\n Vnewton: Attempting damping, relres = 0.152721\n Vnewton: Attempting damping, relres = 0.570236\n Vnewton: Damping accepted, relres = 0.152721\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.527207e-01\n Vprtstp: contraction number = 1.527207e-01\n Vnewton: Using errtol_s: 104780.035977\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.733882e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.206348e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.255423e+04\n Vprtstp: contraction number = 2.255423e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.985893e-02\n Vprtstp: contraction number = 1.955132e-01\n Vnewton: Using errtol_s: 20485.884926\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.801369e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.334308e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.496448e+03\n Vprtstp: contraction number = 5.496448e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.211588e-03\n Vprtstp: contraction number = 2.415220e-01\n Vnewton: Using errtol_s: 4947.791442\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.866579e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.405640e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.444377e+03\n Vprtstp: contraction number = 1.444377e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.894730e-03\n Vprtstp: contraction number = 2.627341e-01\n Vnewton: Using errtol_s: 1299.953373\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.932894e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.513609e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.987236e+02\n Vprtstp: contraction number = 3.987236e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.230404e-04\n Vprtstp: contraction number = 2.760502e-01\n Vnewton: Using errtol_s: 358.852327\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.995736e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.642649e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.137605e+02\n Vprtstp: contraction number = 1.137605e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.492292e-04\n Vprtstp: contraction number = 2.853110e-01\n Vnewton: Using errtol_s: 102.384499\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.061235e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.752165e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.325592e+01\n Vprtstp: contraction number = 3.325592e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.362456e-05\n Vprtstp: contraction number = 2.923327e-01\n Vnewton: Using errtol_s: 29.930336\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.127698e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.877772e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.925690e+00\n Vprtstp: contraction number = 9.925690e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.302035e-05\n Vprtstp: contraction number = 2.984638e-01\n Vnewton: Using errtol_s: 8.933121\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.194590e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.971642e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.021979e+00\n Vprtstp: contraction number = 3.021979e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.964181e-06\n Vprtstp: contraction number = 3.044603e-01\n Vnewton: Using errtol_s: 2.719781\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.261749e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.090168e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.363300e-01\n Vprtstp: contraction number = 9.363300e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.228262e-06\n Vprtstp: contraction number = 3.098400e-01\n Vnewton: Using errtol_s: 0.842697\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.327965e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.198333e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.943527e-01\n Vprtstp: contraction number = 2.943527e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.861268e-07\n Vprtstp: contraction number = 3.143685e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.374092e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.567426e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.210006e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.234237e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -15994,15 +15994,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.810295872225E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.064058027536E+03 kT\n Vpmg_energy:  dielEnergy = 4.029966775084E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.844500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.123600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -16031,162 +16031,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.101207\n+Vacc_SASA: Time elapsed: 0.116650\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.209690e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.522410e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.713900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.756600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.619970e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.239000e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.506259e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.426389e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1545868.713233\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.520750e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.459080e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.195959e+05\n Vprtstp: contraction number = 2.195959e+05\n Vnewton: Attempting damping, relres = 0.180695\n Vnewton: Attempting damping, relres = 0.564482\n Vnewton: Damping accepted, relres = 0.180695\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.806948e-01\n Vprtstp: contraction number = 1.806948e-01\n Vnewton: Using errtol_s: 279330.491277\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.593647e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.575259e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.153850e+04\n Vprtstp: contraction number = 4.153850e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.508737e-02\n Vprtstp: contraction number = 1.941803e-01\n Vnewton: Using errtol_s: 54240.471315\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.669407e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.709361e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.050009e+04\n Vprtstp: contraction number = 1.050009e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.567269e-03\n Vprtstp: contraction number = 2.156693e-01\n Vnewton: Using errtol_s: 11698.005091\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.736585e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.834122e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.909851e+03\n Vprtstp: contraction number = 2.909851e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.738825e-03\n Vprtstp: contraction number = 2.297824e-01\n Vnewton: Using errtol_s: 2687.995161\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.802473e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.933815e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.166574e+02\n Vprtstp: contraction number = 8.166574e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.755829e-04\n Vprtstp: contraction number = 2.735082e-01\n Vnewton: Using errtol_s: 735.188760\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.868648e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.032822e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.418263e+02\n Vprtstp: contraction number = 2.418263e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.407907e-04\n Vprtstp: contraction number = 2.960382e-01\n Vnewton: Using errtol_s: 217.643927\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.935558e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.154878e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.307074e+01\n Vprtstp: contraction number = 7.307074e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.254157e-05\n Vprtstp: contraction number = 3.021618e-01\n Vnewton: Using errtol_s: 65.763679\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.002124e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.260847e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.224627e+01\n Vprtstp: contraction number = 2.224627e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.295171e-05\n Vprtstp: contraction number = 3.044484e-01\n Vnewton: Using errtol_s: 20.021644\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.068605e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.354399e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.802985e+00\n Vprtstp: contraction number = 6.802985e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.960677e-06\n Vprtstp: contraction number = 3.058034e-01\n Vnewton: Using errtol_s: 6.122687\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.135242e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.464430e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.086607e+00\n Vprtstp: contraction number = 2.086607e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.214816e-06\n Vprtstp: contraction number = 3.067192e-01\n Vnewton: Using errtol_s: 1.877946\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.202039e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.594649e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.414261e-01\n Vprtstp: contraction number = 6.414261e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.734363e-07\n Vprtstp: contraction number = 3.074016e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.536562e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.723367e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.268713e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.294386e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -16196,17 +16196,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.218327471785E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.873840524527E+04 kT\n Vpmg_energy:  dielEnergy = 9.358686721845E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.831500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.303000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n Vpbe_ctor2:  bulk ionic strength = 0.275\n Vpbe_ctor2:  xkappa = 0.17076\n@@ -16253,160 +16253,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00502725 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.101219\n+Vacc_SASA: Time elapsed: 0.114764\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.572460e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.216950e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.698000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.728200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.609950e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.074370e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.306463e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.766315e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1578654.561343\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.320752e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.795467e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.749391e+05\n Vprtstp: contraction number = 2.749391e+05\n Vnewton: Attempting damping, relres = 0.208079\n Vnewton: Attempting damping, relres = 0.579104\n Vnewton: Damping accepted, relres = 0.208079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.080792e-01\n Vprtstp: contraction number = 2.080792e-01\n Vnewton: Using errtol_s: 328485.121608\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.399458e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.943381e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.673641e+04\n Vprtstp: contraction number = 5.673641e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.299902e-02\n Vprtstp: contraction number = 2.066474e-01\n Vnewton: Using errtol_s: 67880.597256\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.483224e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.088121e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.510541e+04\n Vprtstp: contraction number = 1.510541e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.991987e-03\n Vprtstp: contraction number = 2.323771e-01\n Vnewton: Using errtol_s: 15773.896333\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.555609e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.210615e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.375823e+03\n Vprtstp: contraction number = 4.375823e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.532644e-03\n Vprtstp: contraction number = 2.534675e-01\n Vnewton: Using errtol_s: 3998.170369\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.627783e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.328426e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.301537e+03\n Vprtstp: contraction number = 1.301537e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.421078e-04\n Vprtstp: contraction number = 2.930170e-01\n Vnewton: Using errtol_s: 1171.531808\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.699352e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.464046e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.070189e+02\n Vprtstp: contraction number = 4.070189e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.320441e-04\n Vprtstp: contraction number = 3.126824e-01\n Vnewton: Using errtol_s: 366.317427\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.770868e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.588081e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.302066e+02\n Vprtstp: contraction number = 1.302066e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.423158e-05\n Vprtstp: contraction number = 3.199029e-01\n Vnewton: Using errtol_s: 117.186019\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.841904e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.710526e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.220788e+01\n Vprtstp: contraction number = 4.220788e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.406296e-05\n Vprtstp: contraction number = 3.241606e-01\n Vnewton: Using errtol_s: 37.987094\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.913586e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.842795e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.382030e+01\n Vprtstp: contraction number = 1.382030e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.879032e-06\n Vprtstp: contraction number = 3.274341e-01\n Vnewton: Using errtol_s: 12.438270\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.985274e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.966243e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.561479e+00\n Vprtstp: contraction number = 4.561479e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.600526e-06\n Vprtstp: contraction number = 3.300565e-01\n Vnewton: Using errtol_s: 4.105331\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.057311e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.093502e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.515099e+00\n Vprtstp: contraction number = 1.515099e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.637667e-07\n Vprtstp: contraction number = 3.321508e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.120580e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.306063e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.441719e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.465723e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -16416,29 +16416,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.207264728497E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.135578758917E+04 kT\n Vpmg_energy:  dielEnergy = 1.066739245337E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.835700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.396800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.200923e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.290931e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:45:44 2025\n+# Creation Date and Time:  Sun Jan  7 09:48:49 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -16708,151 +16708,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.187439\n+Vacc_SASA: Time elapsed: 0.204088\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.309140e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.863740e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.740700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.027600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.630600e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.156850e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.345410e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.500840e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2208581.508242\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.755790e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.047200e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.858538e+05\n Vprtstp: contraction number = 2.858538e+05\n Vnewton: Attempting damping, relres = 0.131715\n Vnewton: Attempting damping, relres = 0.556234\n Vnewton: Damping accepted, relres = 0.131715\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.317149e-01\n Vprtstp: contraction number = 1.317149e-01\n Vnewton: Using errtol_s: 290903.178824\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.533576e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.568472e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.143090e+04\n Vprtstp: contraction number = 5.143090e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.336960e-02\n Vprtstp: contraction number = 1.774256e-01\n Vnewton: Using errtol_s: 51613.668608\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.372577e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.871102e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.206326e+04\n Vprtstp: contraction number = 1.206326e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.129225e-03\n Vprtstp: contraction number = 2.194828e-01\n Vnewton: Using errtol_s: 11328.310511\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.187895e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.190871e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.187128e+03\n Vprtstp: contraction number = 3.187128e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.301872e-03\n Vprtstp: contraction number = 2.538146e-01\n Vnewton: Using errtol_s: 2875.290058\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.985281e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.328123e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.922285e+02\n Vprtstp: contraction number = 8.922285e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.635897e-04\n Vprtstp: contraction number = 2.792822e-01\n Vnewton: Using errtol_s: 803.017471\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.782787e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.646421e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.591681e+02\n Vprtstp: contraction number = 2.591681e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.056114e-04\n Vprtstp: contraction number = 2.904687e-01\n Vnewton: Using errtol_s: 233.251428\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.581411e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.998583e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.682702e+01\n Vprtstp: contraction number = 7.682702e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.130712e-05\n Vprtstp: contraction number = 2.964369e-01\n Vnewton: Using errtol_s: 69.144331\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.382845e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.040857e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.309726e+01\n Vprtstp: contraction number = 2.309726e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.412165e-06\n Vprtstp: contraction number = 3.006398e-01\n Vnewton: Using errtol_s: 20.787535\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.184927e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.183723e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.019037e+00\n Vprtstp: contraction number = 7.019037e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.860267e-06\n Vprtstp: contraction number = 3.038904e-01\n Vnewton: Using errtol_s: 6.317133\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.991472e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.314729e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.152093e+00\n Vprtstp: contraction number = 2.152093e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.769810e-07\n Vprtstp: contraction number = 3.066081e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.181812e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.372819e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.352038e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.376945e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -16862,15 +16862,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.850378362352E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.566988443868E+04 kT\n Vpmg_energy:  dielEnergy = 1.282832279800E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.836300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.633900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -16919,160 +16919,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0167285 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.183941\n+Vacc_SASA: Time elapsed: 0.186111\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.810070e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.491310e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.852500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.683800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.813980e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.151250e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.330897e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.509694e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2261526.211377\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.473648e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.541990e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.556600e+05\n Vprtstp: contraction number = 3.556600e+05\n Vnewton: Attempting damping, relres = 0.156191\n Vnewton: Attempting damping, relres = 0.568968\n Vnewton: Damping accepted, relres = 0.156191\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.561910e-01\n Vprtstp: contraction number = 1.561910e-01\n Vnewton: Using errtol_s: 353229.985787\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.035434e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.705303e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.049885e+04\n Vprtstp: contraction number = 7.049885e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.038701e-02\n Vprtstp: contraction number = 1.945503e-01\n Vnewton: Using errtol_s: 68721.012670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.120181e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.851508e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.762526e+04\n Vprtstp: contraction number = 1.762526e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.209079e-03\n Vprtstp: contraction number = 2.372422e-01\n Vnewton: Using errtol_s: 16303.521422\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.204311e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.973151e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.877060e+03\n Vprtstp: contraction number = 4.877060e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.943013e-03\n Vprtstp: contraction number = 2.695230e-01\n Vnewton: Using errtol_s: 4394.173812\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.289754e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.132490e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.426343e+03\n Vprtstp: contraction number = 1.426343e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.676342e-04\n Vprtstp: contraction number = 2.921413e-01\n Vnewton: Using errtol_s: 1283.719712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.374474e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.291570e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.339166e+02\n Vprtstp: contraction number = 4.339166e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.726822e-04\n Vprtstp: contraction number = 3.042139e-01\n Vnewton: Using errtol_s: 390.525321\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.458154e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.455343e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.354221e+02\n Vprtstp: contraction number = 1.354221e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.389279e-05\n Vprtstp: contraction number = 3.120924e-01\n Vnewton: Using errtol_s: 121.879967\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.543168e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.605052e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.309648e+01\n Vprtstp: contraction number = 4.309648e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.715074e-05\n Vprtstp: contraction number = 3.182380e-01\n Vnewton: Using errtol_s: 38.786838\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.628137e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.754114e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.394777e+01\n Vprtstp: contraction number = 1.394777e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.550675e-06\n Vprtstp: contraction number = 3.236406e-01\n Vnewton: Using errtol_s: 12.552997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.712254e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.904990e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.577150e+00\n Vprtstp: contraction number = 4.577150e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.821529e-06\n Vprtstp: contraction number = 3.281635e-01\n Vnewton: Using errtol_s: 4.119435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.797371e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.017532e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.519139e+00\n Vprtstp: contraction number = 1.519139e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.045585e-07\n Vprtstp: contraction number = 3.318962e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.404703e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.614954e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.657406e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.682043e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -17082,17 +17082,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.837128515027E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951603256216E+04 kT\n Vpmg_energy:  dielEnergy = 1.475141098473E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.820300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.919800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -17119,151 +17119,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.066498\n+Vacc_SASA: Time elapsed: 0.070834\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.503870e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.433610e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.787200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.774000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.685030e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.110240e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.994994e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.303291e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 654975.595106\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.009260e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.334168e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.825232e+04\n Vprtstp: contraction number = 8.825232e+04\n Vnewton: Attempting damping, relres = 0.129536\n Vnewton: Attempting damping, relres = 0.558179\n Vnewton: Damping accepted, relres = 0.129536\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.295360e-01\n Vprtstp: contraction number = 1.295360e-01\n Vnewton: Using errtol_s: 84842.899807\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.081661e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.479643e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.656273e+04\n Vprtstp: contraction number = 1.656273e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.304324e-02\n Vprtstp: contraction number = 1.778907e-01\n Vnewton: Using errtol_s: 15092.761763\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.147347e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.588052e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.788125e+03\n Vprtstp: contraction number = 3.788125e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.206395e-03\n Vprtstp: contraction number = 2.259402e-01\n Vnewton: Using errtol_s: 3410.061436\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.212185e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.709665e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.653659e+02\n Vprtstp: contraction number = 9.653659e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.326515e-03\n Vprtstp: contraction number = 2.547856e-01\n Vnewton: Using errtol_s: 868.834666\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.275902e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.828522e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.601053e+02\n Vprtstp: contraction number = 2.601053e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.574104e-04\n Vprtstp: contraction number = 2.694357e-01\n Vnewton: Using errtol_s: 234.095066\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.339553e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.949078e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.225806e+01\n Vprtstp: contraction number = 7.225806e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.928962e-05\n Vprtstp: contraction number = 2.778029e-01\n Vnewton: Using errtol_s: 65.032277\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.401675e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.080784e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.049231e+01\n Vprtstp: contraction number = 2.049231e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.815843e-05\n Vprtstp: contraction number = 2.835989e-01\n Vnewton: Using errtol_s: 18.443082\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.464657e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.189168e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.907221e+00\n Vprtstp: contraction number = 5.907221e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.117095e-06\n Vprtstp: contraction number = 2.882652e-01\n Vnewton: Using errtol_s: 5.316499\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.528513e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.311670e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.726518e+00\n Vprtstp: contraction number = 1.726518e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.372403e-06\n Vprtstp: contraction number = 2.922725e-01\n Vnewton: Using errtol_s: 1.553866\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.591179e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.430082e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.104456e-01\n Vprtstp: contraction number = 5.104456e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.014018e-07\n Vprtstp: contraction number = 2.956503e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.492291e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.686626e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.217588e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.241214e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -17273,15 +17273,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.824785455447E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.831245180939E+03 kT\n Vpmg_energy:  dielEnergy = 3.413552848131E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.872600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.054800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -17330,160 +17330,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00286585 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.063054\n+Vacc_SASA: Time elapsed: 0.069542\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.716280e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.848960e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.781400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.795300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.686510e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.091700e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.683197e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.576785e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 681119.647673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.697048e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.607821e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.097058e+05\n Vprtstp: contraction number = 1.097058e+05\n Vnewton: Attempting damping, relres = 0.152443\n Vnewton: Attempting damping, relres = 0.570128\n Vnewton: Damping accepted, relres = 0.152443\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.524432e-01\n Vprtstp: contraction number = 1.524432e-01\n Vnewton: Using errtol_s: 103832.028377\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.770117e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.744880e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.238938e+04\n Vprtstp: contraction number = 2.238938e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.984124e-02\n Vprtstp: contraction number = 1.957533e-01\n Vnewton: Using errtol_s: 20325.457528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.835532e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.863170e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.463136e+03\n Vprtstp: contraction number = 5.463136e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.220083e-03\n Vprtstp: contraction number = 2.419498e-01\n Vnewton: Using errtol_s: 4917.740487\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.901580e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.993935e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.437458e+03\n Vprtstp: contraction number = 1.437458e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.899412e-03\n Vprtstp: contraction number = 2.630734e-01\n Vnewton: Using errtol_s: 1293.726521\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.966940e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.123807e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.972446e+02\n Vprtstp: contraction number = 3.972446e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.249023e-04\n Vprtstp: contraction number = 2.763499e-01\n Vnewton: Using errtol_s: 357.521241\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.032530e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.257484e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.134401e+02\n Vprtstp: contraction number = 1.134401e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.498946e-04\n Vprtstp: contraction number = 2.855667e-01\n Vnewton: Using errtol_s: 102.096166\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.100780e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.383617e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.318595e+01\n Vprtstp: contraction number = 3.318595e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.385040e-05\n Vprtstp: contraction number = 2.925415e-01\n Vnewton: Using errtol_s: 29.867366\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.166967e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.512139e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.910309e+00\n Vprtstp: contraction number = 9.910309e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.309503e-05\n Vprtstp: contraction number = 2.986296e-01\n Vnewton: Using errtol_s: 8.919279\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.233195e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.640625e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.018558e+00\n Vprtstp: contraction number = 3.018558e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.988583e-06\n Vprtstp: contraction number = 3.045877e-01\n Vnewton: Using errtol_s: 2.716702\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.301093e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.767012e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.355568e-01\n Vprtstp: contraction number = 9.355568e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.236201e-06\n Vprtstp: contraction number = 3.099350e-01\n Vnewton: Using errtol_s: 0.842001\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.367112e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.888120e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.941742e-01\n Vprtstp: contraction number = 2.941742e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.887082e-07\n Vprtstp: contraction number = 3.144376e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.419229e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.614332e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.417595e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.441109e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -17493,17 +17493,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.816506018339E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.063774350048E+03 kT\n Vpmg_energy:  dielEnergy = 4.029829357702E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.848200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.826400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -17530,162 +17530,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.104133\n+Vacc_SASA: Time elapsed: 0.110340\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.214520e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.564330e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.729000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.741000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.703220e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.034150e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.547948e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.137197e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1525884.348969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.562459e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.161741e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.167719e+05\n Vprtstp: contraction number = 2.167719e+05\n Vnewton: Attempting damping, relres = 0.176913\n Vnewton: Attempting damping, relres = 0.564272\n Vnewton: Damping accepted, relres = 0.176913\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.769126e-01\n Vprtstp: contraction number = 1.769126e-01\n Vnewton: Using errtol_s: 269948.173272\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.636910e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.278835e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.092694e+04\n Vprtstp: contraction number = 4.092694e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.387341e-02\n Vprtstp: contraction number = 1.914697e-01\n Vnewton: Using errtol_s: 51686.903490\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.711963e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.411357e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.034780e+04\n Vprtstp: contraction number = 1.034780e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.283807e-03\n Vprtstp: contraction number = 2.150302e-01\n Vnewton: Using errtol_s: 11114.247135\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.780548e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.532231e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.862719e+03\n Vprtstp: contraction number = 2.862719e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.717625e-03\n Vprtstp: contraction number = 2.358142e-01\n Vnewton: Using errtol_s: 2620.897639\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.847532e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.648106e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.092476e+02\n Vprtstp: contraction number = 8.092476e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.773796e-04\n Vprtstp: contraction number = 2.779300e-01\n Vnewton: Using errtol_s: 728.426056\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.914170e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.766498e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.405150e+02\n Vprtstp: contraction number = 2.405150e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.418612e-04\n Vprtstp: contraction number = 2.971664e-01\n Vnewton: Using errtol_s: 216.463714\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.982066e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.888074e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.272000e+01\n Vprtstp: contraction number = 7.272000e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.289186e-05\n Vprtstp: contraction number = 3.023510e-01\n Vnewton: Using errtol_s: 65.448016\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.049645e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.002017e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.214460e+01\n Vprtstp: contraction number = 2.214460e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.306137e-05\n Vprtstp: contraction number = 3.045186e-01\n Vnewton: Using errtol_s: 19.930141\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.116442e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.120245e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.772692e+00\n Vprtstp: contraction number = 6.772692e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.994682e-06\n Vprtstp: contraction number = 3.058394e-01\n Vnewton: Using errtol_s: 6.095423\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.183850e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.240343e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.077475e+00\n Vprtstp: contraction number = 2.077475e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.225341e-06\n Vprtstp: contraction number = 3.067429e-01\n Vnewton: Using errtol_s: 1.869728\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.250402e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.348238e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.386558e-01\n Vprtstp: contraction number = 6.386558e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.766932e-07\n Vprtstp: contraction number = 3.074192e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.600855e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.796305e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.323329e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.346894e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -17695,17 +17695,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.069846752513E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.873729752993E+04 kT\n Vpmg_energy:  dielEnergy = 9.358408005729E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.840200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.125200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n Vpbe_ctor2:  bulk ionic strength = 0.3\n Vpbe_ctor2:  xkappa = 0.178353\n@@ -17752,160 +17752,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00434174 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.103706\n+Vacc_SASA: Time elapsed: 0.126539\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.586130e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.326300e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.796000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.719400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.693910e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.171520e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.355802e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.533513e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1557370.209900\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.369883e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.565054e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.714539e+05\n Vprtstp: contraction number = 2.714539e+05\n Vnewton: Attempting damping, relres = 0.204551\n Vnewton: Attempting damping, relres = 0.578965\n Vnewton: Damping accepted, relres = 0.204551\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.045506e-01\n Vprtstp: contraction number = 2.045506e-01\n Vnewton: Using errtol_s: 318560.936336\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.445284e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.719275e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.592903e+04\n Vprtstp: contraction number = 5.592903e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.183467e-02\n Vprtstp: contraction number = 2.045200e-01\n Vnewton: Using errtol_s: 65152.068354\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.525172e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.873755e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.489191e+04\n Vprtstp: contraction number = 1.489191e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.724338e-03\n Vprtstp: contraction number = 2.324469e-01\n Vnewton: Using errtol_s: 15144.393716\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.596750e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.009178e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.311238e+03\n Vprtstp: contraction number = 4.311238e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.516326e-03\n Vprtstp: contraction number = 2.587658e-01\n Vnewton: Using errtol_s: 3918.850513\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.666426e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.132157e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.290056e+03\n Vprtstp: contraction number = 1.290056e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.455704e-04\n Vprtstp: contraction number = 2.962933e-01\n Vnewton: Using errtol_s: 1161.129054\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.737293e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.245378e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.045979e+02\n Vprtstp: contraction number = 4.045979e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.338163e-04\n Vprtstp: contraction number = 3.136073e-01\n Vnewton: Using errtol_s: 364.138497\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.807743e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.386570e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.295599e+02\n Vprtstp: contraction number = 1.295599e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.487232e-05\n Vprtstp: contraction number = 3.202186e-01\n Vnewton: Using errtol_s: 116.603918\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.877827e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.533116e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.202377e+01\n Vprtstp: contraction number = 4.202377e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.428543e-05\n Vprtstp: contraction number = 3.243579e-01\n Vnewton: Using errtol_s: 37.821402\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.946954e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.668964e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.376584e+01\n Vprtstp: contraction number = 1.376584e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.955244e-06\n Vprtstp: contraction number = 3.275727e-01\n Vnewton: Using errtol_s: 12.389260\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.016407e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.800496e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.544810e+00\n Vprtstp: contraction number = 4.544810e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.626434e-06\n Vprtstp: contraction number = 3.301512e-01\n Vnewton: Using errtol_s: 4.090329\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.086137e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.933743e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.509859e+00\n Vprtstp: contraction number = 1.509859e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.725435e-07\n Vprtstp: contraction number = 3.322161e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.915937e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.113531e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.512638e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.537502e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -17915,29 +17915,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.058985499757E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.135468016715E+04 kT\n Vpmg_energy:  dielEnergy = 1.066711397255E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.811800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.731600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.230812e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.130709e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:46:33 2025\n+# Creation Date and Time:  Sun Jan  7 09:49:09 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -18207,151 +18207,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.185275\n+Vacc_SASA: Time elapsed: 0.216879\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.296910e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.340670e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.736100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.240500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.619350e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.430820e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.337700e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.557720e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2191468.217175\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.788520e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.118919e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.835462e+05\n Vprtstp: contraction number = 2.835462e+05\n Vnewton: Attempting damping, relres = 0.130770\n Vnewton: Attempting damping, relres = 0.556143\n Vnewton: Damping accepted, relres = 0.130770\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.307700e-01\n Vprtstp: contraction number = 1.307700e-01\n Vnewton: Using errtol_s: 286578.355364\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.535149e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.203321e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.106806e+04\n Vprtstp: contraction number = 5.106806e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.314467e-02\n Vprtstp: contraction number = 1.769876e-01\n Vnewton: Using errtol_s: 50720.810223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.364934e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.518029e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.199262e+04\n Vprtstp: contraction number = 1.199262e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.100754e-03\n Vprtstp: contraction number = 2.203857e-01\n Vnewton: Using errtol_s: 11178.140515\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.168495e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.996313e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.172798e+03\n Vprtstp: contraction number = 3.172798e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.305202e-03\n Vprtstp: contraction number = 2.558841e-01\n Vnewton: Using errtol_s: 2860.308039\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.960006e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.456310e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.902300e+02\n Vprtstp: contraction number = 8.902300e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.656064e-04\n Vprtstp: contraction number = 2.801149e-01\n Vnewton: Using errtol_s: 801.214793\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.755883e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.287850e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.587695e+02\n Vprtstp: contraction number = 2.587695e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.062725e-04\n Vprtstp: contraction number = 2.906745e-01\n Vnewton: Using errtol_s: 232.892741\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.556548e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.739011e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.672901e+01\n Vprtstp: contraction number = 7.672901e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.151135e-05\n Vprtstp: contraction number = 2.965147e-01\n Vnewton: Using errtol_s: 69.056118\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.349689e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.194429e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.307099e+01\n Vprtstp: contraction number = 2.307099e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.474878e-06\n Vprtstp: contraction number = 3.006815e-01\n Vnewton: Using errtol_s: 20.763894\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.158517e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.705886e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.011582e+00\n Vprtstp: contraction number = 7.011582e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.879541e-06\n Vprtstp: contraction number = 3.039133e-01\n Vnewton: Using errtol_s: 6.310424\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.968959e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.158744e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.149903e+00\n Vprtstp: contraction number = 2.149903e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.829299e-07\n Vprtstp: contraction number = 3.066217e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.160037e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.349377e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.680739e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.964113e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -18361,15 +18361,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.760186349323E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.566917500477E+04 kT\n Vpmg_energy:  dielEnergy = 1.282812157004E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.812400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.825700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -18418,160 +18418,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0160678 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.183768\n+Vacc_SASA: Time elapsed: 0.203828\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.789810e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.924730e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.808900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.823200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.696650e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.673040e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.290211e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.035188e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2243053.741102\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.436474e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.051551e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528083e+05\n Vprtstp: contraction number = 3.528083e+05\n Vnewton: Attempting damping, relres = 0.155339\n Vnewton: Attempting damping, relres = 0.568910\n Vnewton: Damping accepted, relres = 0.155339\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.553392e-01\n Vprtstp: contraction number = 1.553392e-01\n Vnewton: Using errtol_s: 348434.112950\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.032158e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.101321e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.998444e+04\n Vprtstp: contraction number = 6.998444e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.017800e-02\n Vprtstp: contraction number = 1.942717e-01\n Vnewton: Using errtol_s: 67690.878524\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.115626e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.156367e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.750872e+04\n Vprtstp: contraction number = 1.750872e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.184752e-03\n Vprtstp: contraction number = 2.380791e-01\n Vnewton: Using errtol_s: 16115.784303\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.199398e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.285058e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.850206e+03\n Vprtstp: contraction number = 4.850206e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.947538e-03\n Vprtstp: contraction number = 2.710655e-01\n Vnewton: Using errtol_s: 4368.432326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.282772e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.423815e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.421336e+03\n Vprtstp: contraction number = 1.421336e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.702989e-04\n Vprtstp: contraction number = 2.928307e-01\n Vnewton: Using errtol_s: 1279.211122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.366067e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.495042e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.327691e+02\n Vprtstp: contraction number = 4.327691e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.736439e-04\n Vprtstp: contraction number = 3.044787e-01\n Vnewton: Using errtol_s: 389.492590\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.450258e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.645946e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.351326e+02\n Vprtstp: contraction number = 1.351326e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.422045e-05\n Vprtstp: contraction number = 3.122508e-01\n Vnewton: Using errtol_s: 121.619374\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.534864e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.791703e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.301940e+01\n Vprtstp: contraction number = 4.301940e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.726105e-05\n Vprtstp: contraction number = 3.183495e-01\n Vnewton: Using errtol_s: 38.717465\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.619250e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.937675e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.392593e+01\n Vprtstp: contraction number = 1.392593e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.587625e-06\n Vprtstp: contraction number = 3.237129e-01\n Vnewton: Using errtol_s: 12.533342\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.701751e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.085930e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.570574e+00\n Vprtstp: contraction number = 4.570574e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.833891e-06\n Vprtstp: contraction number = 3.282059e-01\n Vnewton: Using errtol_s: 4.113517\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.786771e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.237439e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.517041e+00\n Vprtstp: contraction number = 1.517041e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.086957e-07\n Vprtstp: contraction number = 3.319148e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.321861e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.518129e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.330614e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.350784e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -18581,17 +18581,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.747143888593E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951532357684E+04 kT\n Vpmg_energy:  dielEnergy = 1.475121024223E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.787700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.514200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -18618,151 +18618,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.062582\n+Vacc_SASA: Time elapsed: 0.069962\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.471310e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.384370e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.707500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.722200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.601010e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.077500e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.977015e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.498667e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 651047.049796\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.991606e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.528761e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.764819e+04\n Vprtstp: contraction number = 8.764819e+04\n Vnewton: Attempting damping, relres = 0.129306\n Vnewton: Attempting damping, relres = 0.558102\n Vnewton: Damping accepted, relres = 0.129306\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.293065e-01\n Vprtstp: contraction number = 1.293065e-01\n Vnewton: Using errtol_s: 84184.596649\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.063252e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.667031e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.647823e+04\n Vprtstp: contraction number = 1.647823e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.304786e-02\n Vprtstp: contraction number = 1.782421e-01\n Vnewton: Using errtol_s: 15005.240621\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.128151e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.796244e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.775815e+03\n Vprtstp: contraction number = 3.775815e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.220699e-03\n Vprtstp: contraction number = 2.265156e-01\n Vnewton: Using errtol_s: 3398.920946\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.193373e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.922994e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.635341e+02\n Vprtstp: contraction number = 9.635341e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.331987e-03\n Vprtstp: contraction number = 2.551357e-01\n Vnewton: Using errtol_s: 867.186094\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.257292e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.043692e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.598155e+02\n Vprtstp: contraction number = 2.598155e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.591665e-04\n Vprtstp: contraction number = 2.696472e-01\n Vnewton: Using errtol_s: 233.834272\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.322292e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.150727e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.221080e+01\n Vprtstp: contraction number = 7.221080e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.982341e-05\n Vprtstp: contraction number = 2.779308e-01\n Vnewton: Using errtol_s: 64.989737\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.387430e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.275906e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.048426e+01\n Vprtstp: contraction number = 2.048426e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.831721e-05\n Vprtstp: contraction number = 2.836731e-01\n Vnewton: Using errtol_s: 18.435838\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.451748e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.404007e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.905744e+00\n Vprtstp: contraction number = 5.905744e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.164034e-06\n Vprtstp: contraction number = 2.883064e-01\n Vnewton: Using errtol_s: 5.315170\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.516321e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.531612e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.726219e+00\n Vprtstp: contraction number = 1.726219e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.386306e-06\n Vprtstp: contraction number = 2.922949e-01\n Vnewton: Using errtol_s: 1.553597\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.579457e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.652979e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.103781e-01\n Vprtstp: contraction number = 5.103781e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.055409e-07\n Vprtstp: contraction number = 2.956624e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.572201e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.756605e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.257801e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.281846e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -18772,15 +18772,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.829422361663E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.830982023597E+03 kT\n Vpmg_energy:  dielEnergy = 3.413426199926E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.854700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.123600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -18829,160 +18829,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00263165 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.063800\n+Vacc_SASA: Time elapsed: 0.072016\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.697820e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.937190e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.677700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.825300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.579080e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.147990e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.671672e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.815844e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 676873.511924\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.685653e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.846848e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.089080e+05\n Vprtstp: contraction number = 1.089080e+05\n Vnewton: Attempting damping, relres = 0.152173\n Vnewton: Attempting damping, relres = 0.570027\n Vnewton: Damping accepted, relres = 0.152173\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.521734e-01\n Vprtstp: contraction number = 1.521734e-01\n Vnewton: Using errtol_s: 103002.176045\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.758215e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.985919e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.224678e+04\n Vprtstp: contraction number = 2.224678e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.982235e-02\n Vprtstp: contraction number = 1.959760e-01\n Vnewton: Using errtol_s: 20185.957327\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.823391e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.119926e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.434268e+03\n Vprtstp: contraction number = 5.434268e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.226895e-03\n Vprtstp: contraction number = 2.423315e-01\n Vnewton: Using errtol_s: 4891.693818\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.889501e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.260932e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.431460e+03\n Vprtstp: contraction number = 1.431460e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.903352e-03\n Vprtstp: contraction number = 2.633707e-01\n Vnewton: Using errtol_s: 1288.328715\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.955758e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.390546e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.959616e+02\n Vprtstp: contraction number = 3.959616e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.264891e-04\n Vprtstp: contraction number = 2.766115e-01\n Vnewton: Using errtol_s: 356.366550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.019074e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.526060e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.131619e+02\n Vprtstp: contraction number = 1.131619e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.504650e-04\n Vprtstp: contraction number = 2.857895e-01\n Vnewton: Using errtol_s: 101.845804\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.085349e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.657905e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.312512e+01\n Vprtstp: contraction number = 3.312512e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.404458e-05\n Vprtstp: contraction number = 2.927230e-01\n Vnewton: Using errtol_s: 29.812613\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.150853e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.787414e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.896913e+00\n Vprtstp: contraction number = 9.896913e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.315936e-05\n Vprtstp: contraction number = 2.987736e-01\n Vnewton: Using errtol_s: 8.907223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.217622e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.893042e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.015572e+00\n Vprtstp: contraction number = 3.015572e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.009634e-06\n Vprtstp: contraction number = 3.046983e-01\n Vnewton: Using errtol_s: 2.714015\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.285718e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.011793e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.348798e-01\n Vprtstp: contraction number = 9.348798e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.243056e-06\n Vprtstp: contraction number = 3.100174e-01\n Vnewton: Using errtol_s: 0.841392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.352808e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.136251e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.940173e-01\n Vprtstp: contraction number = 2.940173e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.909380e-07\n Vprtstp: contraction number = 3.144974e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.385093e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.567087e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.422668e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.447490e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -18992,15 +18992,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.821085170706E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.063512300781E+03 kT\n Vpmg_energy:  dielEnergy = 4.029703319589E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.869700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.245900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -19029,162 +19029,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.102648\n+Vacc_SASA: Time elapsed: 0.110409\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.236450e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.668200e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.831100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.725800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.760280e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.219620e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.535160e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.385541e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1509004.572180\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.549727e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.418169e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.143767e+05\n Vprtstp: contraction number = 2.143767e+05\n Vnewton: Attempting damping, relres = 0.173607\n Vnewton: Attempting damping, relres = 0.564075\n Vnewton: Damping accepted, relres = 0.173607\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.736069e-01\n Vprtstp: contraction number = 1.736069e-01\n Vnewton: Using errtol_s: 261973.588074\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.623600e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.578355e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.041338e+04\n Vprtstp: contraction number = 4.041338e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.283481e-02\n Vprtstp: contraction number = 1.891331e-01\n Vnewton: Using errtol_s: 49547.880487\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.698118e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.729664e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.021814e+04\n Vprtstp: contraction number = 1.021814e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.057379e-03\n Vprtstp: contraction number = 2.149359e-01\n Vnewton: Using errtol_s: 10649.617829\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.766146e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.847528e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.824157e+03\n Vprtstp: contraction number = 2.824157e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.703748e-03\n Vprtstp: contraction number = 2.414137e-01\n Vnewton: Using errtol_s: 2570.963479\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.833155e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.973599e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.035455e+02\n Vprtstp: contraction number = 8.035455e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.792870e-04\n Vprtstp: contraction number = 2.813133e-01\n Vnewton: Using errtol_s: 723.246303\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.900804e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.106300e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.394281e+02\n Vprtstp: contraction number = 2.394281e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.427997e-04\n Vprtstp: contraction number = 2.979420e-01\n Vnewton: Using errtol_s: 215.485426\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.966987e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.236955e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.242618e+01\n Vprtstp: contraction number = 7.242618e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.319641e-05\n Vprtstp: contraction number = 3.024964e-01\n Vnewton: Using errtol_s: 65.183576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.033889e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.369496e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.205930e+01\n Vprtstp: contraction number = 2.205930e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.315660e-05\n Vprtstp: contraction number = 3.045762e-01\n Vnewton: Using errtol_s: 19.853369\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.100288e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.501529e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.747262e+00\n Vprtstp: contraction number = 6.747262e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.024200e-06\n Vprtstp: contraction number = 3.058693e-01\n Vnewton: Using errtol_s: 6.072536\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.166871e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.621464e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.069809e+00\n Vprtstp: contraction number = 2.069809e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.234475e-06\n Vprtstp: contraction number = 3.067629e-01\n Vnewton: Using errtol_s: 1.862829\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.234760e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.745722e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.363291e-01\n Vprtstp: contraction number = 6.363291e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.795192e-07\n Vprtstp: contraction number = 3.074337e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.572234e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.775476e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.437114e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.462701e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -19194,17 +19194,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.932901630700E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.873629019341E+04 kT\n Vpmg_energy:  dielEnergy = 9.358152654068E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.838900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.170700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n Vpbe_ctor2:  bulk ionic strength = 0.325\n Vpbe_ctor2:  xkappa = 0.185636\n@@ -19251,160 +19251,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00380956 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.102015\n+Vacc_SASA: Time elapsed: 0.109267\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.600400e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.926140e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.776900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.744300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.641170e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.114560e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.339754e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.891257e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1539412.424593\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.354277e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.918150e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.684916e+05\n Vprtstp: contraction number = 2.684916e+05\n Vnewton: Attempting damping, relres = 0.201455\n Vnewton: Attempting damping, relres = 0.578827\n Vnewton: Damping accepted, relres = 0.201455\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.014550e-01\n Vprtstp: contraction number = 2.014550e-01\n Vnewton: Using errtol_s: 310122.358535\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.429347e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.039158e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.524646e+04\n Vprtstp: contraction number = 5.524646e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.083558e-02\n Vprtstp: contraction number = 2.027032e-01\n Vnewton: Using errtol_s: 62862.800070\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.507541e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.154380e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.470940e+04\n Vprtstp: contraction number = 1.470940e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.510864e-03\n Vprtstp: contraction number = 2.329063e-01\n Vnewton: Using errtol_s: 14641.142976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.579833e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.239930e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.258026e+03\n Vprtstp: contraction number = 4.258026e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.506079e-03\n Vprtstp: contraction number = 2.634965e-01\n Vnewton: Using errtol_s: 3857.889813\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.649749e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.336573e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.281004e+03\n Vprtstp: contraction number = 1.281004e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.489530e-04\n Vprtstp: contraction number = 2.988545e-01\n Vnewton: Using errtol_s: 1152.947571\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.719727e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.423981e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.026096e+02\n Vprtstp: contraction number = 4.026096e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.353814e-04\n Vprtstp: contraction number = 3.142806e-01\n Vnewton: Using errtol_s: 362.348997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.789116e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.508861e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.290278e+02\n Vprtstp: contraction number = 1.290278e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.543469e-05\n Vprtstp: contraction number = 3.204786e-01\n Vnewton: Using errtol_s: 116.125091\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.859543e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.591442e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.187301e+01\n Vprtstp: contraction number = 4.187301e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.448058e-05\n Vprtstp: contraction number = 3.245269e-01\n Vnewton: Using errtol_s: 37.685715\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.929678e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.679732e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.372141e+01\n Vprtstp: contraction number = 1.372141e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 8.022069e-06\n Vprtstp: contraction number = 3.276911e-01\n Vnewton: Using errtol_s: 12.349273\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.999778e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.767255e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.531250e+00\n Vprtstp: contraction number = 4.531250e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.649144e-06\n Vprtstp: contraction number = 3.302320e-01\n Vnewton: Using errtol_s: 4.078125\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.069125e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.851147e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.505606e+00\n Vprtstp: contraction number = 1.505606e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.802356e-07\n Vprtstp: contraction number = 3.322717e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.893520e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.084132e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.029116e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.054673e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -19414,29 +19414,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.922197679692E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.135367311591E+04 kT\n Vpmg_energy:  dielEnergy = 1.066685879920E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.825000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.814900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.212362e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.003623e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:47:21 2025\n+# Creation Date and Time:  Sun Jan  7 09:49:29 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -19706,151 +19706,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.187710\n+Vacc_SASA: Time elapsed: 0.186429\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.339890e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.366270e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.843300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.747600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.708620e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.866480e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.479600e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.832900e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2152094.716706\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.902650e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.231990e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.782066e+05\n Vprtstp: contraction number = 2.782066e+05\n Vnewton: Attempting damping, relres = 0.128497\n Vnewton: Attempting damping, relres = 0.555913\n Vnewton: Damping accepted, relres = 0.128497\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.284973e-01\n Vprtstp: contraction number = 1.284973e-01\n Vnewton: Using errtol_s: 276538.353939\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.559954e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.961445e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.023327e+04\n Vprtstp: contraction number = 5.023327e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.262924e-02\n Vprtstp: contraction number = 1.761067e-01\n Vnewton: Using errtol_s: 48700.264198\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.395843e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.778952e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183043e+04\n Vprtstp: contraction number = 1.183043e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.048628e-03\n Vprtstp: contraction number = 2.231020e-01\n Vnewton: Using errtol_s: 10865.126461\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.179784e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.654851e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.142996e+03\n Vprtstp: contraction number = 3.142996e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.315159e-03\n Vprtstp: contraction number = 2.604983e-01\n Vnewton: Using errtol_s: 2830.346955\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.981827e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.623160e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.861041e+02\n Vprtstp: contraction number = 8.861041e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.705677e-04\n Vprtstp: contraction number = 2.817665e-01\n Vnewton: Using errtol_s: 797.496893\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.776164e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.651717e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.579465e+02\n Vprtstp: contraction number = 2.579465e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.078726e-04\n Vprtstp: contraction number = 2.911008e-01\n Vnewton: Using errtol_s: 232.151972\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.590673e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.697795e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.653069e+01\n Vprtstp: contraction number = 7.653069e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.200493e-05\n Vprtstp: contraction number = 2.966920e-01\n Vnewton: Using errtol_s: 68.877633\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.413257e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.707358e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.301874e+01\n Vprtstp: contraction number = 2.301874e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.626375e-06\n Vprtstp: contraction number = 3.007779e-01\n Vnewton: Using errtol_s: 20.716870\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.225860e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.441062e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.996910e+00\n Vprtstp: contraction number = 6.996910e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.926088e-06\n Vprtstp: contraction number = 3.039658e-01\n Vnewton: Using errtol_s: 6.297219\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.044413e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.227502e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.145621e+00\n Vprtstp: contraction number = 2.145621e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.972926e-07\n Vprtstp: contraction number = 3.066526e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.217091e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.416286e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.345425e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.562145e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -19860,15 +19860,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.527227679472E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.566736557939E+04 kT\n Vpmg_energy:  dielEnergy = 1.282759892518E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.812900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.821000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -19917,160 +19917,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0146503 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.182814\n+Vacc_SASA: Time elapsed: 0.185934\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.747140e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.528940e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.752700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.782700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.619010e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.250120e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.348326e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.075753e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2200727.622444\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.485358e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.101454e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.461855e+05\n Vprtstp: contraction number = 3.461855e+05\n Vnewton: Attempting damping, relres = 0.153259\n Vnewton: Attempting damping, relres = 0.568747\n Vnewton: Damping accepted, relres = 0.153259\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.532593e-01\n Vprtstp: contraction number = 1.532593e-01\n Vnewton: Using errtol_s: 337281.994589\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.039391e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.244994e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.878964e+04\n Vprtstp: contraction number = 6.878964e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.969348e-02\n Vprtstp: contraction number = 1.937467e-01\n Vnewton: Using errtol_s: 65347.260012\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.123574e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.378189e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.723760e+04\n Vprtstp: contraction number = 1.723760e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.139932e-03\n Vprtstp: contraction number = 2.404545e-01\n Vnewton: Using errtol_s: 15713.045576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.208021e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.524023e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.791285e+03\n Vprtstp: contraction number = 4.791285e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.959957e-03\n Vprtstp: contraction number = 2.745064e-01\n Vnewton: Using errtol_s: 4313.331787\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.291743e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.657246e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.410218e+03\n Vprtstp: contraction number = 1.410218e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.767187e-04\n Vprtstp: contraction number = 2.942507e-01\n Vnewton: Using errtol_s: 1269.200854\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.377042e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.812124e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.302153e+02\n Vprtstp: contraction number = 4.302153e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.759391e-04\n Vprtstp: contraction number = 3.050692e-01\n Vnewton: Using errtol_s: 387.194118\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.461106e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.966379e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.344961e+02\n Vprtstp: contraction number = 1.344961e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.500295e-05\n Vprtstp: contraction number = 3.126248e-01\n Vnewton: Using errtol_s: 121.046502\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.545472e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.128500e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.285292e+01\n Vprtstp: contraction number = 4.285292e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.752495e-05\n Vprtstp: contraction number = 3.186183e-01\n Vnewton: Using errtol_s: 38.567632\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.630090e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.276715e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.387951e+01\n Vprtstp: contraction number = 1.387951e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.676104e-06\n Vprtstp: contraction number = 3.238871e-01\n Vnewton: Using errtol_s: 12.491560\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.714789e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.399131e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.556799e+00\n Vprtstp: contraction number = 4.556799e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.863529e-06\n Vprtstp: contraction number = 3.283112e-01\n Vnewton: Using errtol_s: 4.101119\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.798791e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.521968e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.512689e+00\n Vprtstp: contraction number = 1.512689e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.186225e-07\n Vprtstp: contraction number = 3.319630e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.397976e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.585478e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.553998e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.579473e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -20080,15 +20080,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.514675732237E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951351537778E+04 kT\n Vpmg_energy:  dielEnergy = 1.475068873214E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.804300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.815300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -20117,151 +20117,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.063298\n+Vacc_SASA: Time elapsed: 0.100404\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.479260e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.385620e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.792900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.805900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.692890e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.071000e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.994442e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.763682e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 642085.519744\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.008410e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.789980e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.625055e+04\n Vprtstp: contraction number = 8.625055e+04\n Vnewton: Attempting damping, relres = 0.128656\n Vnewton: Attempting damping, relres = 0.557901\n Vnewton: Damping accepted, relres = 0.128656\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.286562e-01\n Vprtstp: contraction number = 1.286562e-01\n Vnewton: Using errtol_s: 82608.252849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.079891e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.903625e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.628118e+04\n Vprtstp: contraction number = 1.628118e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.304734e-02\n Vprtstp: contraction number = 1.791390e-01\n Vnewton: Using errtol_s: 14798.361839\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.145319e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.005815e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.747143e+03\n Vprtstp: contraction number = 3.747143e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.253150e-03\n Vprtstp: contraction number = 2.279287e-01\n Vnewton: Using errtol_s: 3372.971529\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.209974e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.106294e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.592593e+02\n Vprtstp: contraction number = 9.592593e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.344585e-03\n Vprtstp: contraction number = 2.559579e-01\n Vnewton: Using errtol_s: 863.338654\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.273716e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.207830e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.591357e+02\n Vprtstp: contraction number = 2.591357e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.632264e-04\n Vprtstp: contraction number = 2.701401e-01\n Vnewton: Using errtol_s: 233.222386\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.337765e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.326516e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.209902e+01\n Vprtstp: contraction number = 7.209902e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.010600e-04\n Vprtstp: contraction number = 2.782286e-01\n Vnewton: Using errtol_s: 64.889141\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.402679e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.438861e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.046499e+01\n Vprtstp: contraction number = 2.046499e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.868541e-05\n Vprtstp: contraction number = 2.838455e-01\n Vnewton: Using errtol_s: 18.418489\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.466526e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.561647e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.902147e+00\n Vprtstp: contraction number = 5.902147e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.272935e-06\n Vprtstp: contraction number = 2.884022e-01\n Vnewton: Using errtol_s: 5.311932\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.528820e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.694154e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.725476e+00\n Vprtstp: contraction number = 1.725476e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.418570e-06\n Vprtstp: contraction number = 2.923472e-01\n Vnewton: Using errtol_s: 1.552929\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.591236e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.819242e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.102067e-01\n Vprtstp: contraction number = 5.102067e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.151478e-07\n Vprtstp: contraction number = 2.956904e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.517084e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.713609e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.146459e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.171496e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -20271,15 +20271,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.836319274152E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.830295346260E+03 kT\n Vpmg_energy:  dielEnergy = 3.413099848091E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.873100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.973000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -20328,160 +20328,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00207488 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.062024\n+Vacc_SASA: Time elapsed: 0.070986\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.725890e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.767540e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.760000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.883800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.745260e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.116270e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.685754e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.966936e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 667195.414501\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.699895e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.998442e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.070575e+05\n Vprtstp: contraction number = 1.070575e+05\n Vnewton: Attempting damping, relres = 0.151420\n Vnewton: Attempting damping, relres = 0.569765\n Vnewton: Damping accepted, relres = 0.151420\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.514203e-01\n Vprtstp: contraction number = 1.514203e-01\n Vnewton: Using errtol_s: 101026.941605\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.773499e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.125893e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.191459e+04\n Vprtstp: contraction number = 2.191459e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.976400e-02\n Vprtstp: contraction number = 1.965654e-01\n Vnewton: Using errtol_s: 19858.405232\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.839962e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.259013e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.366842e+03\n Vprtstp: contraction number = 5.366842e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.240542e-03\n Vprtstp: contraction number = 2.432651e-01\n Vnewton: Using errtol_s: 4830.856278\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.906077e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.386386e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.417443e+03\n Vprtstp: contraction number = 1.417443e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.912054e-03\n Vprtstp: contraction number = 2.640761e-01\n Vnewton: Using errtol_s: 1275.713735\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.970777e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.501228e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.929589e+02\n Vprtstp: contraction number = 3.929589e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.300759e-04\n Vprtstp: contraction number = 2.772285e-01\n Vnewton: Using errtol_s: 353.664179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.037374e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.627631e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.125096e+02\n Vprtstp: contraction number = 1.125096e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.517678e-04\n Vprtstp: contraction number = 2.863133e-01\n Vnewton: Using errtol_s: 101.258773\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.104312e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.752404e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.298207e+01\n Vprtstp: contraction number = 3.298207e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.449052e-05\n Vprtstp: contraction number = 2.931486e-01\n Vnewton: Using errtol_s: 29.683870\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.170497e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.885328e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.865288e+00\n Vprtstp: contraction number = 9.865288e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.330759e-05\n Vprtstp: contraction number = 2.991106e-01\n Vnewton: Using errtol_s: 8.878760\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.236402e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.020010e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.008494e+00\n Vprtstp: contraction number = 3.008494e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.058248e-06\n Vprtstp: contraction number = 3.049575e-01\n Vnewton: Using errtol_s: 2.707645\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.302072e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.157314e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.332652e-01\n Vprtstp: contraction number = 9.332652e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.258910e-06\n Vprtstp: contraction number = 3.102101e-01\n Vnewton: Using errtol_s: 0.839939\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.367395e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.285027e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.936402e-01\n Vprtstp: contraction number = 2.936402e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.961001e-07\n Vprtstp: contraction number = 3.146374e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.390921e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.591040e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.408793e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.432827e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -20491,15 +20491,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.827843084018E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.062828524213E+03 kT\n Vpmg_energy:  dielEnergy = 4.029378526105E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.872900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.015700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -20528,162 +20528,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.101638\n+Vacc_SASA: Time elapsed: 0.164163\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.221390e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.065910e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.770100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.484500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.610520e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.077900e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.543938e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.523909e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1471319.117079\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.557937e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.554980e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.089888e+05\n Vprtstp: contraction number = 2.089888e+05\n Vnewton: Attempting damping, relres = 0.165808\n Vnewton: Attempting damping, relres = 0.563564\n Vnewton: Damping accepted, relres = 0.165808\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.658082e-01\n Vprtstp: contraction number = 1.658082e-01\n Vnewton: Using errtol_s: 243956.756463\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.628439e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.705351e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.927783e+04\n Vprtstp: contraction number = 3.927783e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.048323e-02\n Vprtstp: contraction number = 1.838464e-01\n Vnewton: Using errtol_s: 44850.563282\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.697827e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.837215e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.923271e+03\n Vprtstp: contraction number = 9.923271e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.609400e-03\n Vprtstp: contraction number = 2.168208e-01\n Vnewton: Using errtol_s: 9724.536863\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.764169e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.970806e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.744656e+03\n Vprtstp: contraction number = 2.744656e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.685430e-03\n Vprtstp: contraction number = 2.550050e-01\n Vnewton: Using errtol_s: 2479.805360\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.830038e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.094054e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.927726e+02\n Vprtstp: contraction number = 7.927726e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.849448e-04\n Vprtstp: contraction number = 2.877276e-01\n Vnewton: Using errtol_s: 713.508521\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.895889e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.224434e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.371902e+02\n Vprtstp: contraction number = 2.371902e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.450884e-04\n Vprtstp: contraction number = 2.991854e-01\n Vnewton: Using errtol_s: 213.471337\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.962624e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.348723e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.181744e+01\n Vprtstp: contraction number = 7.181744e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.393045e-05\n Vprtstp: contraction number = 3.027840e-01\n Vnewton: Using errtol_s: 64.635706\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.028482e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.424324e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.188269e+01\n Vprtstp: contraction number = 2.188269e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.338555e-05\n Vprtstp: contraction number = 3.046988e-01\n Vnewton: Using errtol_s: 19.694422\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.094447e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.553026e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.694672e+00\n Vprtstp: contraction number = 6.694672e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.095104e-06\n Vprtstp: contraction number = 3.059346e-01\n Vnewton: Using errtol_s: 6.025205\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.161141e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.688987e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.053963e+00\n Vprtstp: contraction number = 2.053963e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.256401e-06\n Vprtstp: contraction number = 3.068056e-01\n Vnewton: Using errtol_s: 1.848567\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.228923e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.828426e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.315192e-01\n Vprtstp: contraction number = 6.315192e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.862977e-07\n Vprtstp: contraction number = 3.074637e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.426209e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.613283e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.420377e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.445498e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -20693,17 +20693,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.577297422192E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.873373018987E+04 kT\n Vpmg_energy:  dielEnergy = 9.357495652952E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.841400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.907300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n Vpbe_ctor2:  bulk ionic strength = 0.4\n Vpbe_ctor2:  xkappa = 0.205945\n@@ -20750,160 +20750,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00276825 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.103561\n+Vacc_SASA: Time elapsed: 0.107142\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.640890e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.006540e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.816400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.683300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.721150e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.175640e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.335202e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.013931e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1499432.159358\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.349493e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.044233e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.618100e+05\n Vprtstp: contraction number = 2.618100e+05\n Vnewton: Attempting damping, relres = 0.194105\n Vnewton: Attempting damping, relres = 0.578438\n Vnewton: Damping accepted, relres = 0.194105\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.941047e-01\n Vprtstp: contraction number = 1.941047e-01\n Vnewton: Using errtol_s: 291046.875702\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.425673e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.199295e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.372130e+04\n Vprtstp: contraction number = 5.372130e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.856178e-02\n Vprtstp: contraction number = 1.986648e-01\n Vnewton: Using errtol_s: 57820.773992\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.503173e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.352515e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.429172e+04\n Vprtstp: contraction number = 1.429172e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.088822e-03\n Vprtstp: contraction number = 2.356951e-01\n Vnewton: Using errtol_s: 13628.071398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.573059e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.494031e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.146951e+03\n Vprtstp: contraction number = 4.146951e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.494923e-03\n Vprtstp: contraction number = 2.745046e-01\n Vnewton: Using errtol_s: 3740.967765\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.642888e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.633611e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.262928e+03\n Vprtstp: contraction number = 1.262928e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.580508e-04\n Vprtstp: contraction number = 3.038374e-01\n Vnewton: Using errtol_s: 1136.645774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.712846e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.764915e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.984728e+02\n Vprtstp: contraction number = 3.984728e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.391744e-04\n Vprtstp: contraction number = 3.155124e-01\n Vnewton: Using errtol_s: 358.625830\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.784214e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.869658e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.279297e+02\n Vprtstp: contraction number = 1.279297e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.678689e-05\n Vprtstp: contraction number = 3.210497e-01\n Vnewton: Using errtol_s: 115.136728\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.855801e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.014492e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.156614e+01\n Vprtstp: contraction number = 4.156614e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.494913e-05\n Vprtstp: contraction number = 3.249140e-01\n Vnewton: Using errtol_s: 37.409531\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.925950e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.139802e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.363199e+01\n Vprtstp: contraction number = 1.363199e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 8.182289e-06\n Vprtstp: contraction number = 3.279589e-01\n Vnewton: Using errtol_s: 12.268788\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.995548e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.280173e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.504209e+00\n Vprtstp: contraction number = 4.504209e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.703549e-06\n Vprtstp: contraction number = 3.304147e-01\n Vnewton: Using errtol_s: 4.053788\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.065419e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.412365e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.497181e+00\n Vprtstp: contraction number = 1.497181e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.986490e-07\n Vprtstp: contraction number = 3.323961e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.895475e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.093917e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.517748e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.542649e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -20913,29 +20913,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.566888561678E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.135111393094E+04 kT\n Vpmg_energy:  dielEnergy = 1.066620211340E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.822300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.730700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.207335e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.618304e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:48:08 2025\n+# Creation Date and Time:  Sun Jan  7 09:49:50 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -21205,151 +21205,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.188838\n+Vacc_SASA: Time elapsed: 0.243449\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.335620e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.588250e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.748900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.729500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.611320e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.088410e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.349150e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.167380e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2117021.813584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.732070e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.127139e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.733993e+05\n Vprtstp: contraction number = 2.733993e+05\n Vnewton: Attempting damping, relres = 0.126346\n Vnewton: Attempting damping, relres = 0.555677\n Vnewton: Damping accepted, relres = 0.126346\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.263459e-01\n Vprtstp: contraction number = 1.263459e-01\n Vnewton: Using errtol_s: 267477.104304\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.545625e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.843874e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.948638e+04\n Vprtstp: contraction number = 4.948638e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.218275e-02\n Vprtstp: contraction number = 1.755716e-01\n Vnewton: Using errtol_s: 46961.371226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.372965e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.619639e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.168877e+04\n Vprtstp: contraction number = 1.168877e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.021324e-03\n Vprtstp: contraction number = 2.263616e-01\n Vnewton: Using errtol_s: 10630.252373\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.178697e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.776367e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.120176e+03\n Vprtstp: contraction number = 3.120176e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.326708e-03\n Vprtstp: contraction number = 2.642148e-01\n Vnewton: Using errtol_s: 2808.669489\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.966937e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.527148e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.828690e+02\n Vprtstp: contraction number = 8.828690e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.753310e-04\n Vprtstp: contraction number = 2.829040e-01\n Vnewton: Using errtol_s: 794.583820\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.780566e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.522759e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.573077e+02\n Vprtstp: contraction number = 2.573077e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.093881e-04\n Vprtstp: contraction number = 2.914445e-01\n Vnewton: Using errtol_s: 231.577068\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.580927e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.986916e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.638166e+01\n Vprtstp: contraction number = 7.638166e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.247180e-05\n Vprtstp: contraction number = 2.968494e-01\n Vnewton: Using errtol_s: 68.743505\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.392206e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.685247e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.298047e+01\n Vprtstp: contraction number = 2.298047e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.769584e-06\n Vprtstp: contraction number = 3.008636e-01\n Vnewton: Using errtol_s: 20.682422\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.202277e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.632955e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.986364e+00\n Vprtstp: contraction number = 6.986364e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.970082e-06\n Vprtstp: contraction number = 3.040131e-01\n Vnewton: Using errtol_s: 6.287728\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.997888e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.075973e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.142572e+00\n Vprtstp: contraction number = 2.142572e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 9.108619e-07\n Vprtstp: contraction number = 3.066791e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.179923e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.366507e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.073518e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.097846e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -21359,15 +21359,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.282938613188E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.566547142826E+04 kT\n Vpmg_energy:  dielEnergy = 1.282703574681E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.818900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.997700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -21416,160 +21416,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0133684 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.180889\n+Vacc_SASA: Time elapsed: 0.188947\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.767600e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.015680e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.784900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.548300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.636890e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.426740e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.302635e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.250008e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2163354.564593\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.440964e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.281148e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.401998e+05\n Vprtstp: contraction number = 3.401998e+05\n Vnewton: Attempting damping, relres = 0.151250\n Vnewton: Attempting damping, relres = 0.568556\n Vnewton: Damping accepted, relres = 0.151250\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.512496e-01\n Vprtstp: contraction number = 1.512496e-01\n Vnewton: Using errtol_s: 327206.577099\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.034646e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.381785e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.770698e+04\n Vprtstp: contraction number = 6.770698e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.926462e-02\n Vprtstp: contraction number = 1.934856e-01\n Vnewton: Using errtol_s: 63309.757927\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.117555e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.487747e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.699399e+04\n Vprtstp: contraction number = 1.699399e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.115656e-03\n Vprtstp: contraction number = 2.431487e-01\n Vnewton: Using errtol_s: 15393.687585\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.201794e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.560055e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.742003e+03\n Vprtstp: contraction number = 4.742003e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.972961e-03\n Vprtstp: contraction number = 2.772704e-01\n Vnewton: Using errtol_s: 4268.214485\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.285254e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.646311e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.400571e+03\n Vprtstp: contraction number = 1.400571e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.826678e-04\n Vprtstp: contraction number = 2.953265e-01\n Vnewton: Using errtol_s: 1260.517005\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.368986e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.722359e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.279978e+02\n Vprtstp: contraction number = 4.279978e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.780560e-04\n Vprtstp: contraction number = 3.055876e-01\n Vnewton: Using errtol_s: 385.198337\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.451811e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.848373e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.339544e+02\n Vprtstp: contraction number = 1.339544e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.572782e-05\n Vprtstp: contraction number = 3.129791e-01\n Vnewton: Using errtol_s: 120.559033\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.533704e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.994793e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.271452e+01\n Vprtstp: contraction number = 4.271452e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.777012e-05\n Vprtstp: contraction number = 3.188734e-01\n Vnewton: Using errtol_s: 38.443069\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.618413e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.091906e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.384186e+01\n Vprtstp: contraction number = 1.384186e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.758498e-06\n Vprtstp: contraction number = 3.240551e-01\n Vnewton: Using errtol_s: 12.457672\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.700893e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.183301e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.545889e+00\n Vprtstp: contraction number = 4.545889e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.891183e-06\n Vprtstp: contraction number = 3.284161e-01\n Vnewton: Using errtol_s: 4.091300\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.783549e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.253778e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.509299e+00\n Vprtstp: contraction number = 1.509299e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.278996e-07\n Vprtstp: contraction number = 3.320141e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.278695e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.468640e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.062447e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.092368e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -21579,17 +21579,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.270848264537E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951162263981E+04 kT\n Vpmg_energy:  dielEnergy = 1.475012659776E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.779500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.697500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -21616,151 +21616,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.061460\n+Vacc_SASA: Time elapsed: 0.074554\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.449830e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.377930e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.723700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.711700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.574120e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.036820e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.972054e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.445357e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 634193.792999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.985835e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.472431e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.499222e+04\n Vprtstp: contraction number = 8.499222e+04\n Vnewton: Attempting damping, relres = 0.127890\n Vnewton: Attempting damping, relres = 0.557688\n Vnewton: Damping accepted, relres = 0.127890\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.278898e-01\n Vprtstp: contraction number = 1.278898e-01\n Vnewton: Using errtol_s: 81106.914272\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.057270e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.552782e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.610090e+04\n Vprtstp: contraction number = 1.610090e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.303084e-02\n Vprtstp: contraction number = 1.800835e-01\n Vnewton: Using errtol_s: 14606.018111\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.120565e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.626311e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.721077e+03\n Vprtstp: contraction number = 3.721077e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.281325e-03\n Vprtstp: contraction number = 2.293153e-01\n Vnewton: Using errtol_s: 3349.383286\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.184412e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.759306e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.553498e+02\n Vprtstp: contraction number = 9.553498e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.355768e-03\n Vprtstp: contraction number = 2.567099e-01\n Vnewton: Using errtol_s: 859.819863\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.248722e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.885279e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.585067e+02\n Vprtstp: contraction number = 2.585067e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.668537e-04\n Vprtstp: contraction number = 2.705873e-01\n Vnewton: Using errtol_s: 232.656331\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.312410e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.969946e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.199407e+01\n Vprtstp: contraction number = 7.199407e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.021686e-04\n Vprtstp: contraction number = 2.784995e-01\n Vnewton: Using errtol_s: 64.794682\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.376160e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.072555e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.044636e+01\n Vprtstp: contraction number = 2.044636e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.901594e-05\n Vprtstp: contraction number = 2.840006e-01\n Vnewton: Using errtol_s: 18.401729\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.440251e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.164468e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.898540e+00\n Vprtstp: contraction number = 5.898540e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.370763e-06\n Vprtstp: contraction number = 2.884884e-01\n Vnewton: Using errtol_s: 5.308686\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.504326e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.245908e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.724703e+00\n Vprtstp: contraction number = 1.724703e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.447569e-06\n Vprtstp: contraction number = 2.923949e-01\n Vnewton: Using errtol_s: 1.552233\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.568657e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.312143e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.100216e-01\n Vprtstp: contraction number = 5.100216e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.237842e-07\n Vprtstp: contraction number = 2.957156e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.525131e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.707368e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.261560e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.507379e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -21770,17 +21770,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.835376083091E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.829553004280E+03 kT\n Vpmg_energy:  dielEnergy = 3.412753768634E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.853700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.223500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n Vpbe_ctor2:  bulk ionic strength = 0.5\n Vpbe_ctor2:  xkappa = 0.230253\n@@ -21827,160 +21827,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00156468 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.060382\n+Vacc_SASA: Time elapsed: 0.068301\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.656570e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.844460e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.753900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.345400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.610850e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.388860e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.662052e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.433186e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 658696.826144\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.676204e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.467196e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.053855e+05\n Vprtstp: contraction number = 1.053855e+05\n Vnewton: Attempting damping, relres = 0.150549\n Vnewton: Attempting damping, relres = 0.569486\n Vnewton: Damping accepted, relres = 0.150549\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.505490e-01\n Vprtstp: contraction number = 1.505490e-01\n Vnewton: Using errtol_s: 99166.139789\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.749321e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.600507e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.161238e+04\n Vprtstp: contraction number = 2.161238e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.969136e-02\n Vprtstp: contraction number = 1.972206e-01\n Vnewton: Using errtol_s: 19557.601485\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.814847e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.724054e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.305338e+03\n Vprtstp: contraction number = 5.305338e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.249717e-03\n Vprtstp: contraction number = 2.441693e-01\n Vnewton: Using errtol_s: 4775.365541\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.879032e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.789930e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404636e+03\n Vprtstp: contraction number = 1.404636e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.919225e-03\n Vprtstp: contraction number = 2.647311e-01\n Vnewton: Using errtol_s: 1264.187582\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.941955e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.857669e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.902078e+02\n Vprtstp: contraction number = 3.902078e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.331561e-04\n Vprtstp: contraction number = 2.777976e-01\n Vnewton: Using errtol_s: 351.188214\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.007272e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.922976e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.119096e+02\n Vprtstp: contraction number = 1.119096e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.529061e-04\n Vprtstp: contraction number = 2.867943e-01\n Vnewton: Using errtol_s: 100.718769\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.083444e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.976160e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.284972e+01\n Vprtstp: contraction number = 3.284972e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.488371e-05\n Vprtstp: contraction number = 2.935377e-01\n Vnewton: Using errtol_s: 29.564758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.176047e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.030845e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.835792e+00\n Vprtstp: contraction number = 9.835792e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.343898e-05\n Vprtstp: contraction number = 2.994178e-01\n Vnewton: Using errtol_s: 8.852214\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.263943e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.123178e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.001834e+00\n Vprtstp: contraction number = 3.001834e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.101508e-06\n Vprtstp: contraction number = 3.051949e-01\n Vnewton: Using errtol_s: 2.701650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.345415e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.188862e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.317265e-01\n Vprtstp: contraction number = 9.317265e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.273050e-06\n Vprtstp: contraction number = 3.103858e-01\n Vnewton: Using errtol_s: 0.838554\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.413463e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.280911e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.932750e-01\n Vprtstp: contraction number = 2.932750e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.007117e-07\n Vprtstp: contraction number = 3.147651e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.103749e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.291539e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.426490e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.705739e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -21990,15 +21990,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.826778540566E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.062089331006E+03 kT\n Vpmg_energy:  dielEnergy = 4.029034062463E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.841600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.727900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -22027,162 +22027,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.100656\n+Vacc_SASA: Time elapsed: 0.117506\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.211460e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.384880e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.724600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.718200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.704690e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.203800e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.590632e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.514521e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1439349.266881\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.606179e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.546343e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.043544e+05\n Vprtstp: contraction number = 2.043544e+05\n Vnewton: Attempting damping, relres = 0.158631\n Vnewton: Attempting damping, relres = 0.563029\n Vnewton: Damping accepted, relres = 0.158631\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.586310e-01\n Vprtstp: contraction number = 1.586310e-01\n Vnewton: Using errtol_s: 228325.431602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.679950e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.632665e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.831785e+04\n Vprtstp: contraction number = 3.831785e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.847279e-02\n Vprtstp: contraction number = 1.794907e-01\n Vnewton: Using errtol_s: 40982.294833\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.757740e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.726800e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.668291e+03\n Vprtstp: contraction number = 9.668291e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.314045e-03\n Vprtstp: contraction number = 2.217571e-01\n Vnewton: Using errtol_s: 9088.116327\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.846056e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.838597e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.688849e+03\n Vprtstp: contraction number = 2.688849e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.683268e-03\n Vprtstp: contraction number = 2.665910e-01\n Vnewton: Using errtol_s: 2422.810315\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.933561e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.965093e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.856129e+02\n Vprtstp: contraction number = 7.856129e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.912324e-04\n Vprtstp: contraction number = 2.918326e-01\n Vnewton: Using errtol_s: 707.055007\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.008355e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.071683e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.356112e+02\n Vprtstp: contraction number = 2.356112e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473237e-04\n Vprtstp: contraction number = 2.999062e-01\n Vnewton: Using errtol_s: 212.050207\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.075401e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.188781e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.139103e+01\n Vprtstp: contraction number = 7.139103e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.463957e-05\n Vprtstp: contraction number = 3.030034e-01\n Vnewton: Using errtol_s: 64.251934\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.138911e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.315259e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.175983e+01\n Vprtstp: contraction number = 2.175983e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.360604e-05\n Vprtstp: contraction number = 3.047978e-01\n Vnewton: Using errtol_s: 19.583846\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.204039e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.448444e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.658230e+00\n Vprtstp: contraction number = 6.658230e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.163275e-06\n Vprtstp: contraction number = 3.059873e-01\n Vnewton: Using errtol_s: 5.992407\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.268232e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.578148e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.042996e+00\n Vprtstp: contraction number = 2.042996e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.277450e-06\n Vprtstp: contraction number = 3.068378e-01\n Vnewton: Using errtol_s: 1.838697\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.329772e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.689952e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.281914e-01\n Vprtstp: contraction number = 6.281914e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.927971e-07\n Vprtstp: contraction number = 3.074853e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.946484e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.145435e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.266053e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.291140e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -22192,15 +22192,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.196840922494E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.873106662838E+04 kT\n Vpmg_energy:  dielEnergy = 9.356799948261E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.831800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.534600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -22249,160 +22249,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00202496 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.103517\n+Vacc_SASA: Time elapsed: 0.118933\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.614990e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.295210e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.810000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.262200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.614760e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.130580e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.432458e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.853131e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1465724.452340\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.446055e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.885445e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.560590e+05\n Vprtstp: contraction number = 2.560590e+05\n Vnewton: Attempting damping, relres = 0.187284\n Vnewton: Attempting damping, relres = 0.577996\n Vnewton: Damping accepted, relres = 0.187284\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.872842e-01\n Vprtstp: contraction number = 1.872842e-01\n Vnewton: Using errtol_s: 274507.063571\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.521192e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.999591e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.241855e+04\n Vprtstp: contraction number = 5.241855e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.660510e-02\n Vprtstp: contraction number = 1.954521e-01\n Vnewton: Using errtol_s: 53652.984086\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.592999e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.134327e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.392830e+04\n Vprtstp: contraction number = 1.392830e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.808972e-03\n Vprtstp: contraction number = 2.406488e-01\n Vnewton: Using errtol_s: 12911.525544\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.661627e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.240049e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.064869e+03\n Vprtstp: contraction number = 4.064869e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.497826e-03\n Vprtstp: contraction number = 2.835548e-01\n Vnewton: Using errtol_s: 3661.124985\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.735313e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.357010e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.249555e+03\n Vprtstp: contraction number = 1.249555e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.672679e-04\n Vprtstp: contraction number = 3.071743e-01\n Vnewton: Using errtol_s: 1124.603371\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.805237e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.493981e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.953417e+02\n Vprtstp: contraction number = 3.953417e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.427522e-04\n Vprtstp: contraction number = 3.163852e-01\n Vnewton: Using errtol_s: 355.807819\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.872902e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.625134e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.271192e+02\n Vprtstp: contraction number = 1.271192e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.805515e-05\n Vprtstp: contraction number = 3.215425e-01\n Vnewton: Using errtol_s: 114.407339\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.943688e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.751136e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.134607e+01\n Vprtstp: contraction number = 4.134607e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.538777e-05\n Vprtstp: contraction number = 3.252542e-01\n Vnewton: Using errtol_s: 37.211468\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.016699e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.882904e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356940e+01\n Vprtstp: contraction number = 1.356940e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 8.332028e-06\n Vprtstp: contraction number = 3.281907e-01\n Vnewton: Using errtol_s: 12.212457\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.090177e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.993444e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.485660e+00\n Vprtstp: contraction number = 4.485660e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.754334e-06\n Vprtstp: contraction number = 3.305718e-01\n Vnewton: Using errtol_s: 4.037094\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.160230e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.137920e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.491490e+00\n Vprtstp: contraction number = 1.491490e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 9.158205e-07\n Vprtstp: contraction number = 3.325017e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.867170e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.056088e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.390353e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.415754e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -22412,29 +22412,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.186606092212E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.134845139455E+04 kT\n Vpmg_energy:  dielEnergy = 1.066550655218E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.893300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.940700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.295043e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.327805e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:48:44 2025\n+# Creation Date and Time:  Sun Jan  7 09:50:08 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -22704,151 +22704,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.204485\n+Vacc_SASA: Time elapsed: 0.194518\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.360820e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.902090e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.894500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.721600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.746420e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.912610e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.786850e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.380320e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2093191.031761\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.736510e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.046413e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.700910e+05\n Vprtstp: contraction number = 2.700910e+05\n Vnewton: Attempting damping, relres = 0.124805\n Vnewton: Attempting damping, relres = 0.555496\n Vnewton: Damping accepted, relres = 0.124805\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.248046e-01\n Vprtstp: contraction number = 1.248046e-01\n Vnewton: Using errtol_s: 261239.913592\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.792286e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.656478e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.897400e+04\n Vprtstp: contraction number = 4.897400e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.189435e-02\n Vprtstp: contraction number = 1.754290e-01\n Vnewton: Using errtol_s: 45829.056358\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.552258e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.876886e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.159488e+04\n Vprtstp: contraction number = 1.159488e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.014196e-03\n Vprtstp: contraction number = 2.290178e-01\n Vnewton: Using errtol_s: 10495.669115\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.296128e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.451155e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.106549e+03\n Vprtstp: contraction number = 3.106549e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.335806e-03\n Vprtstp: contraction number = 2.664048e-01\n Vnewton: Using errtol_s: 2796.096256\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.056973e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.153114e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.808235e+02\n Vprtstp: contraction number = 8.808235e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.787243e-04\n Vprtstp: contraction number = 2.835176e-01\n Vnewton: Using errtol_s: 792.742402\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.794319e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.718550e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.569082e+02\n Vprtstp: contraction number = 2.569082e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.104617e-04\n Vprtstp: contraction number = 2.916679e-01\n Vnewton: Using errtol_s: 231.217496\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.546517e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.223228e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.629035e+01\n Vprtstp: contraction number = 7.629035e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.280223e-05\n Vprtstp: contraction number = 2.969556e-01\n Vnewton: Using errtol_s: 68.661328\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.293973e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.847004e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.295748e+01\n Vprtstp: contraction number = 2.295748e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.870924e-06\n Vprtstp: contraction number = 3.009224e-01\n Vnewton: Using errtol_s: 20.661731\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.053560e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.310625e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.980126e+00\n Vprtstp: contraction number = 6.980126e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.001214e-06\n Vprtstp: contraction number = 3.040459e-01\n Vnewton: Using errtol_s: 6.282114\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.818176e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.755538e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.140783e+00\n Vprtstp: contraction number = 2.140783e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 9.204627e-07\n Vprtstp: contraction number = 3.066968e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.785038e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.989260e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.556854e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.790143e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -22858,17 +22858,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.091310515028E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.566396275850E+04 kT\n Vpmg_energy:  dielEnergy = 1.282657451494E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.975600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.845300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.6\n Vpbe_ctor2:  xkappa = 0.25223\n@@ -22915,160 +22915,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0123549 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.182762\n+Vacc_SASA: Time elapsed: 0.205556\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.194290e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.970400e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.718100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.755700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.600940e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.907770e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.091936e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.015128e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2138246.077963\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.234313e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.034729e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.360784e+05\n Vprtstp: contraction number = 3.360784e+05\n Vnewton: Attempting damping, relres = 0.149785\n Vnewton: Attempting damping, relres = 0.568394\n Vnewton: Damping accepted, relres = 0.149785\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.497849e-01\n Vprtstp: contraction number = 1.497849e-01\n Vnewton: Using errtol_s: 320277.019000\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.011955e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.101415e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.696106e+04\n Vprtstp: contraction number = 6.696106e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.898319e-02\n Vprtstp: contraction number = 1.934987e-01\n Vnewton: Using errtol_s: 61973.189490\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.092748e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.144266e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.682773e+04\n Vprtstp: contraction number = 1.682773e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.107594e-03\n Vprtstp: contraction number = 2.452316e-01\n Vnewton: Using errtol_s: 15197.785187\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.168265e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.186881e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.709721e+03\n Vprtstp: contraction number = 4.709721e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.982435e-03\n Vprtstp: contraction number = 2.789179e-01\n Vnewton: Using errtol_s: 4238.934308\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.248955e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.227230e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.393997e+03\n Vprtstp: contraction number = 1.393997e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.867426e-04\n Vprtstp: contraction number = 2.959706e-01\n Vnewton: Using errtol_s: 1254.599967\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.325972e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.268423e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.264850e+02\n Vprtstp: contraction number = 4.264850e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.795101e-04\n Vprtstp: contraction number = 3.059436e-01\n Vnewton: Using errtol_s: 383.836806\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.403516e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.308956e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.335898e+02\n Vprtstp: contraction number = 1.335898e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.622871e-05\n Vprtstp: contraction number = 3.132342e-01\n Vnewton: Using errtol_s: 120.230819\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.482039e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.349509e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.262294e+01\n Vprtstp: contraction number = 4.262294e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.794024e-05\n Vprtstp: contraction number = 3.190584e-01\n Vnewton: Using errtol_s: 38.360650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.560815e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.393224e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.381744e+01\n Vprtstp: contraction number = 1.381744e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.815841e-06\n Vprtstp: contraction number = 3.241785e-01\n Vnewton: Using errtol_s: 12.435699\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.639511e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.435115e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.538963e+00\n Vprtstp: contraction number = 4.538963e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.910476e-06\n Vprtstp: contraction number = 3.284952e-01\n Vnewton: Using errtol_s: 4.085067\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.717975e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.477669e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.507189e+00\n Vprtstp: contraction number = 1.507189e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.343844e-07\n Vprtstp: contraction number = 3.320557e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.791659e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.977490e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.959735e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.186390e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -23078,15 +23078,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.079562127761E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951011518926E+04 kT\n Vpmg_energy:  dielEnergy = 1.474966609512E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.805600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.788500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -23115,151 +23115,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.068852\n+Vacc_SASA: Time elapsed: 0.076756\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.081760e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.386330e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.767500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.766600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.924880e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.611970e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.912458e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.638586e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 628877.747769\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.933893e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.653493e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.412647e+04\n Vprtstp: contraction number = 8.412647e+04\n Vnewton: Attempting damping, relres = 0.127232\n Vnewton: Attempting damping, relres = 0.557518\n Vnewton: Damping accepted, relres = 0.127232\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.272321e-01\n Vprtstp: contraction number = 1.272321e-01\n Vnewton: Using errtol_s: 80013.454014\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.022280e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.704038e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.597434e+04\n Vprtstp: contraction number = 1.597434e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.300878e-02\n Vprtstp: contraction number = 1.808409e-01\n Vnewton: Using errtol_s: 14469.707458\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.087397e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.747972e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.702955e+03\n Vprtstp: contraction number = 3.702955e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.299891e-03\n Vprtstp: contraction number = 2.303422e-01\n Vnewton: Using errtol_s: 3332.983791\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.150662e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.789272e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.526036e+02\n Vprtstp: contraction number = 9.526036e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.363298e-03\n Vprtstp: contraction number = 2.572314e-01\n Vnewton: Using errtol_s: 857.348085\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.213004e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.833349e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.580584e+02\n Vprtstp: contraction number = 2.580584e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.693131e-04\n Vprtstp: contraction number = 2.708968e-01\n Vnewton: Using errtol_s: 232.252814\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.276542e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.876434e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.191756e+01\n Vprtstp: contraction number = 7.191756e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.029227e-04\n Vprtstp: contraction number = 2.786869e-01\n Vnewton: Using errtol_s: 64.725819\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.343278e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.916924e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.043225e+01\n Vprtstp: contraction number = 2.043225e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.924102e-05\n Vprtstp: contraction number = 2.841066e-01\n Vnewton: Using errtol_s: 18.389029\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.409829e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.956359e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.895681e+00\n Vprtstp: contraction number = 5.895681e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.437431e-06\n Vprtstp: contraction number = 2.885477e-01\n Vnewton: Using errtol_s: 5.306113\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.473063e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.999750e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.724061e+00\n Vprtstp: contraction number = 1.724061e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.467339e-06\n Vprtstp: contraction number = 2.924277e-01\n Vnewton: Using errtol_s: 1.551655\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.535613e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.048453e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.098608e-01\n Vprtstp: contraction number = 5.098608e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.296724e-07\n Vprtstp: contraction number = 2.957325e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 6.821551e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.043538e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 4.524391e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.719221e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -23269,15 +23269,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.828142417011E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.828945138010E+03 kT\n Vpmg_energy:  dielEnergy = 3.412475614010E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.997000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.374800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -23326,160 +23326,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0012176 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.066544\n+Vacc_SASA: Time elapsed: 0.078759\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.259250e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.892950e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.750500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.806700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.954700e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.054120e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.642212e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.150052e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 653003.444935\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.663032e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.169511e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.042328e+05\n Vprtstp: contraction number = 1.042328e+05\n Vnewton: Attempting damping, relres = 0.149810\n Vnewton: Attempting damping, relres = 0.569263\n Vnewton: Damping accepted, relres = 0.149810\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.498099e-01\n Vprtstp: contraction number = 1.498099e-01\n Vnewton: Using errtol_s: 97826.408096\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.747548e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.260287e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.140231e+04\n Vprtstp: contraction number = 2.140231e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.962843e-02\n Vprtstp: contraction number = 1.977735e-01\n Vnewton: Using errtol_s: 19347.468430\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.812465e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.320397e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.262567e+03\n Vprtstp: contraction number = 5.262567e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.253840e-03\n Vprtstp: contraction number = 2.448270e-01\n Vnewton: Using errtol_s: 4736.782334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.879524e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.389088e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.395696e+03\n Vprtstp: contraction number = 1.395696e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923638e-03\n Vprtstp: contraction number = 2.651889e-01\n Vnewton: Using errtol_s: 1256.142167\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.946472e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.459109e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.882795e+02\n Vprtstp: contraction number = 3.882795e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.351469e-04\n Vprtstp: contraction number = 2.781952e-01\n Vnewton: Using errtol_s: 349.452740\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.020426e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.517617e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114868e+02\n Vprtstp: contraction number = 1.114868e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.536566e-04\n Vprtstp: contraction number = 2.871297e-01\n Vnewton: Using errtol_s: 100.338262\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.096058e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.581024e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.275571e+01\n Vprtstp: contraction number = 3.275571e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.514547e-05\n Vprtstp: contraction number = 2.938077e-01\n Vnewton: Using errtol_s: 29.480150\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.173646e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.669355e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.814633e+00\n Vprtstp: contraction number = 9.814633e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.352699e-05\n Vprtstp: contraction number = 2.996311e-01\n Vnewton: Using errtol_s: 8.833170\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.257200e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.745998e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.996998e+00\n Vprtstp: contraction number = 2.996998e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.130604e-06\n Vprtstp: contraction number = 3.053602e-01\n Vnewton: Using errtol_s: 2.697298\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.347164e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.816484e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.305904e-01\n Vprtstp: contraction number = 9.305904e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.282583e-06\n Vprtstp: contraction number = 3.105075e-01\n Vnewton: Using errtol_s: 0.837531\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.426822e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.858599e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.929997e-01\n Vprtstp: contraction number = 2.929997e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.038259e-07\n Vprtstp: contraction number = 3.148535e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.515041e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.739869e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 7.435127e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.681420e+00\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -23489,15 +23489,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.819478148872E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.061484049390E+03 kT\n Vpmg_energy:  dielEnergy = 4.028757163114E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.272600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.849300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -23526,162 +23526,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.108321\n+Vacc_SASA: Time elapsed: 0.170678\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.145520e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.124520e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.704600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.016800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.234260e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.264160e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.628114e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.039035e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1418682.220089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.657117e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.074238e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.013102e+05\n Vprtstp: contraction number = 2.013102e+05\n Vnewton: Attempting damping, relres = 0.153624\n Vnewton: Attempting damping, relres = 0.562616\n Vnewton: Damping accepted, relres = 0.153624\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.536244e-01\n Vprtstp: contraction number = 1.536244e-01\n Vnewton: Using errtol_s: 217944.143405\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.747695e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.207217e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.768720e+04\n Vprtstp: contraction number = 3.768720e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.718554e-02\n Vprtstp: contraction number = 1.769611e-01\n Vnewton: Using errtol_s: 38567.641801\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.814239e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.299586e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.503404e+03\n Vprtstp: contraction number = 9.503404e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.173770e-03\n Vprtstp: contraction number = 2.270976e-01\n Vnewton: Using errtol_s: 8758.617788\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.880009e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.396914e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660166e+03\n Vprtstp: contraction number = 2.660166e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.688330e-03\n Vprtstp: contraction number = 2.734683e-01\n Vnewton: Using errtol_s: 2395.204376\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.947790e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.487343e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.818054e+02\n Vprtstp: contraction number = 7.818054e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.959721e-04\n Vprtstp: contraction number = 2.937648e-01\n Vnewton: Using errtol_s: 703.626776\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.015281e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.593926e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.347603e+02\n Vprtstp: contraction number = 2.347603e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.489300e-04\n Vprtstp: contraction number = 3.002790e-01\n Vnewton: Using errtol_s: 211.284321\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.095912e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.702538e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.116445e+01\n Vprtstp: contraction number = 7.116445e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.514613e-05\n Vprtstp: contraction number = 3.031366e-01\n Vnewton: Using errtol_s: 64.048016\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.178434e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.836633e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.169522e+01\n Vprtstp: contraction number = 2.169522e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.376326e-05\n Vprtstp: contraction number = 3.048603e-01\n Vnewton: Using errtol_s: 19.525698\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.267909e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.948876e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.639132e+00\n Vprtstp: contraction number = 6.639132e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.211809e-06\n Vprtstp: contraction number = 3.060182e-01\n Vnewton: Using errtol_s: 5.975219\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.361106e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.061526e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.037255e+00\n Vprtstp: contraction number = 2.037255e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.292417e-06\n Vprtstp: contraction number = 3.068556e-01\n Vnewton: Using errtol_s: 1.833530\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.442714e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.186834e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.264492e-01\n Vprtstp: contraction number = 6.264492e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.974141e-07\n Vprtstp: contraction number = 3.074967e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.784380e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.034786e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.228238e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.254437e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -23691,15 +23691,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.888929472568E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.872895947241E+04 kT\n Vpmg_energy:  dielEnergy = 9.356241018508E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.817100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.329400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -23748,160 +23748,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00159488 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.102302\n+Vacc_SASA: Time elapsed: 0.167456\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.418720e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.689840e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.666800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.736400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.033510e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.065340e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.567377e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.342428e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1444108.030883\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.594973e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.371236e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.522925e+05\n Vprtstp: contraction number = 2.522925e+05\n Vnewton: Attempting damping, relres = 0.182497\n Vnewton: Attempting damping, relres = 0.577636\n Vnewton: Damping accepted, relres = 0.182497\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.824967e-01\n Vprtstp: contraction number = 1.824967e-01\n Vnewton: Using errtol_s: 263544.898395\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.710303e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.484131e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.156495e+04\n Vprtstp: contraction number = 5.156495e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.534743e-02\n Vprtstp: contraction number = 1.936881e-01\n Vnewton: Using errtol_s: 51045.503065\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.812262e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.600418e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.369160e+04\n Vprtstp: contraction number = 1.369160e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.672608e-03\n Vprtstp: contraction number = 2.453533e-01\n Vnewton: Using errtol_s: 12524.182385\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.913173e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.702594e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.019157e+03\n Vprtstp: contraction number = 4.019157e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.505566e-03\n Vprtstp: contraction number = 2.889057e-01\n Vnewton: Using errtol_s: 3618.307619\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.005563e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.804256e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.241608e+03\n Vprtstp: contraction number = 1.241608e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.737990e-04\n Vprtstp: contraction number = 3.088321e-01\n Vnewton: Using errtol_s: 1117.449365\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.097316e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.912484e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.934907e+02\n Vprtstp: contraction number = 3.934907e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.452323e-04\n Vprtstp: contraction number = 3.169199e-01\n Vnewton: Using errtol_s: 354.141922\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.183116e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.030528e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.266527e+02\n Vprtstp: contraction number = 1.266527e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.893280e-05\n Vprtstp: contraction number = 3.218695e-01\n Vnewton: Using errtol_s: 113.987497\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.257082e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.156007e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.122303e+01\n Vprtstp: contraction number = 4.122303e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.569111e-05\n Vprtstp: contraction number = 3.254807e-01\n Vnewton: Using errtol_s: 37.100733\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.326155e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.270492e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.353532e+01\n Vprtstp: contraction number = 1.353532e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 8.435513e-06\n Vprtstp: contraction number = 3.283437e-01\n Vnewton: Using errtol_s: 12.181792\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.400099e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.385432e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.475781e+00\n Vprtstp: contraction number = 4.475781e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.789406e-06\n Vprtstp: contraction number = 3.306741e-01\n Vnewton: Using errtol_s: 4.028203\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.484042e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.479911e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.488509e+00\n Vprtstp: contraction number = 1.488509e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 9.276717e-07\n Vprtstp: contraction number = 3.325696e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.897536e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.014294e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.228810e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.253107e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -23911,29 +23911,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.878772494899E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.134634520141E+04 kT\n Vpmg_energy:  dielEnergy = 1.066494761685E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.446200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.353600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.637708e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.656679e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:49:07 2025\n+# Creation Date and Time:  Sun Jan  7 09:50:22 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -24203,151 +24203,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.231015\n+Vacc_SASA: Time elapsed: 0.201533\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.211060e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.226830e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.116800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.285100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.848050e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.049920e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.719430e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.260580e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2075985.759525\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.006432e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.048093e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.676742e+05\n Vprtstp: contraction number = 2.676742e+05\n Vnewton: Attempting damping, relres = 0.123645\n Vnewton: Attempting damping, relres = 0.555352\n Vnewton: Damping accepted, relres = 0.123645\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.236446e-01\n Vprtstp: contraction number = 1.236446e-01\n Vnewton: Using errtol_s: 256684.416130\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.074088e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.702061e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.859973e+04\n Vprtstp: contraction number = 4.859973e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.169836e-02\n Vprtstp: contraction number = 1.754897e-01\n Vnewton: Using errtol_s: 45045.483798\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.913918e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.391511e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.152870e+04\n Vprtstp: contraction number = 1.152870e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.014779e-03\n Vprtstp: contraction number = 2.311133e-01\n Vnewton: Using errtol_s: 10410.609915\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.874043e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.727398e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.097422e+03\n Vprtstp: contraction number = 3.097422e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.342870e-03\n Vprtstp: contraction number = 2.677824e-01\n Vnewton: Using errtol_s: 2787.778355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.983060e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.131740e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.793803e+02\n Vprtstp: contraction number = 8.793803e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.812374e-04\n Vprtstp: contraction number = 2.838975e-01\n Vnewton: Using errtol_s: 791.443333\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.212044e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.523745e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.566243e+02\n Vprtstp: contraction number = 2.566243e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.112541e-04\n Vprtstp: contraction number = 2.918238e-01\n Vnewton: Using errtol_s: 230.962017\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.450903e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.193576e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.622598e+01\n Vprtstp: contraction number = 7.622598e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.304618e-05\n Vprtstp: contraction number = 2.970332e-01\n Vnewton: Using errtol_s: 68.603390\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.609352e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.832163e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.294139e+01\n Vprtstp: contraction number = 2.294139e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.945756e-06\n Vprtstp: contraction number = 3.009654e-01\n Vnewton: Using errtol_s: 20.647248\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.829216e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.003609e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.975781e+00\n Vprtstp: contraction number = 6.975781e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.024203e-06\n Vprtstp: contraction number = 3.040697e-01\n Vnewton: Using errtol_s: 6.278203\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.100194e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.151860e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.139542e+00\n Vprtstp: contraction number = 2.139542e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 9.275536e-07\n Vprtstp: contraction number = 3.067101e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.129209e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.150824e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.179397e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.205957e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -24357,17 +24357,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.936418090819E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.566271448852E+04 kT\n Vpmg_energy:  dielEnergy = 1.282618425876E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.796500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.566900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.7\n Vpbe_ctor2:  xkappa = 0.272439\n@@ -24414,160 +24414,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0114665 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.187668\n+Vacc_SASA: Time elapsed: 0.262468\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.407100e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.401870e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.348300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.824400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.225220e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.304280e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.289917e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.355437e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2120327.174672\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.322485e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.381074e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.330788e+05\n Vprtstp: contraction number = 3.330788e+05\n Vnewton: Attempting damping, relres = 0.148670\n Vnewton: Attempting damping, relres = 0.568259\n Vnewton: Damping accepted, relres = 0.148670\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.486698e-01\n Vprtstp: contraction number = 1.486698e-01\n Vnewton: Using errtol_s: 315228.684259\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.487979e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.456325e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.641464e+04\n Vprtstp: contraction number = 6.641464e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.878895e-02\n Vprtstp: contraction number = 1.936435e-01\n Vnewton: Using errtol_s: 61041.990934\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.637924e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.588394e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.670744e+04\n Vprtstp: contraction number = 1.670744e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.105637e-03\n Vprtstp: contraction number = 2.468182e-01\n Vnewton: Using errtol_s: 15066.274957\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.761610e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.755076e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.686665e+03\n Vprtstp: contraction number = 4.686665e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.989361e-03\n Vprtstp: contraction number = 2.799694e-01\n Vnewton: Using errtol_s: 4218.095910\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.865872e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.915597e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.389137e+03\n Vprtstp: contraction number = 1.389137e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.896382e-04\n Vprtstp: contraction number = 2.963958e-01\n Vnewton: Using errtol_s: 1250.225849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.960911e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.082391e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.253662e+02\n Vprtstp: contraction number = 4.253662e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.805523e-04\n Vprtstp: contraction number = 3.062086e-01\n Vnewton: Using errtol_s: 382.829903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.060963e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.252001e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.333214e+02\n Vprtstp: contraction number = 1.333214e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.659001e-05\n Vprtstp: contraction number = 3.134273e-01\n Vnewton: Using errtol_s: 119.989327\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.175909e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.387694e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.255612e+01\n Vprtstp: contraction number = 4.255612e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.806349e-05\n Vprtstp: contraction number = 3.191993e-01\n Vnewton: Using errtol_s: 38.300511\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.298950e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.515167e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.379985e+01\n Vprtstp: contraction number = 1.379985e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.857525e-06\n Vprtstp: contraction number = 3.242742e-01\n Vnewton: Using errtol_s: 12.419869\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.426028e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.671905e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.534043e+00\n Vprtstp: contraction number = 4.534043e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.924533e-06\n Vprtstp: contraction number = 3.285573e-01\n Vnewton: Using errtol_s: 4.080639\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.562504e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.787387e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.505713e+00\n Vprtstp: contraction number = 1.505713e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.391193e-07\n Vprtstp: contraction number = 3.320906e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.387877e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.415243e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.527516e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.553942e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -24577,17 +24577,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.924946278586E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.950886798741E+04 kT\n Vpmg_energy:  dielEnergy = 1.474927636785E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.506100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.913900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -24614,151 +24614,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.071643\n+Vacc_SASA: Time elapsed: 0.077391\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.512960e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.327820e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.287700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.867300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.270030e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.153760e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.814980e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.018740e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 625058.556229\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.847511e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.046412e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.349434e+04\n Vprtstp: contraction number = 8.349434e+04\n Vnewton: Attempting damping, relres = 0.126666\n Vnewton: Attempting damping, relres = 0.557380\n Vnewton: Damping accepted, relres = 0.126666\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.266665e-01\n Vprtstp: contraction number = 1.266665e-01\n Vnewton: Using errtol_s: 79173.978566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.981991e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.165377e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.587988e+04\n Vprtstp: contraction number = 1.587988e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.298610e-02\n Vprtstp: contraction number = 1.814695e-01\n Vnewton: Using errtol_s: 14367.659528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.102227e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.279505e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.689543e+03\n Vprtstp: contraction number = 3.689543e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.312865e-03\n Vprtstp: contraction number = 2.311338e-01\n Vnewton: Using errtol_s: 3320.851989\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.217647e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.352345e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.505518e+02\n Vprtstp: contraction number = 9.505518e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.368674e-03\n Vprtstp: contraction number = 2.576150e-01\n Vnewton: Using errtol_s: 855.501271\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.336818e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.475234e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.577170e+02\n Vprtstp: contraction number = 2.577170e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.710781e-04\n Vprtstp: contraction number = 2.711224e-01\n Vnewton: Using errtol_s: 231.945545\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.454146e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.589985e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.185767e+01\n Vprtstp: contraction number = 7.185767e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.034654e-04\n Vprtstp: contraction number = 2.788237e-01\n Vnewton: Using errtol_s: 64.671921\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.571542e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.696590e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.042074e+01\n Vprtstp: contraction number = 2.042074e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.940311e-05\n Vprtstp: contraction number = 2.841831e-01\n Vnewton: Using errtol_s: 18.378664\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.688077e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.814601e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.893233e+00\n Vprtstp: contraction number = 5.893233e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.485461e-06\n Vprtstp: contraction number = 2.885906e-01\n Vnewton: Using errtol_s: 5.303910\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.805229e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.890572e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.723486e+00\n Vprtstp: contraction number = 1.723486e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.481587e-06\n Vprtstp: contraction number = 2.924517e-01\n Vnewton: Using errtol_s: 1.551137\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.921252e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.996087e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.097109e-01\n Vprtstp: contraction number = 5.097109e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.339149e-07\n Vprtstp: contraction number = 2.957442e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.206762e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.234250e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.085535e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.110300e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -24768,17 +24768,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.817512164844E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.828431655726E+03 kT\n Vpmg_energy:  dielEnergy = 3.412244339074E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.869200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.796400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n Vpbe_ctor2:  bulk ionic strength = 0.7\n Vpbe_ctor2:  xkappa = 0.272439\n@@ -24825,160 +24825,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.000971631 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.113774\n+Vacc_SASA: Time elapsed: 0.093858\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.240080e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.939370e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.289400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.999800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.131470e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.232960e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.082859e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.164393e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 648940.820048\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.113652e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.196399e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.033896e+05\n Vprtstp: contraction number = 1.033896e+05\n Vnewton: Attempting damping, relres = 0.149178\n Vnewton: Attempting damping, relres = 0.569081\n Vnewton: Damping accepted, relres = 0.149178\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.491779e-01\n Vprtstp: contraction number = 1.491779e-01\n Vnewton: Using errtol_s: 96807.596825\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.245081e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.323937e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.124753e+04\n Vprtstp: contraction number = 2.124753e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.957488e-02\n Vprtstp: contraction number = 1.982525e-01\n Vnewton: Using errtol_s: 19192.349469\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.355675e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.416401e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.231045e+03\n Vprtstp: contraction number = 5.231045e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.255435e-03\n Vprtstp: contraction number = 2.453242e-01\n Vnewton: Using errtol_s: 4708.348197\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.471280e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.542155e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.389072e+03\n Vprtstp: contraction number = 1.389072e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.926494e-03\n Vprtstp: contraction number = 2.655242e-01\n Vnewton: Using errtol_s: 1250.180442\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.590871e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.678990e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.868439e+02\n Vprtstp: contraction number = 3.868439e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.365061e-04\n Vprtstp: contraction number = 2.784884e-01\n Vnewton: Using errtol_s: 348.160728\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.707996e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.792855e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.111703e+02\n Vprtstp: contraction number = 1.111703e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.541795e-04\n Vprtstp: contraction number = 2.873769e-01\n Vnewton: Using errtol_s: 100.053355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.829169e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.865355e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.268464e+01\n Vprtstp: contraction number = 3.268464e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.532954e-05\n Vprtstp: contraction number = 2.940050e-01\n Vnewton: Using errtol_s: 29.416189\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.947211e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.974306e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.798450e+00\n Vprtstp: contraction number = 9.798450e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.358923e-05\n Vprtstp: contraction number = 2.997875e-01\n Vnewton: Using errtol_s: 8.818606\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.061600e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.057420e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.993247e+00\n Vprtstp: contraction number = 2.993247e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.151261e-06\n Vprtstp: contraction number = 3.054817e-01\n Vnewton: Using errtol_s: 2.693923\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.180433e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.125205e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.296932e-01\n Vprtstp: contraction number = 9.296932e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.289368e-06\n Vprtstp: contraction number = 3.105968e-01\n Vnewton: Using errtol_s: 0.836724\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.298837e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.203419e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.927772e-01\n Vprtstp: contraction number = 2.927772e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.060455e-07\n Vprtstp: contraction number = 3.149181e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.313544e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.339940e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.107957e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.133845e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -24988,15 +24988,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.808821595407E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.060972751461E+03 kT\n Vpmg_energy:  dielEnergy = 4.028526891385E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.901700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.148000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -25025,162 +25025,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.110173\n+Vacc_SASA: Time elapsed: 0.107122\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.673150e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.463810e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.943400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.671400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.083340e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.978470e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.537449e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.410573e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1404398.831107\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.568556e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.436306e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.991752e+05\n Vprtstp: contraction number = 1.991752e+05\n Vnewton: Attempting damping, relres = 0.149937\n Vnewton: Attempting damping, relres = 0.562289\n Vnewton: Damping accepted, relres = 0.149937\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.499366e-01\n Vprtstp: contraction number = 1.499366e-01\n Vnewton: Using errtol_s: 210570.777586\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.705230e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.539889e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.724441e+04\n Vprtstp: contraction number = 3.724441e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.631656e-02\n Vprtstp: contraction number = 1.755180e-01\n Vnewton: Using errtol_s: 36958.952617\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.828191e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.650021e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.392042e+03\n Vprtstp: contraction number = 9.392042e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.102282e-03\n Vprtstp: contraction number = 2.318799e-01\n Vnewton: Using errtol_s: 8570.037199\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.943085e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.749822e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.643900e+03\n Vprtstp: contraction number = 2.643900e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.694653e-03\n Vprtstp: contraction number = 2.777081e-01\n Vnewton: Using errtol_s: 2379.968912\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.062205e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.873531e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.795002e+02\n Vprtstp: contraction number = 7.795002e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.995386e-04\n Vprtstp: contraction number = 2.947734e-01\n Vnewton: Using errtol_s: 701.551412\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.171573e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.961578e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.342462e+02\n Vprtstp: contraction number = 2.342462e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.501153e-04\n Vprtstp: contraction number = 3.005079e-01\n Vnewton: Using errtol_s: 210.821708\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.286239e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.040143e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.102938e+01\n Vprtstp: contraction number = 7.102938e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.551873e-05\n Vprtstp: contraction number = 3.032252e-01\n Vnewton: Using errtol_s: 63.926447\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.405432e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.140671e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.165701e+01\n Vprtstp: contraction number = 2.165701e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.387876e-05\n Vprtstp: contraction number = 3.049021e-01\n Vnewton: Using errtol_s: 19.491311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.521146e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.243002e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.627865e+00\n Vprtstp: contraction number = 6.627865e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.247425e-06\n Vprtstp: contraction number = 3.060378e-01\n Vnewton: Using errtol_s: 5.965078\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.638317e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.342368e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.033869e+00\n Vprtstp: contraction number = 2.033869e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.303392e-06\n Vprtstp: contraction number = 3.068664e-01\n Vnewton: Using errtol_s: 1.830482\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.753354e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.432121e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.254212e-01\n Vprtstp: contraction number = 6.254212e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.007972e-07\n Vprtstp: contraction number = 3.075032e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.316231e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.341708e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.112650e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.135342e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -25190,17 +25190,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.631424094606E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.872722745686E+04 kT\n Vpmg_energy:  dielEnergy = 9.355776117184E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.576300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.192700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n Vpbe_ctor2:  bulk ionic strength = 0.7\n Vpbe_ctor2:  xkappa = 0.272439\n@@ -25247,160 +25247,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00130951 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.110623\n+Vacc_SASA: Time elapsed: 0.117710\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.012560e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.138750e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.760700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.699300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.015750e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.747780e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.920169e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.589492e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1429289.662203\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.949694e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.614652e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.496624e+05\n Vprtstp: contraction number = 2.496624e+05\n Vnewton: Attempting damping, relres = 0.178955\n Vnewton: Attempting damping, relres = 0.577343\n Vnewton: Damping accepted, relres = 0.178955\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.789551e-01\n Vprtstp: contraction number = 1.789551e-01\n Vnewton: Using errtol_s: 255778.622825\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.088243e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.731189e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.096661e+04\n Vprtstp: contraction number = 5.096661e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.449699e-02\n Vprtstp: contraction number = 1.927690e-01\n Vnewton: Using errtol_s: 49306.188432\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.214108e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.844302e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352983e+04\n Vprtstp: contraction number = 1.352983e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.601027e-03\n Vprtstp: contraction number = 2.493269e-01\n Vnewton: Using errtol_s: 12293.359097\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.330204e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.943445e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.990835e+03\n Vprtstp: contraction number = 3.990835e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.513298e-03\n Vprtstp: contraction number = 2.922090e-01\n Vnewton: Using errtol_s: 3592.230783\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.450519e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.063705e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.236351e+03\n Vprtstp: contraction number = 1.236351e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.785110e-04\n Vprtstp: contraction number = 3.097567e-01\n Vnewton: Using errtol_s: 1112.717700\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.566268e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.131685e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.922762e+02\n Vprtstp: contraction number = 3.922762e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.470100e-04\n Vprtstp: contraction number = 3.172852e-01\n Vnewton: Using errtol_s: 353.048870\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.682032e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.199949e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.263525e+02\n Vprtstp: contraction number = 1.263525e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.956210e-05\n Vprtstp: contraction number = 3.221007e-01\n Vnewton: Using errtol_s: 113.717282\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.793821e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.303753e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.114546e+01\n Vprtstp: contraction number = 4.114546e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.590862e-05\n Vprtstp: contraction number = 3.256402e-01\n Vnewton: Using errtol_s: 37.030918\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.892428e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.408196e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.351428e+01\n Vprtstp: contraction number = 1.351428e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 8.509716e-06\n Vprtstp: contraction number = 3.284512e-01\n Vnewton: Using errtol_s: 12.162848\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.989104e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.468786e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.469783e+00\n Vprtstp: contraction number = 4.469783e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.814548e-06\n Vprtstp: contraction number = 3.307453e-01\n Vnewton: Using errtol_s: 4.022804\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.081377e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.545266e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.486721e+00\n Vprtstp: contraction number = 1.486721e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 9.361638e-07\n Vprtstp: contraction number = 3.326161e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.236101e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.259403e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.037245e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.057165e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -25410,29 +25410,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.621321814807E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.134461409198E+04 kT\n Vpmg_energy:  dielEnergy = 1.066448263473E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.298500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.109300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.234424e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.709881e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:49:30 2025\n+# Creation Date and Time:  Sun Jan  7 09:50:40 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -25702,151 +25702,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.209386\n+Vacc_SASA: Time elapsed: 0.222732\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.940580e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.493770e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.757500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.739400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.918920e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.206620e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.483140e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.407070e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2063009.659222\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.001345e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.149607e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.658306e+05\n Vprtstp: contraction number = 2.658306e+05\n Vnewton: Attempting damping, relres = 0.122739\n Vnewton: Attempting damping, relres = 0.555235\n Vnewton: Damping accepted, relres = 0.122739\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.227391e-01\n Vprtstp: contraction number = 1.227391e-01\n Vnewton: Using errtol_s: 253211.880914\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.389586e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.728345e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.831485e+04\n Vprtstp: contraction number = 4.831485e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.156033e-02\n Vprtstp: contraction number = 1.756599e-01\n Vnewton: Using errtol_s: 44479.169236\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.603103e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.229891e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.148001e+04\n Vprtstp: contraction number = 1.148001e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.018325e-03\n Vprtstp: contraction number = 2.327573e-01\n Vnewton: Using errtol_s: 10352.852780\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.751962e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.773163e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.090763e+03\n Vprtstp: contraction number = 3.090763e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.348386e-03\n Vprtstp: contraction number = 2.686924e-01\n Vnewton: Using errtol_s: 2781.733245\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.837839e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.614097e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.782780e+02\n Vprtstp: contraction number = 8.782780e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.831544e-04\n Vprtstp: contraction number = 2.841578e-01\n Vnewton: Using errtol_s: 790.451228\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.903291e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.870537e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.564053e+02\n Vprtstp: contraction number = 2.564053e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.118584e-04\n Vprtstp: contraction number = 2.919407e-01\n Vnewton: Using errtol_s: 230.764871\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.034025e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.124832e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.617617e+01\n Vprtstp: contraction number = 7.617617e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.323230e-05\n Vprtstp: contraction number = 2.970927e-01\n Vnewton: Using errtol_s: 68.558559\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.152110e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.024715e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.292888e+01\n Vprtstp: contraction number = 2.292888e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.000286e-05\n Vprtstp: contraction number = 3.009981e-01\n Vnewton: Using errtol_s: 20.635996\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.024510e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.168148e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.972403e+00\n Vprtstp: contraction number = 6.972403e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.041752e-06\n Vprtstp: contraction number = 3.040882e-01\n Vnewton: Using errtol_s: 6.275163\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.136472e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.313347e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.138578e+00\n Vprtstp: contraction number = 2.138578e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 9.329670e-07\n Vprtstp: contraction number = 3.067203e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.159801e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.181788e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.279729e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.305099e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -25856,17 +25856,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.808172570835E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.566165331536E+04 kT\n Vpmg_energy:  dielEnergy = 1.282584652691E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.205800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.018400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.8\n Vpbe_ctor2:  xkappa = 0.29125\n@@ -25913,160 +25913,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0106595 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.184427\n+Vacc_SASA: Time elapsed: 0.186116\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.329840e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.598060e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.871300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.699900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.951390e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.747520e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.312684e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.448057e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2106967.008420\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.341868e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.469199e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.308151e+05\n Vprtstp: contraction number = 3.308151e+05\n Vnewton: Attempting damping, relres = 0.147795\n Vnewton: Attempting damping, relres = 0.568147\n Vnewton: Damping accepted, relres = 0.147795\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.477951e-01\n Vprtstp: contraction number = 1.477951e-01\n Vnewton: Using errtol_s: 311399.390533\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.481677e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.558290e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.599748e+04\n Vprtstp: contraction number = 6.599748e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.864948e-02\n Vprtstp: contraction number = 1.938459e-01\n Vnewton: Using errtol_s: 60363.499136\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.602284e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.657631e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.661676e+04\n Vprtstp: contraction number = 1.661676e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.106188e-03\n Vprtstp: contraction number = 2.480390e-01\n Vnewton: Using errtol_s: 14972.503442\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.709890e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.763323e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.669116e+03\n Vprtstp: contraction number = 4.669116e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.994461e-03\n Vprtstp: contraction number = 2.806653e-01\n Vnewton: Using errtol_s: 4202.262595\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.825724e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.859665e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.385353e+03\n Vprtstp: contraction number = 1.385353e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.917609e-04\n Vprtstp: contraction number = 2.967022e-01\n Vnewton: Using errtol_s: 1246.820661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.946508e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.930616e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.244924e+02\n Vprtstp: contraction number = 4.244924e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.813239e-04\n Vprtstp: contraction number = 3.064141e-01\n Vnewton: Using errtol_s: 382.043458\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.071822e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.003957e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.331120e+02\n Vprtstp: contraction number = 1.331120e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.685939e-05\n Vprtstp: contraction number = 3.135792e-01\n Vnewton: Using errtol_s: 119.800865\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.194121e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.136082e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.250410e+01\n Vprtstp: contraction number = 4.250410e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.815581e-05\n Vprtstp: contraction number = 3.193107e-01\n Vnewton: Using errtol_s: 38.253693\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.317839e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.218328e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.378625e+01\n Vprtstp: contraction number = 1.378625e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.888858e-06\n Vprtstp: contraction number = 3.243511e-01\n Vnewton: Using errtol_s: 12.407629\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.435387e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.289491e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.530276e+00\n Vprtstp: contraction number = 4.530276e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.935127e-06\n Vprtstp: contraction number = 3.286082e-01\n Vnewton: Using errtol_s: 4.077249\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.554638e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.407125e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.504596e+00\n Vprtstp: contraction number = 1.504596e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.426945e-07\n Vprtstp: contraction number = 3.321201e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.347309e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.369507e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.001527e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.025019e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -26076,15 +26076,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.796939220773E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.950780776080E+04 kT\n Vpmg_energy:  dielEnergy = 1.474893902492E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.858500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.405600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -26113,151 +26113,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.069398\n+Vacc_SASA: Time elapsed: 0.069859\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.402590e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.246670e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.661400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.730100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.098420e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.955730e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.788162e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.577132e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 622184.484743\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.814537e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.600746e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.301310e+04\n Vprtstp: contraction number = 8.301310e+04\n Vnewton: Attempting damping, relres = 0.126177\n Vnewton: Attempting damping, relres = 0.557265\n Vnewton: Damping accepted, relres = 0.126177\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.261770e-01\n Vprtstp: contraction number = 1.261770e-01\n Vnewton: Using errtol_s: 78505.344097\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.934108e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.709744e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.580629e+04\n Vprtstp: contraction number = 1.580629e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.296474e-02\n Vprtstp: contraction number = 1.820042e-01\n Vnewton: Using errtol_s: 14288.305999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.036236e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.805217e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.679149e+03\n Vprtstp: contraction number = 3.679149e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.322303e-03\n Vprtstp: contraction number = 2.317597e-01\n Vnewton: Using errtol_s: 3311.454085\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.132810e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.893614e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.489453e+02\n Vprtstp: contraction number = 9.489453e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.372672e-03\n Vprtstp: contraction number = 2.579095e-01\n Vnewton: Using errtol_s: 854.055318\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.231615e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.977243e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.574445e+02\n Vprtstp: contraction number = 2.574445e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.723980e-04\n Vprtstp: contraction number = 2.712942e-01\n Vnewton: Using errtol_s: 231.700267\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.332298e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.062758e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.180833e+01\n Vprtstp: contraction number = 7.180833e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.038719e-04\n Vprtstp: contraction number = 2.789272e-01\n Vnewton: Using errtol_s: 64.627514\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.442752e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.174612e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.041084e+01\n Vprtstp: contraction number = 2.041084e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.952461e-05\n Vprtstp: contraction number = 2.842404e-01\n Vnewton: Using errtol_s: 18.369753\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.550471e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.262921e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.891035e+00\n Vprtstp: contraction number = 5.891035e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.521479e-06\n Vprtstp: contraction number = 2.886229e-01\n Vnewton: Using errtol_s: 5.301932\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.662036e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.352944e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.722947e+00\n Vprtstp: contraction number = 1.722947e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.492271e-06\n Vprtstp: contraction number = 2.924694e-01\n Vnewton: Using errtol_s: 1.550653\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.779189e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.439392e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.095658e-01\n Vprtstp: contraction number = 5.095658e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.370953e-07\n Vprtstp: contraction number = 2.957524e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.089873e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.113758e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.426403e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.652566e+00\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -26267,15 +26267,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.805001041922E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.827988101886E+03 kT\n Vpmg_energy:  dielEnergy = 3.412047294485E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.414400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.199500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -26324,160 +26324,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.000791536 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.070048\n+Vacc_SASA: Time elapsed: 0.070125\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.761270e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.657880e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.750800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.752200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.102750e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.897270e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.936759e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.573811e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 645906.037357\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.965993e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.602497e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.027473e+05\n Vprtstp: contraction number = 1.027473e+05\n Vnewton: Attempting damping, relres = 0.148634\n Vnewton: Attempting damping, relres = 0.568930\n Vnewton: Damping accepted, relres = 0.148634\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.486339e-01\n Vprtstp: contraction number = 1.486339e-01\n Vnewton: Using errtol_s: 96003.523693\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.104606e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.705676e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.112857e+04\n Vprtstp: contraction number = 2.112857e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.952923e-02\n Vprtstp: contraction number = 1.986709e-01\n Vnewton: Using errtol_s: 19073.107408\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.219390e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.795450e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.206787e+03\n Vprtstp: contraction number = 5.206787e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.255653e-03\n Vprtstp: contraction number = 2.457109e-01\n Vnewton: Using errtol_s: 4686.469778\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.334736e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.889873e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.383944e+03\n Vprtstp: contraction number = 1.383944e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.928400e-03\n Vprtstp: contraction number = 2.657790e-01\n Vnewton: Using errtol_s: 1245.565289\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.452766e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.003012e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.857274e+02\n Vprtstp: contraction number = 3.857274e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.374712e-04\n Vprtstp: contraction number = 2.787135e-01\n Vnewton: Using errtol_s: 347.155903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.570435e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.112321e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.109221e+02\n Vprtstp: contraction number = 1.109221e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.545581e-04\n Vprtstp: contraction number = 2.875654e-01\n Vnewton: Using errtol_s: 99.830021\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.687782e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.247380e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.262844e+01\n Vprtstp: contraction number = 3.262844e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.546421e-05\n Vprtstp: contraction number = 2.941561e-01\n Vnewton: Using errtol_s: 29.365605\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.807964e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.368218e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.785490e+00\n Vprtstp: contraction number = 9.785490e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.363502e-05\n Vprtstp: contraction number = 2.999067e-01\n Vnewton: Using errtol_s: 8.806942\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.926216e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.480726e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990197e+00\n Vprtstp: contraction number = 2.990197e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.166516e-06\n Vprtstp: contraction number = 3.055746e-01\n Vnewton: Using errtol_s: 2.691178\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.045260e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.601544e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.289503e-01\n Vprtstp: contraction number = 9.289503e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.294392e-06\n Vprtstp: contraction number = 3.106652e-01\n Vnewton: Using errtol_s: 0.836055\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.162356e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.732603e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.925887e-01\n Vprtstp: contraction number = 2.925887e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.076906e-07\n Vprtstp: contraction number = 3.149670e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.322711e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.349362e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.272039e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.294248e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -26487,15 +26487,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.796314557167E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.060531082527E+03 kT\n Vpmg_energy:  dielEnergy = 4.028330665485E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.844600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.030200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -26524,162 +26524,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.107942\n+Vacc_SASA: Time elapsed: 0.117060\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.654000e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.483250e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.008200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.749400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.029190e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.224510e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.400547e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.988325e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1394036.370554\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.430342e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.020610e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.976078e+05\n Vprtstp: contraction number = 1.976078e+05\n Vnewton: Attempting damping, relres = 0.147111\n Vnewton: Attempting damping, relres = 0.562025\n Vnewton: Damping accepted, relres = 0.147111\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.471110e-01\n Vprtstp: contraction number = 1.471110e-01\n Vnewton: Using errtol_s: 205078.018083\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.566568e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.116556e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.691787e+04\n Vprtstp: contraction number = 3.691787e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.570682e-02\n Vprtstp: contraction number = 1.747444e-01\n Vnewton: Using errtol_s: 35836.239165\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.693393e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.200506e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.313783e+03\n Vprtstp: contraction number = 9.313783e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.063883e-03\n Vprtstp: contraction number = 2.358862e-01\n Vnewton: Using errtol_s: 8453.273025\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.808109e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.308556e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.633660e+03\n Vprtstp: contraction number = 2.633660e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.700470e-03\n Vprtstp: contraction number = 2.804259e-01\n Vnewton: Using errtol_s: 2370.516473\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.926614e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.428323e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.779603e+02\n Vprtstp: contraction number = 7.779603e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.022576e-04\n Vprtstp: contraction number = 2.953640e-01\n Vnewton: Using errtol_s: 700.165343\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.049218e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.505007e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.339032e+02\n Vprtstp: contraction number = 2.339032e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.510097e-04\n Vprtstp: contraction number = 3.006618e-01\n Vnewton: Using errtol_s: 210.512957\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.168221e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.636536e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.094002e+01\n Vprtstp: contraction number = 7.094002e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.579940e-05\n Vprtstp: contraction number = 3.032879e-01\n Vnewton: Using errtol_s: 63.846030\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.279714e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.716376e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.163184e+01\n Vprtstp: contraction number = 2.163184e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.396567e-05\n Vprtstp: contraction number = 3.049313e-01\n Vnewton: Using errtol_s: 19.468652\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.394163e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.820370e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.620444e+00\n Vprtstp: contraction number = 6.620444e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.274207e-06\n Vprtstp: contraction number = 3.060510e-01\n Vnewton: Using errtol_s: 5.958400\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.511153e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.914638e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.031637e+00\n Vprtstp: contraction number = 2.031637e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.311640e-06\n Vprtstp: contraction number = 3.068733e-01\n Vnewton: Using errtol_s: 1.828474\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.627182e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.986485e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.247427e-01\n Vprtstp: contraction number = 6.247427e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.033384e-07\n Vprtstp: contraction number = 3.075070e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.321878e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.345346e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.108323e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.134002e+01\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -26689,17 +26689,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.410814502422E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.872576445438E+04 kT\n Vpmg_energy:  dielEnergy = 9.355379703968E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.932700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.076900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n Vpbe_ctor2:  bulk ionic strength = 0.8\n Vpbe_ctor2:  xkappa = 0.29125\n@@ -26746,160 +26746,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00110224 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.161137\n+Vacc_SASA: Time elapsed: 0.112289\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.945920e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.167890e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.397800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.851000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.106680e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.817840e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.802585e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.162342e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1418623.682815\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.832375e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.183404e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.477376e+05\n Vprtstp: contraction number = 2.477376e+05\n Vnewton: Attempting damping, relres = 0.176231\n Vnewton: Attempting damping, relres = 0.577102\n Vnewton: Damping accepted, relres = 0.176231\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.762312e-01\n Vprtstp: contraction number = 1.762312e-01\n Vnewton: Using errtol_s: 250005.771686\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.972765e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.280842e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.052668e+04\n Vprtstp: contraction number = 5.052668e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.389791e-02\n Vprtstp: contraction number = 1.923491e-01\n Vnewton: Using errtol_s: 48088.378660\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.095588e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.373801e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.341451e+04\n Vprtstp: contraction number = 1.341451e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.561128e-03\n Vprtstp: contraction number = 2.525562e-01\n Vnewton: Using errtol_s: 12145.019085\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.221232e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.443660e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.971688e+03\n Vprtstp: contraction number = 3.971688e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.519877e-03\n Vprtstp: contraction number = 2.943394e-01\n Vnewton: Using errtol_s: 3574.757814\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.343808e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.577090e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.232605e+03\n Vprtstp: contraction number = 1.232605e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.819875e-04\n Vprtstp: contraction number = 3.103276e-01\n Vnewton: Using errtol_s: 1109.346049\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.468124e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.650328e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.914134e+02\n Vprtstp: contraction number = 3.914134e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.483197e-04\n Vprtstp: contraction number = 3.175495e-01\n Vnewton: Using errtol_s: 352.272271\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.594882e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.757395e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.261412e+02\n Vprtstp: contraction number = 1.261412e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.002626e-05\n Vprtstp: contraction number = 3.222710e-01\n Vnewton: Using errtol_s: 113.527152\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.716758e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.897031e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.109151e+01\n Vprtstp: contraction number = 4.109151e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.606919e-05\n Vprtstp: contraction number = 3.257579e-01\n Vnewton: Using errtol_s: 36.982365\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.833013e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.995178e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.349979e+01\n Vprtstp: contraction number = 1.349979e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 8.564509e-06\n Vprtstp: contraction number = 3.285300e-01\n Vnewton: Using errtol_s: 12.149816\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.948246e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.104273e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.465689e+00\n Vprtstp: contraction number = 4.465689e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.833112e-06\n Vprtstp: contraction number = 3.307968e-01\n Vnewton: Using errtol_s: 4.019120\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.057128e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.231882e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.485509e+00\n Vprtstp: contraction number = 1.485509e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 9.424331e-07\n Vprtstp: contraction number = 3.326494e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.350722e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.376723e+01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.188573e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.210201e+01\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -26909,19 +26909,19 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.400773657781E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.134315194179E+04 kT\n Vpmg_energy:  dielEnergy = 1.066408609760E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.051700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.045900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.237268e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.433392e+01\n"}, {"source1": "./usr/share/apbs/examples/solv/io.mc", "source2": "./usr/share/apbs/examples/solv/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:37:20 2025\n+# Creation Date and Time:  Sun Jan  7 09:46:17 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path methanol.pqr\n@@ -245,32 +245,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000439\n+Vacc_SASA: Time elapsed: 0.010845\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.848300e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.362000e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.030000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.299600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.108600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.718700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.455550e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.346460e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.930795e-01\n Vprtstp: contraction number = 2.930795e-01\n Vprtstp: iteration = 2\n@@ -299,30 +299,30 @@\n Vprtstp: contraction number = 3.064107e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.158998e-06\n Vprtstp: contraction number = 3.114698e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.836605e-07\n Vprtstp: contraction number = 3.166565e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.795278e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.916114e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.040517e+00\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.128872e+00\n Vpmg_setPart:  lower corner = (-7.69135, -8, -8.2417)\n Vpmg_setPart:  upper corner = (8.30865, 8, 7.7583)\n Vpmg_setPart:  actual minima = (-7.69135, -8, -8.2417)\n Vpmg_setPart:  actual maxima = (8.30865, 8, 7.7583)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.481476875907E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.100000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.000000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 2.83039\n Vpbe_ctor2:  solute dimensions = 3.775 x 3.775 x 4.8153\n Vpbe_ctor2:  solute charge = 5.55112e-17\n@@ -345,32 +345,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000385\n+Vacc_SASA: Time elapsed: 0.002573\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.104200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.741200e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.804000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.853000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.927100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.609700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.080510e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.290839e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.518468e-01\n Vprtstp: contraction number = 1.518468e-01\n Vprtstp: iteration = 2\n@@ -387,32 +387,32 @@\n Vprtstp: contraction number = 1.057725e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.782567e-06\n Vprtstp: contraction number = 1.074900e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.936135e-07\n Vprtstp: contraction number = 1.086150e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.151205e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.268640e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.467060e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.200510e-01\n Vpmg_setPart:  lower corner = (-7.69135, -8, -8.2417)\n Vpmg_setPart:  upper corner = (8.30865, 8, 7.7583)\n Vpmg_setPart:  actual minima = (-7.69135, -8, -8.2417)\n Vpmg_setPart:  actual maxima = (8.30865, 8, 7.7583)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.510541428496E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.500000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.700000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 2.54275\n Vpbe_ctor2:  solute dimensions = 3.775 x 3.775 x 4.733\n Vpbe_ctor2:  solute charge = -1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -433,32 +433,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000124\n+Vacc_SASA: Time elapsed: 0.000120\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.643900e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.553000e-03\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.049000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.564000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.900300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.002300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.362147e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.028016e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.228747e-01\n Vprtstp: contraction number = 1.228747e-01\n Vprtstp: iteration = 2\n@@ -484,32 +484,32 @@\n Vprtstp: contraction number = 3.196112e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.915327e-06\n Vprtstp: contraction number = 3.214910e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.179105e-07\n Vprtstp: contraction number = 3.226135e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.647319e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.760127e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 9.288000e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.986760e-01\n Vpmg_setPart:  lower corner = (-8, -8, -8.12785)\n Vpmg_setPart:  upper corner = (8, 8, 7.87215)\n Vpmg_setPart:  actual minima = (-8, -8, -8.12785)\n Vpmg_setPart:  actual maxima = (8, 8, 7.87215)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.191047608004E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.500000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.500000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 2.54275\n Vpbe_ctor2:  solute dimensions = 3.775 x 3.775 x 4.733\n Vpbe_ctor2:  solute charge = -1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -530,32 +530,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000119\n+Vacc_SASA: Time elapsed: 0.000121\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.271900e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.644000e-03\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.744000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.577000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.496600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.581400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.132125e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.048280e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.134958e-01\n Vprtstp: contraction number = 1.134958e-01\n Vprtstp: iteration = 2\n@@ -572,42 +572,42 @@\n Vprtstp: contraction number = 1.069805e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.498256e-06\n Vprtstp: contraction number = 1.078455e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.625625e-07\n Vprtstp: contraction number = 1.085012e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.147488e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.256403e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.290070e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.048510e-01\n Vpmg_setPart:  lower corner = (-8, -8, -8.12785)\n Vpmg_setPart:  upper corner = (8, 8, 7.87215)\n Vpmg_setPart:  actual minima = (-8, -8, -8.12785)\n Vpmg_setPart:  actual maxima = (8, 8, 7.87215)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.504084363930E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.400000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.100000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 6.280523e+00\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.695806e+00\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Fri Feb  7 13:37:26 2025\n+# Creation Date and Time:  Sun Jan  7 09:46:18 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path methanol.pqr\n@@ -848,32 +848,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001304\n+Vacc_SASA: Time elapsed: 0.006934\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.788300e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.715200e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.258000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.494000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.000100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.225200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.737630e-01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.708320e-01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.392714e-01\n Vprtstp: contraction number = 2.392714e-01\n Vprtstp: iteration = 2\n@@ -893,32 +893,32 @@\n Vprtstp: contraction number = 1.556589e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.217054e-06\n Vprtstp: contraction number = 1.639311e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.821154e-07\n Vprtstp: contraction number = 1.723528e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.306816e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.426935e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.649210e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.457370e-01\n Vpmg_setPart:  lower corner = (-7.69135, -8, -8.2417)\n Vpmg_setPart:  upper corner = (8.30865, 8, 7.7583)\n Vpmg_setPart:  actual minima = (-7.69135, -8, -8.2417)\n Vpmg_setPart:  actual maxima = (8.30865, 8, 7.7583)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.481634746029E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.100000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.800000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 2.83039\n Vpbe_ctor2:  solute dimensions = 3.775 x 3.775 x 4.8153\n Vpbe_ctor2:  solute charge = 5.55112e-17\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -939,32 +939,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000185\n+Vacc_SASA: Time elapsed: 0.000184\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.188200e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.847700e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.729000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.894000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.882900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 6.035500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.638652e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.068254e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.514442e-01\n Vprtstp: contraction number = 1.514442e-01\n Vprtstp: iteration = 2\n@@ -981,32 +981,32 @@\n Vprtstp: contraction number = 1.045560e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.694780e-06\n Vprtstp: contraction number = 1.061179e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.817099e-07\n Vprtstp: contraction number = 1.072174e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.138935e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.253766e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.692820e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.450280e-01\n Vpmg_setPart:  lower corner = (-7.69135, -8, -8.2417)\n Vpmg_setPart:  upper corner = (8.30865, 8, 7.7583)\n Vpmg_setPart:  actual minima = (-7.69135, -8, -8.2417)\n Vpmg_setPart:  actual maxima = (8.30865, 8, 7.7583)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.511763544580E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.200000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.400000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 0.000000e+00\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 2.54275\n Vpbe_ctor2:  solute dimensions = 3.775 x 3.775 x 4.733\n Vpbe_ctor2:  solute charge = -1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1027,32 +1027,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000121\n+Vacc_SASA: Time elapsed: 0.000122\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.928900e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.631600e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.976000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.994000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.664100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.888000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.928770e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.871983e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.159916e-01\n Vprtstp: contraction number = 1.159916e-01\n Vprtstp: iteration = 2\n@@ -1069,30 +1069,30 @@\n Vprtstp: contraction number = 1.378576e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 3.539643e-06\n Vprtstp: contraction number = 1.515814e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.760895e-07\n Vprtstp: contraction number = 1.627536e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.153957e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.264677e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.650670e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.347820e-01\n Vpmg_setPart:  lower corner = (-8, -8, -8.12785)\n Vpmg_setPart:  upper corner = (8, 8, 7.87215)\n Vpmg_setPart:  actual minima = (-8, -8, -8.12785)\n Vpmg_setPart:  actual maxima = (8, 8, 7.87215)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.192183682119E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.600000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.300000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 2.54275\n Vpbe_ctor2:  solute dimensions = 3.775 x 3.775 x 4.733\n Vpbe_ctor2:  solute charge = -1\n@@ -1115,32 +1115,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000121\n+Vacc_SASA: Time elapsed: 0.000119\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.746100e-02\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.444400e-02\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.335000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.920000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 7.823300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 5.925500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.233718e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.667058e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.128724e-01\n Vprtstp: contraction number = 1.128724e-01\n Vprtstp: iteration = 2\n@@ -1157,32 +1157,32 @@\n Vprtstp: contraction number = 1.067766e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.477665e-06\n Vprtstp: contraction number = 1.075719e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.598211e-07\n Vprtstp: contraction number = 1.081578e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.140035e+00\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.252608e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.653220e-01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.309710e-01\n Vpmg_setPart:  lower corner = (-8, -8, -8.12785)\n Vpmg_setPart:  upper corner = (8, 8, 7.87215)\n Vpmg_setPart:  actual minima = (-8, -8, -8.12785)\n Vpmg_setPart:  actual maxima = (8, 8, 7.87215)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.505883286802E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.500000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.200000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.374210e+00\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.352583e+00\n"}]}]}]}]}