I: pbuilder: network access will be disabled during build
I: Current time: Tue Jan 28 11:37:59 -12 2025
I: pbuilder-time-stamp: 1738107479
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [pdb2pqr_3.6.1+dfsg-1.dsc]
I: copying [./pdb2pqr_3.6.1+dfsg.orig.tar.xz]
I: copying [./pdb2pqr_3.6.1+dfsg-1.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: unsupported subcommand
dpkg-source: info: extracting pdb2pqr in pdb2pqr-3.6.1+dfsg
dpkg-source: info: unpacking pdb2pqr_3.6.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking pdb2pqr_3.6.1+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying skip-network-tests.patch
dpkg-source: info: applying unversioned_docutils.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/39115/tmp/hooks/D02_print_environment starting
I: set
  BUILDDIR='/build/reproducible-path'
  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
  BUILDUSERNAME='pbuilder1'
  BUILD_ARCH='i386'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 '
  DISTRIBUTION='trixie'
  HOME='/root'
  HOST_ARCH='i386'
  IFS=' 	
  '
  INVOCATION_ID='c688e272ae844878bf1538564f975498'
  LANG='C'
  LANGUAGE='en_US:en'
  LC_ALL='C'
  LD_LIBRARY_PATH='/usr/lib/libeatmydata'
  LD_PRELOAD='libeatmydata.so'
  MAIL='/var/mail/root'
  OPTIND='1'
  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
  PBCURRENTCOMMANDLINEOPERATION='build'
  PBUILDER_OPERATION='build'
  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
  PBUILDER_SYSCONFDIR='/etc'
  PPID='39115'
  PS1='# '
  PS2='> '
  PS4='+ '
  PWD='/'
  SHELL='/bin/bash'
  SHLVL='2'
  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.vygaQaMG/pbuilderrc_8hcC --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.vygaQaMG/b1 --logfile b1/build.log pdb2pqr_3.6.1+dfsg-1.dsc'
  SUDO_GID='112'
  SUDO_UID='107'
  SUDO_USER='jenkins'
  TERM='unknown'
  TZ='/usr/share/zoneinfo/Etc/GMT+12'
  USER='root'
  _='/usr/bin/systemd-run'
  http_proxy='http://46.16.76.132:3128'
I: uname -a
  Linux ionos12-i386 6.1.0-30-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.124-1 (2025-01-12) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/39115/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), dh-python, dh-sequence-sphinxdoc, help2man, python3-dev, python3-numpy, python3-pdbx, python3-pandas, python3-propka, python3-pytest, python3-setuptools, python3-sphinx-rtd-theme, python3-testfixtures
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19841 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on dh-python; however:
  Package dh-python is not installed.
 pbuilder-satisfydepends-dummy depends on dh-sequence-sphinxdoc; however:
  Package dh-sequence-sphinxdoc is not installed.
 pbuilder-satisfydepends-dummy depends on help2man; however:
  Package help2man is not installed.
 pbuilder-satisfydepends-dummy depends on python3-dev; however:
  Package python3-dev is not installed.
 pbuilder-satisfydepends-dummy depends on python3-numpy; however:
  Package python3-numpy is not installed.
 pbuilder-satisfydepends-dummy depends on python3-pdbx; however:
  Package python3-pdbx is not installed.
 pbuilder-satisfydepends-dummy depends on python3-pandas; however:
  Package python3-pandas is not installed.
 pbuilder-satisfydepends-dummy depends on python3-propka; however:
  Package python3-propka is not installed.
 pbuilder-satisfydepends-dummy depends on python3-pytest; however:
  Package python3-pytest is not installed.
 pbuilder-satisfydepends-dummy depends on python3-setuptools; however:
  Package python3-setuptools is not installed.
 pbuilder-satisfydepends-dummy depends on python3-sphinx-rtd-theme; however:
  Package python3-sphinx-rtd-theme is not installed.
 pbuilder-satisfydepends-dummy depends on python3-testfixtures; however:
  Package python3-testfixtures is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-font-awesome{a} fonts-lato{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} liblapack3{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-autocommand{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-dateutil{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pdbx{a} python3-pkg-resources{a} python3-pluggy{a} python3-propka{a} python3-pygments{a} python3-pytest{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-rtd-theme{a} python3-sphinxcontrib.jquery{a} python3-testfixtures{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-urllib3{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} sphinx-rtd-theme-common{a} tzdata{a} xml-core{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  curl javascript-common libarchive-cpio-perl libjson-xs-perl libltdl-dev libmail-sendmail-perl libpaper-utils lynx python3-bottleneck python3-bs4 python3-html5lib python3-lxml python3-matplotlib python3-numexpr python3-odf python3-openpyxl python3-pil python3-scipy python3-tables wget 
0 packages upgraded, 113 newly installed, 0 to remove and 0 not upgraded.
Need to get 71.9 MB of archives. After unpacking 333 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 fonts-lato all 2.015-1 [2780 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 liblocale-gettext-perl i386 1.07-7+b1 [15.4 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 libpython3.13-minimal i386 3.13.1-3 [858 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 python3.13-minimal i386 3.13.1-3 [2264 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 python3-minimal i386 3.13.1-2 [27.0 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 media-types all 10.1.0 [26.9 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 netbase all 6.4 [12.8 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 tzdata all 2024b-6 [257 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 libffi8 i386 3.4.6-1 [21.2 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 libpython3.13-stdlib i386 3.13.1-3 [1980 kB]
Get: 14 http://deb.debian.org/debian trixie/main i386 python3.13 i386 3.13.1-3 [740 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 libpython3-stdlib i386 3.13.1-2 [9952 B]
Get: 16 http://deb.debian.org/debian trixie/main i386 python3 i386 3.13.1-2 [28.0 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 sgml-base all 1.31 [15.4 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 openssl i386 3.4.0-2 [1427 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 ca-certificates all 20241223 [164 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 22 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-1 [96.1 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 29 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-5 [301 kB]
Get: 31 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 32 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 33 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 34 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 35 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.23 [90.6 kB]
Get: 36 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-2 [539 kB]
Get: 37 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 38 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 39 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB]
Get: 40 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-1 [8584 B]
Get: 41 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 42 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 43 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 44 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 45 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 46 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 47 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 48 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 49 http://deb.debian.org/debian trixie/main i386 debhelper all 13.23 [919 kB]
Get: 50 http://deb.debian.org/debian trixie/main i386 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 51 http://deb.debian.org/debian trixie/main i386 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 52 http://deb.debian.org/debian trixie/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 53 http://deb.debian.org/debian trixie/main i386 python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 54 http://deb.debian.org/debian trixie/main i386 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 55 http://deb.debian.org/debian trixie/main i386 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 56 http://deb.debian.org/debian trixie/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 57 http://deb.debian.org/debian trixie/main i386 python3-pkg-resources all 75.6.0-1 [222 kB]
Get: 58 http://deb.debian.org/debian trixie/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 59 http://deb.debian.org/debian trixie/main i386 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 60 http://deb.debian.org/debian trixie/main i386 python3-setuptools all 75.6.0-1 [720 kB]
Get: 61 http://deb.debian.org/debian trixie/main i386 dh-python all 6.20250108 [113 kB]
Get: 62 http://deb.debian.org/debian trixie/main i386 xml-core all 0.19 [20.1 kB]
Get: 63 http://deb.debian.org/debian trixie/main i386 docutils-common all 0.21.2+dfsg-2 [128 kB]
Get: 64 http://deb.debian.org/debian trixie/main i386 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB]
Get: 65 http://deb.debian.org/debian trixie/main i386 help2man i386 1.49.3 [198 kB]
Get: 66 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-4 [143 kB]
Get: 67 http://deb.debian.org/debian trixie/main i386 libexpat1-dev i386 2.6.4-1 [165 kB]
Get: 68 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14.2.0-12 [735 kB]
Get: 69 http://deb.debian.org/debian trixie/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 70 http://deb.debian.org/debian trixie/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 71 http://deb.debian.org/debian trixie/main i386 libjs-sphinxdoc all 8.1.3-4 [30.4 kB]
Get: 72 http://deb.debian.org/debian trixie/main i386 libjson-perl all 4.10000-1 [87.5 kB]
Get: 73 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-4 [2194 kB]
Get: 74 http://deb.debian.org/debian trixie/main i386 libpython3.13 i386 3.13.1-3 [2199 kB]
Get: 75 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Get: 76 http://deb.debian.org/debian trixie/main i386 libpython3.13-dev i386 3.13.1-3 [5191 kB]
Get: 77 http://deb.debian.org/debian trixie/main i386 libpython3-dev i386 3.13.1-2 [10.2 kB]
Get: 78 http://deb.debian.org/debian trixie/main i386 python-babel-localedata all 2.16.0-1 [5696 kB]
Get: 79 http://deb.debian.org/debian trixie/main i386 python3-alabaster all 0.7.16-0.1 [27.9 kB]
Get: 80 http://deb.debian.org/debian trixie/main i386 python3-babel all 2.16.0-1 [114 kB]
Get: 81 http://deb.debian.org/debian trixie/main i386 python3-certifi all 2024.12.14+ds-1 [9624 B]
Get: 82 http://deb.debian.org/debian trixie/main i386 python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get: 83 http://deb.debian.org/debian trixie/main i386 python3-charset-normalizer i386 3.4.0-1+b1 [139 kB]
Get: 84 http://deb.debian.org/debian trixie/main i386 python3-dateutil all 2.9.0-3 [79.3 kB]
Get: 85 http://deb.debian.org/debian trixie/main i386 python3-defusedxml all 0.7.1-3 [43.4 kB]
Get: 86 http://deb.debian.org/debian trixie/main i386 python3.13-dev i386 3.13.1-3 [505 kB]
Get: 87 http://deb.debian.org/debian trixie/main i386 python3-dev i386 3.13.1-2 [26.1 kB]
Get: 88 http://deb.debian.org/debian trixie/main i386 python3-roman all 4.2-1 [10.4 kB]
Get: 89 http://deb.debian.org/debian trixie/main i386 python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get: 90 http://deb.debian.org/debian trixie/main i386 python3-idna all 3.8-2 [41.6 kB]
Get: 91 http://deb.debian.org/debian trixie/main i386 python3-imagesize all 1.4.1-1 [6688 B]
Get: 92 http://deb.debian.org/debian trixie/main i386 python3-iniconfig all 1.1.1-2 [6396 B]
Get: 93 http://deb.debian.org/debian trixie/main i386 python3-markupsafe i386 2.1.5-1+b2 [13.9 kB]
Get: 94 http://deb.debian.org/debian trixie/main i386 python3-jinja2 all 3.1.5-1 [107 kB]
Get: 95 http://deb.debian.org/debian trixie/main i386 python3-numpy i386 1:1.26.4+ds-13 [4751 kB]
Get: 96 http://deb.debian.org/debian trixie/main i386 python3-packaging all 24.2-1 [55.3 kB]
Get: 97 http://deb.debian.org/debian trixie/main i386 python3-tz all 2024.2-1 [31.0 kB]
Get: 98 http://deb.debian.org/debian trixie/main i386 python3-pandas-lib i386 2.2.3+dfsg-5+b1 [6860 kB]
Get: 99 http://deb.debian.org/debian trixie/main i386 python3-pandas all 2.2.3+dfsg-5 [3096 kB]
Get: 100 http://deb.debian.org/debian trixie/main i386 python3-pdbx all 2.0.1-2 [17.4 kB]
Get: 101 http://deb.debian.org/debian trixie/main i386 python3-pluggy all 1.5.0-1 [26.9 kB]
Get: 102 http://deb.debian.org/debian trixie/main i386 python3-propka all 3.5.1-2 [68.2 kB]
Get: 103 http://deb.debian.org/debian trixie/main i386 python3-pygments all 2.18.0+dfsg-2 [836 kB]
Get: 104 http://deb.debian.org/debian trixie/main i386 python3-pytest all 8.3.4-1 [250 kB]
Get: 105 http://deb.debian.org/debian trixie/main i386 python3-urllib3 all 2.3.0-1 [114 kB]
Get: 106 http://deb.debian.org/debian trixie/main i386 python3-requests all 2.32.3+dfsg-1 [71.9 kB]
Get: 107 http://deb.debian.org/debian trixie/main i386 python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get: 108 http://deb.debian.org/debian trixie/main i386 sphinx-common all 8.1.3-4 [616 kB]
Get: 109 http://deb.debian.org/debian trixie/main i386 python3-sphinx all 8.1.3-4 [468 kB]
Get: 110 http://deb.debian.org/debian trixie/main i386 sphinx-rtd-theme-common all 3.0.2+dfsg-1 [1023 kB]
Get: 111 http://deb.debian.org/debian trixie/main i386 python3-sphinxcontrib.jquery all 4.1-5 [7348 B]
Get: 112 http://deb.debian.org/debian trixie/main i386 python3-sphinx-rtd-theme all 3.0.2+dfsg-1 [29.5 kB]
Get: 113 http://deb.debian.org/debian trixie/main i386 python3-testfixtures all 8.3.0-2 [87.2 kB]
Fetched 71.9 MB in 1s (73.3 MB/s)
Preconfiguring packages ...
Selecting previously unselected package fonts-lato.
(Reading database ... 
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Current default time zone: 'Etc/UTC'
Local time is now:      Tue Jan 28 23:38:35 UTC 2025.
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Run 'dpkg-reconfigure tzdata' if you wish to change it.

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done.
Reading package lists...
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Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/pdb2pqr-3.6.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../pdb2pqr_3.6.1+dfsg-1_source.changes
dpkg-buildpackage: info: source package pdb2pqr
dpkg-buildpackage: info: source version 3.6.1+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
 debian/rules clean
dh clean --buildsystem pybuild --with python3
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/pdb2pqr-3.6.1+dfsg'
dh_auto_clean
I: pybuild base:311: python3.13 setup.py clean 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
running clean
removing '/build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build' (and everything under it)
'build/bdist.linux-i686' does not exist -- can't clean it
'build/scripts-3.13' does not exist -- can't clean it
rm -rf pdb2pqr.egg-info
make[1]: Leaving directory '/build/reproducible-path/pdb2pqr-3.6.1+dfsg'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules binary
dh binary --buildsystem pybuild --with python3
   dh_update_autotools_config -O--buildsystem=pybuild
   dh_autoreconf -O--buildsystem=pybuild
   dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:311: python3.13 setup.py config 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
running config
   debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/pdb2pqr-3.6.1+dfsg'
dh_auto_build
I: pybuild base:311: /usr/bin/python3 setup.py build 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
running build
running build_py
creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/io.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/aa.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/na.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/psize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/cells.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/config.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/definitions.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/pdb.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/main.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/_version.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/residue.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/forcefield.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/run.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/__main__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/cif.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/utilities.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/quatfit.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/debump.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/biomolecule.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/inputgen.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr
creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/hydrogens
copying pdb2pqr/hydrogens/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/hydrogens
copying pdb2pqr/hydrogens/optimize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/hydrogens
copying pdb2pqr/hydrogens/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/hydrogens
creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/ligand
copying pdb2pqr/ligand/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/ligand
copying pdb2pqr/ligand/mol2.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/ligand
copying pdb2pqr/ligand/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/ligand
copying pdb2pqr/ligand/peoe.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/ligand
creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/AA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/HYDROGENS.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/TOPOLOGY.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/NA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/PATCHES.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/PARSE.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/SWANSON.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/AMBER.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/CHARMM.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/PEOEPB.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/TYL06.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/CHARMM.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/PEOEPB.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/SWANSON.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/AMBER.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/TYL06.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/PARSE.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat
PYTHONPATH=. python3 -m sphinx -N -bhtml docs/source build/html
Running Sphinx v8.1.3
loading translations [en]... done
WARNING: html_static_path entry '_static' does not exist
loading intersphinx inventory 'python' from https://docs.python.org/3/objects.inv ...
WARNING: failed to reach any of the inventories with the following issues:
intersphinx inventory 'https://docs.python.org/3/objects.inv' not fetchable due to <class 'requests.exceptions.ProxyError'>: HTTPSConnectionPool(host='docs.python.org', port=443): Max retries exceeded with url: /3/objects.inv (Caused by ProxyError('Unable to connect to proxy', NewConnectionError('<urllib3.connection.HTTPSConnection object at 0xf4388030>: Failed to establish a new connection: [Errno 111] Connection refused')))
[autosummary] generating autosummary for: api/aa.rst, api/biomolecule.rst, api/cells.rst, api/cif.rst, api/config.rst, api/debump.rst, api/definitions.rst, api/forcefield.rst, api/hydrogens.rst, api/index.rst, ..., formats/xml-names.rst, getting.rst, help.rst, index.rst, releases.rst, supporting.rst, using/algorithms.rst, using/examples.rst, using/index.rst, using/other-software.rst
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 39 source files that are out of date
updating environment: [new config] 39 added, 0 changed, 0 removed
reading sources... [  3%] api/aa
reading sources... [  5%] api/biomolecule
reading sources... [  8%] api/cells
reading sources... [ 10%] api/cif
reading sources... [ 13%] api/config
reading sources... [ 15%] api/debump
reading sources... [ 18%] api/definitions
reading sources... [ 21%] api/forcefield
reading sources... [ 23%] api/hydrogens
reading sources... [ 26%] api/index
reading sources... [ 28%] api/inputgen
reading sources... [ 31%] api/io
reading sources... [ 33%] api/ligand
reading sources... [ 36%] api/main
reading sources... [ 38%] api/na
reading sources... [ 41%] api/pdb
reading sources... [ 44%] api/psize
reading sources... [ 46%] api/quatfit
reading sources... [ 49%] api/residue
reading sources... [ 51%] api/run
reading sources... [ 54%] api/structures
reading sources... [ 56%] api/topology
reading sources... [ 59%] api/utilities
reading sources... [ 62%] extending
reading sources... [ 64%] formats/dat
reading sources... [ 67%] formats/index
reading sources... [ 69%] formats/mol2
reading sources... [ 72%] formats/pdb
reading sources... [ 74%] formats/pqr
reading sources... [ 77%] formats/xml-names
reading sources... [ 79%] getting
reading sources... [ 82%] help
reading sources... [ 85%] index
reading sources... [ 87%] releases
reading sources... [ 90%] supporting
reading sources... [ 92%] using/algorithms
reading sources... [ 95%] using/examples
reading sources... [ 97%] using/index
reading sources... [100%] using/other-software

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
copying assets... 
copying static files... 
Writing evaluated template result to /build/reproducible-path/pdb2pqr-3.6.1+dfsg/build/html/_static/language_data.js
Writing evaluated template result to /build/reproducible-path/pdb2pqr-3.6.1+dfsg/build/html/_static/documentation_options.js
Writing evaluated template result to /build/reproducible-path/pdb2pqr-3.6.1+dfsg/build/html/_static/basic.css
Writing evaluated template result to /build/reproducible-path/pdb2pqr-3.6.1+dfsg/build/html/_static/js/versions.js
copying static files: done
copying extra files... 
copying extra files: done
copying assets: done
writing output... [  3%] api/aa
writing output... [  5%] api/biomolecule
writing output... [  8%] api/cells
writing output... [ 10%] api/cif
writing output... [ 13%] api/config
writing output... [ 15%] api/debump
writing output... [ 18%] api/definitions
writing output... [ 21%] api/forcefield
writing output... [ 23%] api/hydrogens
writing output... [ 26%] api/index
writing output... [ 28%] api/inputgen
writing output... [ 31%] api/io
writing output... [ 33%] api/ligand
writing output... [ 36%] api/main
writing output... [ 38%] api/na
writing output... [ 41%] api/pdb
writing output... [ 44%] api/psize
writing output... [ 46%] api/quatfit
writing output... [ 49%] api/residue
writing output... [ 51%] api/run
writing output... [ 54%] api/structures
writing output... [ 56%] api/topology
writing output... [ 59%] api/utilities
writing output... [ 62%] extending
writing output... [ 64%] formats/dat
writing output... [ 67%] formats/index
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make[1]: Leaving directory '/build/reproducible-path/pdb2pqr-3.6.1+dfsg'
   dh_auto_test -O--buildsystem=pybuild
I: pybuild base:311: cd /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build; python3.13 -m pytest tests
============================= test session starts ==============================
platform linux -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0
rootdir: /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build
configfile: pytest.ini
plugins: typeguard-4.4.1

----------------------------- live log collection ------------------------------
WARNING  py.warnings:warnings.py:110 /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/tests/core_test.py:81: PytestUnknownMarkWarning: Unknown pytest.mark.long_test - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html
  @pytest.mark.long_test

ERROR    regression_test:regression_test.py:173 Need to reinstate the --apbs-input test with a temporary directory as path
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tests/core_test.py::test_long_pdb[4GS3] SKIPPED (not running tests r...) [ 64%]
tests/core_test.py::test_long_pdb[2VWR] SKIPPED (not running tests r...) [ 65%]
tests/core_test.py::test_long_pdb[2ESK] SKIPPED (not running tests r...) [ 65%]
tests/core_test.py::test_long_pdb[2EBB] SKIPPED (not running tests r...) [ 65%]
tests/core_test.py::test_long_pdb[4ZQA] SKIPPED (not running tests r...) [ 66%]
tests/core_test.py::test_broken_backbone[4MGP] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_broken_backbone_4MGP_0/4MGP.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP
XFAIL                                                                    [ 66%]
tests/core_test.py::test_broken_backbone[1EJG] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_broken_backbone_1EJG_0/1EJG.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG
XFAIL                                                                    [ 66%]
tests/core_test.py::test_broken_backbone[3U7T] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_broken_backbone_3U7T_0/3U7T.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T
XFAIL                                                                    [ 67%]
tests/core_test.py::test_broken_backbone[2V75] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_broken_backbone_2V75_0/2V75.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75
XFAIL                                                                    [ 67%]
tests/core_test.py::test_protonated_terminals[C-terminal HID] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/cterm_hid.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber).
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output.
INFO     common:common.py:198 0 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 67%]
tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/5vav_cyclic_peptide.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
INFO     PDB2PQR3.6.1:main.py:459 This biomolecule is clean.  No repair needed.
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber).
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output.
INFO     common:common.py:198 0 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 68%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 68%]
tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED     [ 68%]
tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED           [ 68%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 69%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 69%]
tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 69%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 70%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 70%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 70%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 71%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 71%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 71%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 72%]
tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 72%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 72%]
tests/io_test.py::test_read_pqr[tests/data/1HPX_with-ph=7.00_titration_state_method=propka_ligand=LIG_1HPX_ff=AMBER.pqr] PASSED [ 73%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 73%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED     [ 73%]
tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 74%]
tests/io_test.py::test_read_qcd PASSED                                   [ 74%]
tests/io_test.py::test_dx2cube 
-------------------------------- live log call ---------------------------------
INFO     io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr...
INFO     io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx...
INFO     io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-pbuilder1/pytest-0/test_dx2cube0/test.cube...
INFO     io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-pbuilder1/pytest-0/test_dx2cube0/test.cube...
INFO     io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube...
INFO     io_test:io_test.py:68 No differences found in output
PASSED                                                                   [ 74%]
tests/ligand_test.py::test_peoe_charges 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
PASSED                                                                   [ 75%]
tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 ->  0.00
PASSED                                                                   [ 75%]
tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 -> -0.00
PASSED                                                                   [ 75%]
tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
INFO     ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00
PASSED                                                                   [ 75%]
tests/ligand_test.py::test_assign_parameters[acetate.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00
PASSED                                                                   [ 76%]
tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 -> -0.00
PASSED                                                                   [ 76%]
tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type.
WARNING  pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type.
INFO     ligand_test:ligand_test.py:73 Total charge:  1.00 ->  1.00
PASSED                                                                   [ 76%]
tests/ligand_test.py::test_assign_parameters[adp.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order.
INFO     ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00
PASSED                                                                   [ 77%]
tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 -> -0.00
PASSED                                                                   [ 77%]
tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 ->  0.00
PASSED                                                                   [ 77%]
tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 ->  0.00
PASSED                                                                   [ 78%]
tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00
PASSED                                                                   [ 78%]
tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 ->  0.00
PASSED                                                                   [ 78%]
tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 -> -0.00
PASSED                                                                   [ 79%]
tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 
-------------------------------- live log call ---------------------------------
INFO     ligand_test:ligand_test.py:73 Total charge:  0.00 ->  0.00
PASSED                                                                   [ 79%]
tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type.
WARNING  pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type.
INFO     ligand_test:ligand_test.py:73 Total charge:  1.00 ->  1.00
PASSED                                                                   [ 79%]
tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
PASSED                                                                   [ 80%]
tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
PASSED                                                                   [ 80%]
tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order.
PASSED                                                                   [ 80%]
tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED            [ 81%]
tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED       [ 81%]
tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type.
PASSED                                                                   [ 81%]
tests/ligand_test.py::test_formal_charge[adp.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order.
WARNING  pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order.
PASSED                                                                   [ 81%]
tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED         [ 82%]
tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED        [ 82%]
tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED            [ 82%]
tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED         [ 83%]
tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED           [ 83%]
tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED        [ 83%]
tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED            [ 84%]
tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 
-------------------------------- live log call ---------------------------------
WARNING  pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type.
PASSED                                                                   [ 84%]
tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED           [ 84%]
tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED                 [ 85%]
tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED                 [ 85%]
tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED     [ 85%]
tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED                [ 86%]
tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED             [ 86%]
tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED                [ 86%]
tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED                [ 87%]
tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED                [ 87%]
tests/ligand_test.py::test_rings[acetate.mol2] PASSED                    [ 87%]
tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED               [ 87%]
tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED              [ 88%]
tests/ligand_test.py::test_rings[adp.mol2] PASSED                        [ 88%]
tests/ligand_test.py::test_rings[anthracene.mol2] PASSED                 [ 88%]
tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED                [ 89%]
tests/ligand_test.py::test_rings[ethanol.mol2] PASSED                    [ 89%]
tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED                 [ 89%]
tests/ligand_test.py::test_rings[glycerol.mol2] PASSED                   [ 90%]
tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED                [ 90%]
tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED                    [ 90%]
tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED        [ 91%]
tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%]
tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%]
tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%]
tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%]
tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%]
tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%]
tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%]
tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%]
tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%]
tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%]
tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%]
tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%]
tests/regression_test.py::test_basic[1AFS basic local] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_basic_1AFS_basic_local_0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES.  Parsing as new residue.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333
WARNING  pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333
WARNING  pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 95%]
tests/regression_test.py::test_forcefields[1AFS whitespace AMBER] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP.  Parsing as new residue.
WARNING  pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES.  Parsing as new residue.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 95%]
tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa1/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
WARNING  pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 5 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 95%]
tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa2/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 96%]
tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa3/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 96%]
tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa4/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 96%]
tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_forcefields_1AFS_whitespa5/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 97%]
tests/regression_test.py::test_other_options[1AFS whitespace clean] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_other_options_1AFS_whites0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps.
INFO     common:common.py:198 0 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 97%]
tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_other_options_1A1P_assign0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output.
INFO     common:common.py:198 0 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 97%]
tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_other_options_1A1P_nodebu0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
INFO     PDB2PQR3.6.1:main.py:459 This biomolecule is clean.  No repair needed.
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization...
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output.
INFO     common:common.py:198 0 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 98%]
tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_other_options_1AFS_chain_0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 98%]
tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_other_options_1AFS_neutra0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 98%]
tests/regression_test.py::test_other_options[1AFS drop-water AMBER] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_other_options_1AFS_drop_w0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:768 Dropping water from structure.
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 99%]
tests/regression_test.py::test_other_options[1AFS userff usernames whitespace] 
-------------------------------- live log call ---------------------------------
INFO     pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-pbuilder1/pytest-0/test_other_options_1AFS_userff0/output.log
INFO     PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software.
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Jurrus E, et al.  Improvements to the APBS biomolecular solvation software suite.  Protein Sci 27 112-128 (2018).
INFO     PDB2PQR3.6.1:main.py:242 Please cite:  Dolinsky TJ, et al.  PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
INFO     PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments.
INFO     PDB2PQR3.6.1:main.py:763 Loading topology files.
INFO     PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb
INFO     PDB2PQR3.6.1:main.py:770 Setting up molecule.
INFO     PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms.
INFO     PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains.
INFO     PDB2PQR3.6.1:main.py:604 Loading forcefield.
INFO     PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule.
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319
WARNING  pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288
INFO     pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928
INFO     PDB2PQR3.6.1:main.py:623 Updating disulfide bridges.
INFO     PDB2PQR3.6.1:main.py:626 Debumping biomolecule.
INFO     PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule.
INFO     PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again).
INFO     PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds
INFO     PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states.
INFO     PDB2PQR3.6.1:main.py:713 Regenerating headers.
INFO     PDB2PQR3.6.1:main.py:738 Regenerating PDB lines.
WARNING  PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output.
WARNING  PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output.
WARNING  common:common.py:186 6 atoms have position differences > 0
INFO     common:common.py:198 0 atoms have position differences > 0.01
INFO     common:common.py:198 0 atoms have charge differences > 0
INFO     common:common.py:198 0 atoms have charge differences > 0.01
INFO     common:common.py:198 0 atoms have radius differences > 0
INFO     common:common.py:198 0 atoms have radius differences > 0.01
PASSED                                                                   [ 99%]
tests/test_version.py::test_version_exists PASSED                        [ 99%]
tests/test_version.py::test_version PASSED                               [100%]

============ 92 passed, 220 skipped, 4 xfailed in 160.99s (0:02:40) ============
   create-stamp debian/debhelper-build-stamp
   dh_testroot -O--buildsystem=pybuild
   dh_prep -O--buildsystem=pybuild
   dh_installdirs -O--buildsystem=pybuild
   dh_auto_install -O--buildsystem=pybuild
I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
running build
running build_py
running install_lib
creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages
creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/.pytest_cache
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/.pytest_cache/CACHEDIR.TAG -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/.pytest_cache
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/.pytest_cache/README.md -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/.pytest_cache
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/.pytest_cache/.gitignore -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/.pytest_cache
creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/.pytest_cache/v
creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/.pytest_cache/v/cache
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/.pytest_cache/v/cache/stepwise -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/.pytest_cache/v/cache
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/.pytest_cache/v/cache/nodeids -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/.pytest_cache/v/cache
creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/io.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/aa.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/na.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/psize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/cells.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/config.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/definitions.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/pdb.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/main.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/_version.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/hydrogens
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/hydrogens/structures.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/hydrogens
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/hydrogens/optimize.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/hydrogens
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/hydrogens/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/hydrogens
creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/hydrogens/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/hydrogens/__pycache__/optimize.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/hydrogens/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/hydrogens/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/hydrogens/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/hydrogens/__pycache__/structures.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/hydrogens/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/residue.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/forcefield.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/run.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__main__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/cif.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/utilities.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/quatfit.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/PARSE.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/CHARMM.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/PEOEPB.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/SWANSON.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/AA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/SWANSON.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/AMBER.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/AMBER.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/CHARMM.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/HYDROGENS.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/TOPOLOGY.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/NA.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/TYL06.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/PEOEPB.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/TYL06.DAT -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/PARSE.names -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/dat/PATCHES.xml -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/dat
creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/pdb.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/io.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/biomolecule.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/main.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/quatfit.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/cells.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/forcefield.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/aa.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/cif.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/na.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/definitions.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/utilities.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/_version.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/residue.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/config.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/psize.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/inputgen.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/debump.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/__pycache__/structures.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/debump.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/biomolecule.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/inputgen.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr
creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/ligand
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/ligand/topology.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/ligand
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/ligand/mol2.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/ligand
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/ligand/__init__.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/ligand
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/ligand/peoe.py -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/ligand
creating /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/ligand/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/ligand/__pycache__/peoe.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/ligand/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/ligand/__pycache__/mol2.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/ligand/__pycache__
copying /build/reproducible-path/pdb2pqr-3.6.1+dfsg/.pybuild/cpython3_3.13/build/pdb2pqr/ligand/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/ligand/__pycache__
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/io.py to io.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/topology.py to topology.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/aa.py to aa.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/na.py to na.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/psize.py to psize.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/structures.py to structures.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/cells.py to cells.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/config.py to config.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/definitions.py to definitions.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/pdb.py to pdb.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/main.py to main.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/_version.py to _version.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/hydrogens/structures.py to structures.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/hydrogens/optimize.py to optimize.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/hydrogens/__init__.py to __init__.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/residue.py to residue.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/forcefield.py to forcefield.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/run.py to run.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__init__.py to __init__.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/__main__.py to __main__.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/cif.py to cif.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/utilities.py to utilities.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/quatfit.py to quatfit.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/debump.py to debump.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/biomolecule.py to biomolecule.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/inputgen.py to inputgen.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/ligand/topology.py to topology.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/ligand/mol2.py to mol2.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/ligand/__init__.py to __init__.cpython-313.pyc
byte-compiling /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr/ligand/peoe.py to peoe.cpython-313.pyc
running install_egg_info
running egg_info
creating pdb2pqr.egg-info
writing pdb2pqr.egg-info/PKG-INFO
writing dependency_links to pdb2pqr.egg-info/dependency_links.txt
writing entry points to pdb2pqr.egg-info/entry_points.txt
writing requirements to pdb2pqr.egg-info/requires.txt
writing top-level names to pdb2pqr.egg-info/top_level.txt
writing manifest file 'pdb2pqr.egg-info/SOURCES.txt'
reading manifest file 'pdb2pqr.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'pdb2pka'
adding license file 'LICENSE.md'
adding license file 'COPYING'
writing manifest file 'pdb2pqr.egg-info/SOURCES.txt'
Copying pdb2pqr.egg-info to /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/lib/python3.13/dist-packages/pdb2pqr-3.6.1.egg-info
Skipping SOURCES.txt
running install_scripts
Installing dx2cube script to /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/bin
Installing inputgen script to /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/bin
Installing pdb2pqr script to /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/bin
Installing pdb2pqr30 script to /build/reproducible-path/pdb2pqr-3.6.1+dfsg/debian/tmp/usr/bin
   dh_install -O--buildsystem=pybuild
   debian/rules override_dh_installdocs
make[1]: Entering directory '/build/reproducible-path/pdb2pqr-3.6.1+dfsg'
dh_installdocs
dh_installdocs -p pdb2pqr-doc --doc-main-package pdb2pqr build/html
make[1]: Leaving directory '/build/reproducible-path/pdb2pqr-3.6.1+dfsg'
   dh_sphinxdoc -O--buildsystem=pybuild
   dh_installchangelogs -O--buildsystem=pybuild
   dh_installexamples -O--buildsystem=pybuild
   debian/rules override_dh_installman
make[1]: Entering directory '/build/reproducible-path/pdb2pqr-3.6.1+dfsg'
PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/dx2cube --no-info --version-string 3.6.1+dfsg > dx2cube.1
PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/inputgen --no-info --version-string 3.6.1+dfsg > inputgen.1
PYTHONPATH=. help2man debian/pdb2pqr/usr/bin/pdb2pqr30 --no-info --version-string 3.6.1+dfsg > pdb2pqr30.1
dh_installman
make[1]: Leaving directory '/build/reproducible-path/pdb2pqr-3.6.1+dfsg'
   dh_python3 -O--buildsystem=pybuild
   dh_installsystemduser -O--buildsystem=pybuild
   dh_perl -O--buildsystem=pybuild
   dh_link -O--buildsystem=pybuild
   dh_strip_nondeterminism -O--buildsystem=pybuild
   dh_compress -O--buildsystem=pybuild
   dh_fixperms -O--buildsystem=pybuild
   dh_missing -O--buildsystem=pybuild
   dh_installdeb -O--buildsystem=pybuild
   dh_gencontrol -O--buildsystem=pybuild
dpkg-gencontrol: warning: package pdb2pqr-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined
   dh_md5sums -O--buildsystem=pybuild
   dh_builddeb -O--buildsystem=pybuild
dpkg-deb: building package 'pdb2pqr-doc' in '../pdb2pqr-doc_3.6.1+dfsg-1_all.deb'.
dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_3.6.1+dfsg-1_all.deb'.
dpkg-deb: building package 'python3-pdb2pqr' in '../python3-pdb2pqr_3.6.1+dfsg-1_all.deb'.
 dpkg-genbuildinfo --build=binary -O../pdb2pqr_3.6.1+dfsg-1_i386.buildinfo
 dpkg-genchanges --build=binary -O../pdb2pqr_3.6.1+dfsg-1_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/39115 and its subdirectories
I: Current time: Tue Jan 28 11:42:29 -12 2025
I: pbuilder-time-stamp: 1738107749