0s autopkgtest [12:17:36]: starting date and time: 2024-03-22 12:17:36+0000 0s autopkgtest [12:17:36]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [12:17:36]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lbp8gt2l/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:sphinx --apt-upgrade pdb2pqr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/7.2.6-6 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos02-s390x-13.secgroup --name adt-noble-s390x-pdb2pqr-20240322-121736-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 81s autopkgtest [12:18:57]: testbed dpkg architecture: s390x 81s autopkgtest [12:18:57]: testbed apt version: 2.7.12 81s autopkgtest [12:18:57]: @@@@@@@@@@@@@@@@@@@@ test bed setup 82s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 82s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 83s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [54.0 kB] 83s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 83s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3807 kB] 84s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [665 kB] 84s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 84s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 84s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 84s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [3992 kB] 84s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 84s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [45.1 kB] 84s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 86s Fetched 9195 kB in 3s (2994 kB/s) 86s Reading package lists... 88s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s Calculating upgrade... 89s The following packages will be upgraded: 89s cloud-init debianutils fonts-ubuntu-console python3-markupsafe 89s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s Need to get 719 kB of archives. 89s After this operation, 11.3 kB disk space will be freed. 89s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x debianutils s390x 5.17 [90.1 kB] 89s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 89s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x python3-markupsafe s390x 2.1.5-1build1 [12.8 kB] 89s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x cloud-init all 24.1.2-0ubuntu1 [597 kB] 90s Preconfiguring packages ... 90s Fetched 719 kB in 0s (1503 kB/s) 90s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52171 files and directories currently installed.) 90s Preparing to unpack .../debianutils_5.17_s390x.deb ... 90s Unpacking debianutils (5.17) over (5.16) ... 90s Setting up debianutils (5.17) ... 90s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52171 files and directories currently installed.) 90s Preparing to unpack .../fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 90s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 90s Preparing to unpack .../python3-markupsafe_2.1.5-1build1_s390x.deb ... 90s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 90s Preparing to unpack .../cloud-init_24.1.2-0ubuntu1_all.deb ... 90s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 90s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 90s Setting up cloud-init (24.1.2-0ubuntu1) ... 91s Setting up python3-markupsafe (2.1.5-1build1) ... 91s Processing triggers for man-db (2.12.0-3) ... 92s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 93s Unknown architecture, assuming PC-style ttyS0 93s sh: Attempting to set up Debian/Ubuntu apt sources automatically 93s sh: Distribution appears to be Ubuntu 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s eatmydata is already the newest version (131-1). 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 95s dbus is already the newest version (1.14.10-4ubuntu1). 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 95s rng-tools-debian is already the newest version (2.4). 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 95s The following packages will be REMOVED: 95s cloud-init* python3-configobj* python3-debconf* 95s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 95s After this operation, 3256 kB disk space will be freed. 96s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52170 files and directories currently installed.) 96s Removing cloud-init (24.1.2-0ubuntu1) ... 96s Removing python3-configobj (5.0.8-3) ... 96s Removing python3-debconf (1.5.86) ... 96s Processing triggers for man-db (2.12.0-3) ... 96s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 51781 files and directories currently installed.) 96s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 97s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 97s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 97s invoke-rc.d: policy-rc.d denied execution of try-restart. 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s linux-generic is already the newest version (6.8.0-11.11+1). 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 98s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 98s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 99s Reading package lists... 99s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s Calculating upgrade... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 100s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s autopkgtest [12:19:16]: rebooting testbed after setup commands that affected boot 119s autopkgtest [12:19:35]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 121s autopkgtest [12:19:37]: @@@@@@@@@@@@@@@@@@@@ apt-source pdb2pqr 125s Get:1 http://ftpmaster.internal/ubuntu noble/universe pdb2pqr 3.6.1+dfsg-1 (dsc) [1860 B] 125s Get:2 http://ftpmaster.internal/ubuntu noble/universe pdb2pqr 3.6.1+dfsg-1 (tar) [7570 kB] 125s Get:3 http://ftpmaster.internal/ubuntu noble/universe pdb2pqr 3.6.1+dfsg-1 (diff) [9876 B] 125s gpgv: Signature made Mon Jun 12 17:36:50 2023 UTC 125s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 125s gpgv: Can't check signature: No public key 125s dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found 126s autopkgtest [12:19:42]: testing package pdb2pqr version 3.6.1+dfsg-1 127s autopkgtest [12:19:43]: build not needed 129s autopkgtest [12:19:45]: test installation-test: preparing testbed 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 134s Starting pkgProblemResolver with broken count: 0 134s Starting 2 pkgProblemResolver with broken count: 0 134s Done 134s The following additional packages will be installed: 134s docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr python3-docutils 134s python3-numpy python3-pdb2pqr python3-pdbx python3-propka python3-roman 134s sgml-base xml-core 134s Suggested packages: 134s apbs docutils-doc fonts-linuxlibertine | ttf-linux-libertine 134s texlive-lang-french texlive-latex-base texlive-latex-recommended gcc 134s gfortran python3-dev python3-pytest python-pdbx-doc python-propka-doc 134s sgml-base-doc debhelper 134s Recommended packages: 134s libpaper-utils python3-pil 134s The following NEW packages will be installed: 134s autopkgtest-satdep docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr 134s python3-docutils python3-numpy python3-pdb2pqr python3-pdbx python3-propka 134s python3-roman sgml-base xml-core 134s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 134s Need to get 9781 kB/9781 kB of archives. 134s After this operation, 45.8 MB of additional disk space will be used. 134s Get:1 /tmp/autopkgtest.esSSmN/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [704 B] 134s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x sgml-base all 1.31 [11.4 kB] 134s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x xml-core all 0.19 [20.3 kB] 134s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x docutils-common all 0.20.1+dfsg-3 [132 kB] 134s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libblas3 s390x 3.12.0-3 [245 kB] 134s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libgfortran5 s390x 14-20240303-1ubuntu1 [598 kB] 134s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x liblapack3 s390x 3.12.0-3 [2979 kB] 135s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x python3-numpy s390x 1:1.24.2-2 [5137 kB] 135s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x python3-roman all 3.3-3 [9632 B] 135s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x python3-docutils all 0.20.1+dfsg-3 [393 kB] 135s Get:11 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pdbx all 2.0.1-2 [16.5 kB] 135s Get:12 http://ftpmaster.internal/ubuntu noble/universe s390x python3-propka all 3.5.1-1 [85.5 kB] 135s Get:13 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pdb2pqr all 3.6.1+dfsg-1 [145 kB] 135s Get:14 http://ftpmaster.internal/ubuntu noble/universe s390x pdb2pqr all 3.6.1+dfsg-1 [10.4 kB] 136s Fetched 9781 kB in 1s (6604 kB/s) 136s Selecting previously unselected package sgml-base. 136s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 51726 files and directories currently installed.) 136s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 136s Unpacking sgml-base (1.31) ... 136s Selecting previously unselected package xml-core. 136s Preparing to unpack .../01-xml-core_0.19_all.deb ... 136s Unpacking xml-core (0.19) ... 136s Selecting previously unselected package docutils-common. 136s Preparing to unpack .../02-docutils-common_0.20.1+dfsg-3_all.deb ... 136s Unpacking docutils-common (0.20.1+dfsg-3) ... 136s Selecting previously unselected package libblas3:s390x. 136s Preparing to unpack .../03-libblas3_3.12.0-3_s390x.deb ... 136s Unpacking libblas3:s390x (3.12.0-3) ... 136s Selecting previously unselected package libgfortran5:s390x. 136s Preparing to unpack .../04-libgfortran5_14-20240303-1ubuntu1_s390x.deb ... 136s Unpacking libgfortran5:s390x (14-20240303-1ubuntu1) ... 136s Selecting previously unselected package liblapack3:s390x. 136s Preparing to unpack .../05-liblapack3_3.12.0-3_s390x.deb ... 136s Unpacking liblapack3:s390x (3.12.0-3) ... 136s Selecting previously unselected package python3-numpy. 136s Preparing to unpack .../06-python3-numpy_1%3a1.24.2-2_s390x.deb ... 136s Unpacking python3-numpy (1:1.24.2-2) ... 136s Selecting previously unselected package python3-roman. 136s Preparing to unpack .../07-python3-roman_3.3-3_all.deb ... 136s Unpacking python3-roman (3.3-3) ... 136s Selecting previously unselected package python3-docutils. 136s Preparing to unpack .../08-python3-docutils_0.20.1+dfsg-3_all.deb ... 136s Unpacking python3-docutils (0.20.1+dfsg-3) ... 136s Selecting previously unselected package python3-pdbx. 136s Preparing to unpack .../09-python3-pdbx_2.0.1-2_all.deb ... 136s Unpacking python3-pdbx (2.0.1-2) ... 136s Selecting previously unselected package python3-propka. 136s Preparing to unpack .../10-python3-propka_3.5.1-1_all.deb ... 136s Unpacking python3-propka (3.5.1-1) ... 136s Selecting previously unselected package python3-pdb2pqr. 136s Preparing to unpack .../11-python3-pdb2pqr_3.6.1+dfsg-1_all.deb ... 136s Unpacking python3-pdb2pqr (3.6.1+dfsg-1) ... 136s Selecting previously unselected package pdb2pqr. 136s Preparing to unpack .../12-pdb2pqr_3.6.1+dfsg-1_all.deb ... 136s Unpacking pdb2pqr (3.6.1+dfsg-1) ... 136s Selecting previously unselected package autopkgtest-satdep. 136s Preparing to unpack .../13-1-autopkgtest-satdep.deb ... 136s Unpacking autopkgtest-satdep (0) ... 136s Setting up python3-propka (3.5.1-1) ... 136s Setting up python3-pdbx (2.0.1-2) ... 137s Setting up python3-roman (3.3-3) ... 137s Setting up libblas3:s390x (3.12.0-3) ... 137s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 137s Setting up libgfortran5:s390x (14-20240303-1ubuntu1) ... 137s Setting up sgml-base (1.31) ... 137s Setting up liblapack3:s390x (3.12.0-3) ... 137s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 137s Setting up python3-numpy (1:1.24.2-2) ... 139s Setting up xml-core (0.19) ... 139s Processing triggers for libc-bin (2.39-0ubuntu2) ... 139s Processing triggers for man-db (2.12.0-3) ... 139s Processing triggers for sgml-base (1.31) ... 139s Setting up docutils-common (0.20.1+dfsg-3) ... 139s Processing triggers for sgml-base (1.31) ... 139s Setting up python3-docutils (0.20.1+dfsg-3) ... 140s Setting up python3-pdb2pqr (3.6.1+dfsg-1) ... 140s Setting up pdb2pqr (3.6.1+dfsg-1) ... 140s Setting up autopkgtest-satdep (0) ... 142s (Reading database ... 53240 files and directories currently installed.) 142s Removing autopkgtest-satdep (0) ... 142s autopkgtest [12:19:58]: test installation-test: [----------------------- 143s Run pdb2pqr... 143s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 143s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 143s INFO: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). 143s INFO:Checking and transforming input arguments. 143s INFO:Loading topology files. 143s INFO:Loading molecule: examples/1a1p/1a1p.pdb 143s INFO:Setting up molecule. 143s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 143s INFO:Created biomolecule object with 14 residues and 208 atoms. 143s INFO:Setting termini states for biomolecule chains. 143s INFO:Loading forcefield. 143s INFO:Loading hydrogen topology definitions. 143s INFO:This biomolecule is clean. No repair needed. 143s INFO:Updating disulfide bridges. 143s INFO:Debumping biomolecule. 143s INFO:Adding hydrogens to biomolecule. 143s INFO:Debumping biomolecule (again). 143s INFO:Optimizing hydrogen bonds 143s INFO:Applying force field to biomolecule states. 143s INFO:Regenerating headers. 143s INFO:Regenerating PDB lines. 143s WARNING:Ignoring 852 header lines in output. 143s WARNING:Ignoring 3 missing lines in output. 143s autopkgtest [12:19:59]: test installation-test: -----------------------] 144s autopkgtest [12:20:00]: test installation-test: - - - - - - - - - - results - - - - - - - - - - 144s installation-test PASS 144s autopkgtest [12:20:00]: test pdb2pka-test: preparing testbed 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s Starting pkgProblemResolver with broken count: 0 146s Starting 2 pkgProblemResolver with broken count: 0 146s Done 146s The following additional packages will be installed: 146s fonts-font-awesome fonts-lato libjs-jquery libjs-sphinxdoc libjs-underscore 146s pdb2pqr-doc sphinx-rtd-theme-common 146s Recommended packages: 146s javascript-common 146s The following NEW packages will be installed: 146s autopkgtest-satdep fonts-font-awesome fonts-lato libjs-jquery 146s libjs-sphinxdoc libjs-underscore pdb2pqr-doc sphinx-rtd-theme-common 146s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 146s Need to get 5162 kB/5162 kB of archives. 146s After this operation, 20.1 MB of additional disk space will be used. 146s Get:1 /tmp/autopkgtest.esSSmN/2-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [720 B] 146s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x fonts-lato all 2.015-1 [2781 kB] 147s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 147s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 147s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 147s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libjs-sphinxdoc all 7.2.6-4 [149 kB] 147s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB] 147s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x pdb2pqr-doc all 3.6.1+dfsg-1 [258 kB] 148s Fetched 5162 kB in 1s (4161 kB/s) 148s Selecting previously unselected package fonts-lato. 148s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 53240 files and directories currently installed.) 148s Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... 148s Unpacking fonts-lato (2.015-1) ... 148s Selecting previously unselected package fonts-font-awesome. 148s Preparing to unpack .../1-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 148s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 148s Selecting previously unselected package libjs-jquery. 148s Preparing to unpack .../2-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 148s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 148s Selecting previously unselected package libjs-underscore. 148s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 148s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 148s Selecting previously unselected package libjs-sphinxdoc. 148s Preparing to unpack .../4-libjs-sphinxdoc_7.2.6-4_all.deb ... 148s Unpacking libjs-sphinxdoc (7.2.6-4) ... 148s Selecting previously unselected package sphinx-rtd-theme-common. 148s Preparing to unpack .../5-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... 148s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 148s Selecting previously unselected package pdb2pqr-doc. 148s Preparing to unpack .../6-pdb2pqr-doc_3.6.1+dfsg-1_all.deb ... 148s Unpacking pdb2pqr-doc (3.6.1+dfsg-1) ... 148s Selecting previously unselected package autopkgtest-satdep. 148s Preparing to unpack .../7-2-autopkgtest-satdep.deb ... 148s Unpacking autopkgtest-satdep (0) ... 148s Setting up fonts-lato (2.015-1) ... 148s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 148s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 148s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 148s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 148s Setting up libjs-sphinxdoc (7.2.6-4) ... 148s Setting up pdb2pqr-doc (3.6.1+dfsg-1) ... 148s Setting up autopkgtest-satdep (0) ... 151s (Reading database ... 53574 files and directories currently installed.) 151s Removing autopkgtest-satdep (0) ... 151s autopkgtest [12:20:07]: test pdb2pka-test: [----------------------- 151s Run pdb2pqr... 152s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 152s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 152s INFO: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). 152s INFO:Checking and transforming input arguments. 152s INFO:Loading topology files. 152s INFO:Loading molecule: 1a1p/1a1p.pdb 152s INFO:Setting up molecule. 152s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 152s INFO:Created biomolecule object with 14 residues and 208 atoms. 152s INFO:Setting termini states for biomolecule chains. 152s INFO:Loading forcefield. 152s INFO:Loading hydrogen topology definitions. 152s INFO:This biomolecule is clean. No repair needed. 152s INFO:Updating disulfide bridges. 152s INFO:Debumping biomolecule. 152s INFO:Adding hydrogens to biomolecule. 152s INFO:Debumping biomolecule (again). 152s INFO:Optimizing hydrogen bonds 152s INFO:Applying force field to biomolecule states. 152s INFO:Regenerating headers. 152s INFO:Regenerating PDB lines. 152s WARNING:Ignoring 852 header lines in output. 152s WARNING:Ignoring 3 missing lines in output. 152s autopkgtest [12:20:08]: test pdb2pka-test: -----------------------] 152s pdb2pka-test PASS 152s autopkgtest [12:20:08]: test pdb2pka-test: - - - - - - - - - - results - - - - - - - - - - 153s autopkgtest [12:20:09]: test command1: preparing testbed 156s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s Starting pkgProblemResolver with broken count: 0 156s Starting 2 pkgProblemResolver with broken count: 0 156s Done 156s The following additional packages will be installed: 156s python3-dateutil python3-iniconfig python3-packaging python3-pandas 156s python3-pandas-lib python3-pluggy python3-pytest python3-testfixtures 156s Suggested packages: 156s python-pandas-doc python3-statsmodels python-testfixtures-doc 156s Recommended packages: 156s python3-scipy python3-matplotlib python3-bottleneck python3-numexpr 156s python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml 156s python3-tables 156s The following NEW packages will be installed: 156s autopkgtest-satdep python3-dateutil python3-iniconfig python3-packaging 156s python3-pandas python3-pandas-lib python3-pluggy python3-pytest 156s python3-testfixtures 156s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 156s Need to get 12.4 MB/12.4 MB of archives. 156s After this operation, 66.0 MB of additional disk space will be used. 156s Get:1 /tmp/autopkgtest.esSSmN/3-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [744 B] 156s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x python3-dateutil all 2.8.2-3 [79.2 kB] 156s Get:3 http://ftpmaster.internal/ubuntu noble/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 156s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x python3-packaging all 23.2-1 [40.6 kB] 156s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pandas-lib s390x 2.1.4+dfsg-4ubuntu2 [8852 kB] 157s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 158s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pluggy all 1.4.0-1 [20.4 kB] 158s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x python3-pytest all 7.4.4-1 [305 kB] 158s Get:9 http://ftpmaster.internal/ubuntu noble/universe s390x python3-testfixtures all 8.1.0-1 [73.5 kB] 158s Fetched 12.4 MB in 2s (7504 kB/s) 158s Selecting previously unselected package python3-dateutil. 158s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 53574 files and directories currently installed.) 158s Preparing to unpack .../0-python3-dateutil_2.8.2-3_all.deb ... 158s Unpacking python3-dateutil (2.8.2-3) ... 158s Selecting previously unselected package python3-iniconfig. 158s Preparing to unpack .../1-python3-iniconfig_1.1.1-2_all.deb ... 158s Unpacking python3-iniconfig (1.1.1-2) ... 158s Selecting previously unselected package python3-packaging. 158s Preparing to unpack .../2-python3-packaging_23.2-1_all.deb ... 158s Unpacking python3-packaging (23.2-1) ... 158s Selecting previously unselected package python3-pandas-lib:s390x. 158s Preparing to unpack .../3-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_s390x.deb ... 158s Unpacking python3-pandas-lib:s390x (2.1.4+dfsg-4ubuntu2) ... 158s Selecting previously unselected package python3-pandas. 158s Preparing to unpack .../4-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 158s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 159s Selecting previously unselected package python3-pluggy. 159s Preparing to unpack .../5-python3-pluggy_1.4.0-1_all.deb ... 159s Unpacking python3-pluggy (1.4.0-1) ... 159s Selecting previously unselected package python3-pytest. 159s Preparing to unpack .../6-python3-pytest_7.4.4-1_all.deb ... 159s Unpacking python3-pytest (7.4.4-1) ... 159s Selecting previously unselected package python3-testfixtures. 159s Preparing to unpack .../7-python3-testfixtures_8.1.0-1_all.deb ... 159s Unpacking python3-testfixtures (8.1.0-1) ... 159s Selecting previously unselected package autopkgtest-satdep. 159s Preparing to unpack .../8-3-autopkgtest-satdep.deb ... 159s Unpacking autopkgtest-satdep (0) ... 159s Setting up python3-iniconfig (1.1.1-2) ... 159s Setting up python3-pandas-lib:s390x (2.1.4+dfsg-4ubuntu2) ... 159s Setting up python3-testfixtures (8.1.0-1) ... 159s Setting up python3-packaging (23.2-1) ... 159s Setting up python3-pluggy (1.4.0-1) ... 159s Setting up python3-dateutil (2.8.2-3) ... 159s Setting up python3-pytest (7.4.4-1) ... 160s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 163s Setting up autopkgtest-satdep (0) ... 163s Processing triggers for man-db (2.12.0-3) ... 166s (Reading database ... 55587 files and directories currently installed.) 166s Removing autopkgtest-satdep (0) ... 167s autopkgtest [12:20:23]: test command1: pytest-3 167s autopkgtest [12:20:23]: test command1: [----------------------- 167s ============================= test session starts ============================== 167s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 167s rootdir: /tmp/autopkgtest.esSSmN/build.E5J/src 167s configfile: pytest.ini 167s 167s ----------------------------- live log collection ------------------------------ 167s WARNING py.warnings:warnings.py:110 /tmp/autopkgtest.esSSmN/build.E5J/src/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 167s @pytest.mark.long_test 167s 167s ERROR regression_test:regression_test.py:173 Need to reinstate the --apbs-input test with a temporary directory as path 167s collected 316 items 167s 167s tests/core_test.py::test_short_pdb[4E8M] SKIPPED (not running tests ...) [ 0%] 167s tests/core_test.py::test_short_pdb[7BNA] SKIPPED (not running tests ...) [ 0%] 167s tests/core_test.py::test_short_pdb[1K1I] SKIPPED (not running tests ...) [ 0%] 167s tests/core_test.py::test_short_pdb[5D8V] SKIPPED (not running tests ...) [ 1%] 167s tests/core_test.py::test_short_pdb[1NAJ] SKIPPED (not running tests ...) [ 1%] 167s tests/core_test.py::test_short_pdb[4UN3] SKIPPED (not running tests ...) [ 1%] 167s tests/core_test.py::test_short_pdb[1AQO] SKIPPED (not running tests ...) [ 2%] 167s tests/core_test.py::test_short_pdb[1FAS] SKIPPED (not running tests ...) 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[ 33%] 167s tests/core_test.py::test_long_pdb[1KFN] SKIPPED (not running tests r...) [ 34%] 167s tests/core_test.py::test_long_pdb[3LMO] SKIPPED (not running tests r...) [ 34%] 167s tests/core_test.py::test_long_pdb[4NPN] SKIPPED (not running tests r...) [ 34%] 167s tests/core_test.py::test_long_pdb[1ZLM] SKIPPED (not running tests r...) [ 35%] 167s tests/core_test.py::test_long_pdb[1NH9] SKIPPED (not running tests r...) [ 35%] 167s tests/core_test.py::test_long_pdb[4ZQA] SKIPPED (not running tests r...) [ 35%] 167s tests/core_test.py::test_long_pdb[4HTI] SKIPPED (not running tests r...) [ 36%] 167s tests/core_test.py::test_long_pdb[2HP7] SKIPPED (not running tests r...) [ 36%] 167s tests/core_test.py::test_long_pdb[1UG4] SKIPPED (not running tests r...) [ 36%] 167s tests/core_test.py::test_long_pdb[3ZZP] SKIPPED (not running tests r...) [ 37%] 167s tests/core_test.py::test_long_pdb[2HDZ] SKIPPED (not running tests r...) [ 37%] 167s tests/core_test.py::test_long_pdb[1FAS] SKIPPED (not running tests r...) [ 37%] 167s tests/core_test.py::test_long_pdb[3CQT] SKIPPED (not running tests r...) [ 37%] 167s tests/core_test.py::test_long_pdb[1TGN] SKIPPED (not running tests r...) [ 38%] 167s tests/core_test.py::test_long_pdb[1P1L] SKIPPED (not running tests r...) [ 38%] 167s tests/core_test.py::test_long_pdb[2OO2] SKIPPED (not running tests r...) [ 38%] 167s tests/core_test.py::test_long_pdb[2IWN] SKIPPED (not running tests r...) [ 39%] 167s tests/core_test.py::test_long_pdb[3RFF] SKIPPED (not running tests r...) [ 39%] 167s tests/core_test.py::test_long_pdb[1ZVA] SKIPPED (not running tests r...) [ 39%] 167s tests/core_test.py::test_long_pdb[3S0A] SKIPPED (not running tests r...) [ 40%] 167s tests/core_test.py::test_long_pdb[2YGS] SKIPPED (not running tests r...) [ 40%] 167s tests/core_test.py::test_long_pdb[2VWR] SKIPPED (not running tests r...) [ 40%] 167s tests/core_test.py::test_long_pdb[1X3O] SKIPPED (not running tests r...) [ 41%] 167s tests/core_test.py::test_long_pdb[1ZZK] SKIPPED (not running tests r...) [ 41%] 167s tests/core_test.py::test_long_pdb[2YXF] SKIPPED (not running tests r...) [ 41%] 167s tests/core_test.py::test_long_pdb[3KT2] SKIPPED (not running tests r...) [ 42%] 167s tests/core_test.py::test_long_pdb[4POY] SKIPPED (not running tests r...) [ 42%] 167s tests/core_test.py::test_long_pdb[3NGP] SKIPPED (not running tests r...) [ 42%] 167s tests/core_test.py::test_long_pdb[2J70] SKIPPED (not running tests r...) [ 43%] 167s tests/core_test.py::test_long_pdb[3LAA] SKIPPED (not running tests r...) [ 43%] 167s tests/core_test.py::test_long_pdb[1R7J] SKIPPED (not running tests r...) [ 43%] 167s tests/core_test.py::test_long_pdb[1HUF] SKIPPED (not running tests r...) [ 43%] 167s tests/core_test.py::test_long_pdb[1SJV] SKIPPED (not running tests r...) [ 44%] 167s tests/core_test.py::test_long_pdb[2HC8] SKIPPED (not running tests r...) [ 44%] 167s tests/core_test.py::test_long_pdb[3HRN] SKIPPED (not running tests r...) [ 44%] 167s tests/core_test.py::test_long_pdb[2TGI] SKIPPED (not running tests r...) [ 45%] 167s tests/core_test.py::test_long_pdb[1E7G] SKIPPED (not running tests r...) [ 45%] 167s tests/core_test.py::test_long_pdb[4Q2Q] SKIPPED (not running tests r...) [ 45%] 167s tests/core_test.py::test_long_pdb[1TIG] SKIPPED (not running tests r...) [ 46%] 167s tests/core_test.py::test_long_pdb[2CMP] SKIPPED (not running tests r...) [ 46%] 167s tests/core_test.py::test_long_pdb[2PMR] SKIPPED (not running tests r...) [ 46%] 167s tests/core_test.py::test_long_pdb[1J2A] SKIPPED (not running tests r...) [ 47%] 167s tests/core_test.py::test_long_pdb[1IS5] SKIPPED (not running tests r...) [ 47%] 167s tests/core_test.py::test_long_pdb[2SFA] SKIPPED (not running tests r...) [ 47%] 167s tests/core_test.py::test_long_pdb[3IDW] SKIPPED (not running tests r...) [ 48%] 167s tests/core_test.py::test_long_pdb[4ZMK] SKIPPED (not running tests r...) [ 48%] 167s tests/core_test.py::test_long_pdb[1X91] SKIPPED (not running tests r...) [ 48%] 167s tests/core_test.py::test_long_pdb[2JCP] SKIPPED (not running tests r...) [ 49%] 167s tests/core_test.py::test_long_pdb[3HRO] SKIPPED (not running tests r...) [ 49%] 167s tests/core_test.py::test_long_pdb[5V0O] SKIPPED (not running tests r...) [ 49%] 167s tests/core_test.py::test_long_pdb[1DUP] SKIPPED (not running tests r...) [ 50%] 167s tests/core_test.py::test_long_pdb[1NXO] SKIPPED (not running tests r...) [ 50%] 167s tests/core_test.py::test_long_pdb[2QVO] SKIPPED (not running tests r...) [ 50%] 167s tests/core_test.py::test_long_pdb[1I2T] SKIPPED (not running tests r...) [ 50%] 167s tests/core_test.py::test_long_pdb[3CE7] SKIPPED (not running tests r...) [ 51%] 167s tests/core_test.py::test_long_pdb[1DF4] SKIPPED (not running tests r...) [ 51%] 167s tests/core_test.py::test_long_pdb[1AFS] SKIPPED (not running tests r...) [ 51%] 167s tests/core_test.py::test_long_pdb[4HS2] SKIPPED (not running tests r...) [ 52%] 167s tests/core_test.py::test_long_pdb[3CSR] SKIPPED (not running tests r...) [ 52%] 167s tests/core_test.py::test_long_pdb[2IVY] SKIPPED (not running tests r...) [ 52%] 167s tests/core_test.py::test_long_pdb[2NSN] SKIPPED (not running tests r...) [ 53%] 167s tests/core_test.py::test_long_pdb[1NKD] SKIPPED (not running tests r...) [ 53%] 167s tests/core_test.py::test_long_pdb[4TTW] SKIPPED (not running tests r...) [ 53%] 167s tests/core_test.py::test_long_pdb[3RFI] SKIPPED (not running tests r...) [ 54%] 167s tests/core_test.py::test_long_pdb[1Z0P] SKIPPED (not running tests r...) [ 54%] 167s tests/core_test.py::test_long_pdb[2SGA] SKIPPED (not running tests r...) [ 54%] 167s tests/core_test.py::test_long_pdb[1YQB] SKIPPED (not running tests r...) [ 55%] 167s tests/core_test.py::test_long_pdb[3ZSL] SKIPPED (not running tests r...) [ 55%] 167s tests/core_test.py::test_long_pdb[4L9E] SKIPPED (not running tests r...) [ 55%] 167s tests/core_test.py::test_long_pdb[1JQ0] SKIPPED (not running tests r...) [ 56%] 167s tests/core_test.py::test_long_pdb[4IL7] SKIPPED (not running tests r...) [ 56%] 167s tests/core_test.py::test_long_pdb[1WOU] SKIPPED (not running tests r...) [ 56%] 167s tests/core_test.py::test_long_pdb[3B7H] SKIPPED (not running tests r...) [ 56%] 167s tests/core_test.py::test_long_pdb[1HOE] SKIPPED (not running tests r...) [ 57%] 167s tests/core_test.py::test_long_pdb[2ESK] SKIPPED (not running tests r...) [ 57%] 167s tests/core_test.py::test_long_pdb[3TSV] SKIPPED (not running tests r...) [ 57%] 167s tests/core_test.py::test_long_pdb[1H75] SKIPPED (not running tests r...) [ 58%] 167s tests/core_test.py::test_long_pdb[2CWR] SKIPPED (not running tests r...) [ 58%] 167s tests/core_test.py::test_long_pdb[4EO0] SKIPPED (not running tests r...) [ 58%] 167s tests/core_test.py::test_long_pdb[3T1S] SKIPPED (not running tests r...) [ 59%] 167s tests/core_test.py::test_long_pdb[4CVD] SKIPPED (not running tests r...) [ 59%] 167s tests/core_test.py::test_long_pdb[1RJ1] SKIPPED (not running tests r...) [ 59%] 167s tests/core_test.py::test_long_pdb[2FI9] SKIPPED (not running tests r...) [ 60%] 167s tests/core_test.py::test_long_pdb[1LN4] SKIPPED (not running tests r...) [ 60%] 167s tests/core_test.py::test_long_pdb[1X6J] SKIPPED (not running tests r...) [ 60%] 167s tests/core_test.py::test_long_pdb[4CRH] SKIPPED (not running tests r...) [ 61%] 167s tests/core_test.py::test_long_pdb[3H0X] SKIPPED (not running tests r...) [ 61%] 167s tests/core_test.py::test_long_pdb[2P5K] SKIPPED (not running tests r...) [ 61%] 167s tests/core_test.py::test_long_pdb[1OPC] SKIPPED (not running tests r...) [ 62%] 167s tests/core_test.py::test_long_pdb[2CJJ] SKIPPED (not running tests r...) [ 62%] 167s tests/core_test.py::test_long_pdb[1OPS] SKIPPED (not running tests r...) [ 62%] 167s tests/core_test.py::test_long_pdb[3JTE] SKIPPED (not running tests r...) [ 62%] 167s tests/core_test.py::test_long_pdb[3FH2] SKIPPED (not running tests r...) [ 63%] 167s tests/core_test.py::test_long_pdb[1TUD] SKIPPED (not running tests r...) [ 63%] 167s tests/core_test.py::test_long_pdb[3RVC] SKIPPED (not running tests r...) [ 63%] 167s tests/core_test.py::test_long_pdb[3C97] SKIPPED (not running tests r...) [ 64%] 167s tests/core_test.py::test_long_pdb[1TG0] SKIPPED (not running tests r...) [ 64%] 167s tests/core_test.py::test_long_pdb[4S11] SKIPPED (not running tests r...) [ 64%] 167s tests/core_test.py::test_long_pdb[3US6] SKIPPED (not running tests r...) [ 65%] 167s tests/core_test.py::test_long_pdb[2G7O] SKIPPED (not running tests r...) [ 65%] 167s tests/core_test.py::test_long_pdb[4AXT] SKIPPED (not running tests r...) [ 65%] 167s tests/core_test.py::test_long_pdb[1TQG] SKIPPED (not running tests r...) [ 66%] 167s tests/core_test.py::test_broken_backbone[2V75] 167s -------------------------------- live log call --------------------------------- 167s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_2V75_0/2V75.log 167s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 167s 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). 167s 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). 167s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 167s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 168s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 169s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 169s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 169s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 90 residues and 687 atoms. 169s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 169s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 169s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 169s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 8 missing atoms in biomolecule. 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 169s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 169s CRITICAL PDB2PQR3.6.1:main.py:800 Too few atoms present to reconstruct or cap residue ASN A 95 in structure! This error is generally caused by missing backbone atoms in this biomolecule; you must use an external program to complete gaps in the biomolecule backbone. Heavy atoms missing from ASN A 95: C O CB CG OD1 ND2 OXT CA 169s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 169s XFAIL [ 66%] 169s tests/core_test.py::test_broken_backbone[4MGP] 169s -------------------------------- live log call --------------------------------- 169s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_4MGP_0/4MGP.log 169s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 169s 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). 169s 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). 169s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 169s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 169s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP 170s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 170s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 170s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 23 residues and 163 atoms. 170s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in MET A 21. 170s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in MET A 21. 170s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in MET A 21. 170s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: SD in MET A 21. 170s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE in MET A 21. 170s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in MET A 21. At least one of the instances is being ignored. 170s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 170s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 170s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 170s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 12 missing atoms in biomolecule. 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 170s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 170s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 11 at coordinates 1.430, -1.683, -11.529 170s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 11 at coordinates 1.940, -0.315, -11.800 170s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CG to residue LYS A 14 at coordinates -1.600, -8.819, -6.913 170s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CD to residue LYS A 14 at coordinates -2.056, -8.844, -8.361 170s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 14 at coordinates -3.548, -9.031, -8.498 170s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 14 at coordinates -3.947, -9.048, -9.928 170s CRITICAL PDB2PQR3.6.1:main.py:800 Too few atoms present to reconstruct or cap residue SER A 23 in structure! This error is generally caused by missing backbone atoms in this biomolecule; you must use an external program to complete gaps in the biomolecule backbone. Heavy atoms missing from SER A 23: C O CB OG OXT CA 170s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 170s XFAIL [ 66%] 170s tests/core_test.py::test_broken_backbone[1EJG] 170s -------------------------------- live log call --------------------------------- 170s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_1EJG_0/1EJG.log 170s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 170s 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). 170s 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). 170s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 170s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 170s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG 171s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 171s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 171s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 650 atoms. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in THR A 1. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 1. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 1. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 1. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 1. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H1 in THR A 1. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H2 in THR A 1. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H3 in THR A 1. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 1. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 1. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 1. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 1. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 1. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 1. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 1. At least one of the instances is being ignored. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 2. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 2. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 2. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 2. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 2. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 2. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 2. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 2. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 2. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 2. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 2. At least one of the instances is being ignored. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 7. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 7. At least one of the instances is being ignored. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in VAL A 8. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in VAL A 8. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in VAL A 8. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in VAL A 8. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in VAL A 8. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in VAL A 8. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in VAL A 8. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in VAL A 8. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG11 in VAL A 8. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in VAL A 8. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in VAL A 8. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in VAL A 8. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in VAL A 8. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in VAL A 8. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in VAL A 8. At least one of the instances is being ignored. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NE in ARG A 10. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in ARG A 10. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH1 in ARG A 10. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH2 in ARG A 10. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE in ARG A 10. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH11 in ARG A 10. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH12 in ARG A 10. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH21 in ARG A 10. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH22 in ARG A 10. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ARG A 10. At least one of the instances is being ignored. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ASN A 12. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASN A 12. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 12. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 12. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 12. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ASN A 12. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASN A 12. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASN A 12. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 12. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 12. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 12. At least one of the instances is being ignored. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PHE A 13. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in PHE A 13. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in PHE A 13. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in PHE A 13. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in PHE A 13. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in PHE A 13. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in PHE A 13. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PHE A 13. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in PHE A 13. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in PHE A 13. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HZ in PHE A 13. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PHE A 13. At least one of the instances is being ignored. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 19. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 19. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 19. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 19. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 19. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 19. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 19. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 19. At least one of the instances is being ignored. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in SER A 22. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in SER A 22. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in SER A 22. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in SER A 22. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in SER A 22. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in SER A 22. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in SER A 22. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in SER A 22. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in SER A 22. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in SER A 22. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in SER A 22. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in SER A 22. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in SER A 22. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in SER A 22. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in SER A 22. At least one of the instances is being ignored. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in GLU A 23. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in GLU A 23. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE1 in GLU A 23. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE2 in GLU A 23. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in GLU A 23. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in GLU A 23. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in GLU A 23. At least one of the instances is being ignored. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 25. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 25. At least one of the instances is being ignored. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in TYR A 29. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in TYR A 29. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in TYR A 29. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in TYR A 29. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in TYR A 29. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in TYR A 29. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OH in TYR A 29. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in TYR A 29. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in TYR A 29. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in TYR A 29. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in TYR A 29. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH in TYR A 29. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in TYR A 29. At least one of the instances is being ignored. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 34. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 34. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 34. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 34. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 34. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 34. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 34. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 34. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 34. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 34. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 34. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 34. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 34. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 34. At least one of the instances is being ignored. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 36. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 36. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 36. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 36. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 36. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 36. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 36. At least one of the instances is being ignored. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 39. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 39. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 39. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 39. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 39. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 39. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 39. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 39. At least one of the instances is being ignored. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASP A 43. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASP A 43. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASP A 43. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD2 in ASP A 43. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASP A 43. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASP A 43. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASP A 43. At least one of the instances is being ignored. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 46. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 46. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 46. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 46. 171s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 46. 171s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 46. At least one of the instances is being ignored. 171s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 171s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 171s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 171s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 171s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 171s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 171s CRITICAL PDB2PQR3.6.1:main.py:800 Unable to debump biomolecule. Biomolecular structure is incomplete: Found gap in biomolecule structure for atom ATOM 405 CG SER 22 4.661 14.854 -4.058 0.0000 0.0000 171s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 171s XFAIL [ 67%] 171s tests/core_test.py::test_broken_backbone[3U7T] 171s -------------------------------- live log call --------------------------------- 171s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_3U7T_0/3U7T.log 171s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 171s 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). 171s 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). 171s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 171s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 171s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T 172s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 172s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 172s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 652 atoms. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in PRO A 22. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in PRO A 22. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in PRO A 22. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in PRO A 22. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 22. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in PRO A 22. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in PRO A 22. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 22. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 22. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in PRO A 22. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 22. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in PRO A 22. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 22. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 22. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 22. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 22. 172s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 22. At least one of the instances is being ignored. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in LEU A 25. 172s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in LEU A 25. At least one of the instances is being ignored. 172s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 172s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 172s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 172s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 172s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 172s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 172s CRITICAL PDB2PQR3.6.1:main.py:800 Unable to debump biomolecule. Biomolecular structure is incomplete: Found gap in biomolecule structure for atom ATOM 313 OG PRO 22 -13.108 -5.696 -15.739 0.0000 0.0000 172s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 172s XFAIL [ 67%] 172s tests/core_test.py::test_protonated_terminals[C-terminal HID] 172s -------------------------------- live log call --------------------------------- 172s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log 172s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 172s 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). 172s 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). 172s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 172s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 172s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/cterm_hid.pdb 172s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 172s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms. 172s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 172s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 172s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 172s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 172s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 172s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule. 172s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 172s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402 172s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 172s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 172s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 172s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 172s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 172s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 172s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 172s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 172s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 172s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 172s INFO common:common.py:198 0 atoms have position differences > 0 172s INFO common:common.py:198 0 atoms have position differences > 0.01 172s INFO common:common.py:198 0 atoms have charge differences > 0 172s INFO common:common.py:198 0 atoms have charge differences > 0.01 172s INFO common:common.py:198 0 atoms have radius differences > 0 172s INFO common:common.py:198 0 atoms have radius differences > 0.01 172s PASSED [ 67%] 172s tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 172s -------------------------------- live log call --------------------------------- 172s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log 172s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 172s 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). 172s 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). 172s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 172s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 172s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/5vav_cyclic_peptide.pdb 172s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 172s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms. 172s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 172s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 172s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 172s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 172s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 172s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 172s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 172s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 172s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 172s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 172s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 172s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 172s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 172s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 172s INFO common:common.py:198 0 atoms have position differences > 0 172s INFO common:common.py:198 0 atoms have position differences > 0.01 172s INFO common:common.py:198 0 atoms have charge differences > 0 172s INFO common:common.py:198 0 atoms have charge differences > 0.01 172s INFO common:common.py:198 0 atoms have radius differences > 0 172s INFO common:common.py:198 0 atoms have radius differences > 0.01 172s PASSED [ 68%] 172s tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 68%] 172s tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 68%] 172s tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 68%] 172s tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 69%] 172s tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 69%] 172s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 69%] 172s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 70%] 172s tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 70%] 172s tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 70%] 173s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 71%] 173s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 71%] 173s tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 71%] 173s tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 72%] 173s tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 72%] 173s tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 72%] 173s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 73%] 173s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 73%] 173s 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%] 173s tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 74%] 173s tests/io_test.py::test_read_qcd PASSED [ 74%] 173s tests/io_test.py::test_dx2cube 173s -------------------------------- live log call --------------------------------- 173s INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... 173s INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... 173s INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 174s INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 174s INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... 175s INFO io_test:io_test.py:68 No differences found in output 175s PASSED [ 74%] 175s tests/ligand_test.py::test_peoe_charges 175s -------------------------------- live log call --------------------------------- 175s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 175s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 175s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 175s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 175s PASSED [ 75%] 176s tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 176s -------------------------------- live log call --------------------------------- 176s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 176s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 176s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 176s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 176s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 176s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 176s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 176s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 176s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 176s PASSED [ 75%] 176s tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 176s -------------------------------- live log call --------------------------------- 176s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 176s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 176s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 176s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 176s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 176s PASSED [ 75%] 177s tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 177s -------------------------------- live log call --------------------------------- 177s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 177s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 177s PASSED [ 75%] 177s tests/ligand_test.py::test_assign_parameters[acetate.mol2] 177s -------------------------------- live log call --------------------------------- 177s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 177s PASSED [ 76%] 177s tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 177s -------------------------------- live log call --------------------------------- 177s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 177s PASSED [ 76%] 177s tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 177s -------------------------------- live log call --------------------------------- 177s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 177s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 177s PASSED [ 76%] 177s tests/ligand_test.py::test_assign_parameters[adp.mol2] 177s -------------------------------- live log call --------------------------------- 177s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 177s INFO ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00 177s PASSED [ 77%] 177s tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 177s -------------------------------- live log call --------------------------------- 177s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 177s PASSED [ 77%] 177s tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 177s -------------------------------- live log call --------------------------------- 177s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 177s PASSED [ 77%] 177s tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 177s -------------------------------- live log call --------------------------------- 177s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 177s PASSED [ 78%] 177s tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 177s -------------------------------- live log call --------------------------------- 177s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 177s PASSED [ 78%] 177s tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 177s -------------------------------- live log call --------------------------------- 177s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 177s PASSED [ 78%] 177s tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 177s -------------------------------- live log call --------------------------------- 177s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 177s PASSED [ 79%] 177s tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 177s -------------------------------- live log call --------------------------------- 177s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 177s PASSED [ 79%] 177s tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 177s -------------------------------- live log call --------------------------------- 177s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 177s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 177s PASSED [ 79%] 177s tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 177s -------------------------------- live log call --------------------------------- 177s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 177s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 177s PASSED [ 80%] 178s tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 178s -------------------------------- live log call --------------------------------- 178s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 178s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 178s PASSED [ 80%] 178s tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 178s -------------------------------- live log call --------------------------------- 178s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 178s PASSED [ 80%] 178s tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED [ 81%] 178s tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED [ 81%] 178s tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 178s -------------------------------- live log call --------------------------------- 178s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 178s PASSED [ 81%] 178s tests/ligand_test.py::test_formal_charge[adp.mol2] 178s -------------------------------- live log call --------------------------------- 178s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 178s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 178s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 178s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 178s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 178s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 178s PASSED [ 81%] 178s tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED [ 82%] 178s tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED [ 82%] 178s tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED [ 82%] 178s tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED [ 83%] 178s tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED [ 83%] 178s tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED [ 83%] 178s tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED [ 84%] 178s tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 178s -------------------------------- live log call --------------------------------- 178s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 178s PASSED [ 84%] 178s tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED [ 84%] 178s tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED [ 85%] 178s tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED [ 85%] 178s tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED [ 85%] 178s tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED [ 86%] 178s tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED [ 86%] 178s tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED [ 86%] 179s tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED [ 87%] 179s tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED [ 87%] 179s tests/ligand_test.py::test_rings[acetate.mol2] PASSED [ 87%] 179s tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED [ 87%] 179s tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED [ 88%] 179s tests/ligand_test.py::test_rings[adp.mol2] PASSED [ 88%] 179s tests/ligand_test.py::test_rings[anthracene.mol2] PASSED [ 88%] 179s tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED [ 89%] 179s tests/ligand_test.py::test_rings[ethanol.mol2] PASSED [ 89%] 179s tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED [ 89%] 179s tests/ligand_test.py::test_rings[glycerol.mol2] PASSED [ 90%] 179s tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED [ 90%] 179s tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED [ 90%] 179s tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED [ 91%] 179s tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%] 179s tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%] 179s tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%] 179s tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%] 179s tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%] 179s tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%] 179s tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%] 179s tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%] 179s tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%] 179s tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%] 179s tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%] 179s tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] 179s tests/regression_test.py::test_basic[1AFS basic local] 179s -------------------------------- live log call --------------------------------- 179s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_basic_1AFS_basic_local_0/output.log 179s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 179s 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). 179s 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). 179s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 179s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 179s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 179s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 179s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 179s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 179s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 179s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 179s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 179s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 179s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 179s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 179s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 179s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 179s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 179s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 179s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 179s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 179s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 179s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 179s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 179s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 179s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 180s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 180s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 181s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 181s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 181s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 181s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 181s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 181s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 181s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 181s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 181s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 181s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 181s WARNING pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages 183s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 183s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 183s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 183s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 183s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 183s WARNING common:common.py:186 6 atoms have position differences > 0 183s INFO common:common.py:198 0 atoms have position differences > 0.01 183s INFO common:common.py:198 0 atoms have charge differences > 0 183s INFO common:common.py:198 0 atoms have charge differences > 0.01 183s INFO common:common.py:198 0 atoms have radius differences > 0 183s INFO common:common.py:198 0 atoms have radius differences > 0.01 183s PASSED [ 95%] 183s tests/regression_test.py::test_forcefields[1AFS whitespace AMBER] 183s -------------------------------- live log call --------------------------------- 183s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa0/output.log 183s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 183s 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). 183s 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). 183s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 183s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 183s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 183s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 183s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 183s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 183s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 183s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 183s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 183s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 183s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 183s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 183s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 183s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 183s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 183s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 183s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 183s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 183s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 184s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 184s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 184s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 184s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 184s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 184s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 185s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 187s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 187s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 187s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 187s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 187s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 187s WARNING common:common.py:186 6 atoms have position differences > 0 187s INFO common:common.py:198 0 atoms have position differences > 0.01 187s INFO common:common.py:198 0 atoms have charge differences > 0 187s INFO common:common.py:198 0 atoms have charge differences > 0.01 187s INFO common:common.py:198 0 atoms have radius differences > 0 187s INFO common:common.py:198 0 atoms have radius differences > 0.01 187s PASSED [ 95%] 187s tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] 187s -------------------------------- live log call --------------------------------- 187s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa1/output.log 187s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 188s 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). 188s 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). 188s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 188s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 188s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 188s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 188s WARNING pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages 188s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 188s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 188s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 188s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 188s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 188s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 188s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 188s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 188s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 188s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 188s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 188s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 188s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 188s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 188s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 188s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 188s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 189s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 191s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 191s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 191s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 192s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 192s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 192s WARNING common:common.py:186 5 atoms have position differences > 0 192s INFO common:common.py:198 0 atoms have position differences > 0.01 192s INFO common:common.py:198 0 atoms have charge differences > 0 192s INFO common:common.py:198 0 atoms have charge differences > 0.01 192s INFO common:common.py:198 0 atoms have radius differences > 0 192s INFO common:common.py:198 0 atoms have radius differences > 0.01 192s PASSED [ 95%] 192s tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] 192s -------------------------------- live log call --------------------------------- 192s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa2/output.log 192s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 192s 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). 192s 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). 192s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 192s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 192s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 192s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 192s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 192s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 192s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 192s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 192s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 192s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 192s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 192s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 192s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 192s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 192s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 192s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 192s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 192s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 192s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 192s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 192s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 193s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 196s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 196s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 196s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 196s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 196s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 196s WARNING common:common.py:186 6 atoms have position differences > 0 196s INFO common:common.py:198 0 atoms have position differences > 0.01 196s INFO common:common.py:198 0 atoms have charge differences > 0 196s INFO common:common.py:198 0 atoms have charge differences > 0.01 196s INFO common:common.py:198 0 atoms have radius differences > 0 196s INFO common:common.py:198 0 atoms have radius differences > 0.01 196s PASSED [ 96%] 196s tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] 196s -------------------------------- live log call --------------------------------- 196s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa3/output.log 196s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 196s 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). 196s 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). 196s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 196s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 196s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 196s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 196s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 196s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 196s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 196s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 196s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 196s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 196s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 196s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 196s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 196s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 196s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 196s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 196s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 196s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 196s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 196s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 197s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 197s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 200s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 200s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 200s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 200s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 200s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 200s WARNING common:common.py:186 6 atoms have position differences > 0 200s INFO common:common.py:198 0 atoms have position differences > 0.01 200s INFO common:common.py:198 0 atoms have charge differences > 0 200s INFO common:common.py:198 0 atoms have charge differences > 0.01 200s INFO common:common.py:198 0 atoms have radius differences > 0 200s INFO common:common.py:198 0 atoms have radius differences > 0.01 200s PASSED [ 96%] 200s tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] 200s -------------------------------- live log call --------------------------------- 200s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa4/output.log 200s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 200s 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). 200s 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). 200s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 200s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 200s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 200s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 200s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 200s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 200s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 200s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 200s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 200s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 200s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 200s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 200s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 200s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 200s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 200s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 200s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 200s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 200s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 200s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 201s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 201s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 204s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 204s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 204s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 204s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output. 204s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 204s WARNING common:common.py:186 6 atoms have position differences > 0 204s INFO common:common.py:198 0 atoms have position differences > 0.01 204s INFO common:common.py:198 0 atoms have charge differences > 0 204s INFO common:common.py:198 0 atoms have charge differences > 0.01 204s INFO common:common.py:198 0 atoms have radius differences > 0 204s INFO common:common.py:198 0 atoms have radius differences > 0.01 204s PASSED [ 96%] 204s tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] 204s -------------------------------- live log call --------------------------------- 204s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa5/output.log 204s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 204s 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). 204s 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). 204s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 204s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 204s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 204s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 204s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 204s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 204s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 204s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 204s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 204s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 204s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 204s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 204s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 204s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 204s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 204s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 204s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 204s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 204s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 204s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 205s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 206s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 208s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 208s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 208s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 208s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 208s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 208s WARNING common:common.py:186 6 atoms have position differences > 0 208s INFO common:common.py:198 0 atoms have position differences > 0.01 208s INFO common:common.py:198 0 atoms have charge differences > 0 208s INFO common:common.py:198 0 atoms have charge differences > 0.01 208s INFO common:common.py:198 0 atoms have radius differences > 0 208s INFO common:common.py:198 0 atoms have radius differences > 0.01 208s PASSED [ 97%] 208s tests/regression_test.py::test_other_options[1AFS whitespace clean] 208s -------------------------------- live log call --------------------------------- 208s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_whites0/output.log 208s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 208s 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). 208s 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). 208s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 208s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 208s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 208s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 208s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 208s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 208s INFO PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps. 208s INFO common:common.py:198 0 atoms have position differences > 0 208s INFO common:common.py:198 0 atoms have position differences > 0.01 208s INFO common:common.py:198 0 atoms have charge differences > 0 208s INFO common:common.py:198 0 atoms have charge differences > 0.01 208s INFO common:common.py:198 0 atoms have radius differences > 0 208s INFO common:common.py:198 0 atoms have radius differences > 0.01 208s PASSED [ 97%] 208s tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] 208s -------------------------------- live log call --------------------------------- 208s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_assign0/output.log 208s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 208s 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). 208s 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). 208s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 208s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 209s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 209s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 209s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 209s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 209s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 209s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 209s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 209s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 209s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 209s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 209s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 209s INFO common:common.py:198 0 atoms have position differences > 0 209s INFO common:common.py:198 0 atoms have position differences > 0.01 209s INFO common:common.py:198 0 atoms have charge differences > 0 209s INFO common:common.py:198 0 atoms have charge differences > 0.01 209s INFO common:common.py:198 0 atoms have radius differences > 0 209s INFO common:common.py:198 0 atoms have radius differences > 0.01 209s PASSED [ 97%] 209s tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] 209s -------------------------------- live log call --------------------------------- 209s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_nodebu0/output.log 209s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 209s 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). 209s 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). 209s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 209s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 209s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 209s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 209s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 209s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 209s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 209s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 209s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 209s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 209s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 209s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 209s INFO pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization... 209s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 209s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 209s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 209s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 209s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 209s INFO common:common.py:198 0 atoms have position differences > 0 209s INFO common:common.py:198 0 atoms have position differences > 0.01 209s INFO common:common.py:198 0 atoms have charge differences > 0 209s INFO common:common.py:198 0 atoms have charge differences > 0.01 209s INFO common:common.py:198 0 atoms have radius differences > 0 209s INFO common:common.py:198 0 atoms have radius differences > 0.01 209s PASSED [ 98%] 209s tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] 209s -------------------------------- live log call --------------------------------- 209s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_chain_0/output.log 209s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 209s 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). 209s 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). 209s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 209s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 209s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 209s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 209s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 209s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 209s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 209s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 209s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 209s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 209s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 209s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 209s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 209s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 209s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 209s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 209s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 209s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 209s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 209s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 210s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 210s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 213s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 213s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 213s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 213s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 213s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 213s WARNING common:common.py:186 6 atoms have position differences > 0 213s INFO common:common.py:198 0 atoms have position differences > 0.01 213s INFO common:common.py:198 0 atoms have charge differences > 0 213s INFO common:common.py:198 0 atoms have charge differences > 0.01 213s INFO common:common.py:198 0 atoms have radius differences > 0 213s INFO common:common.py:198 0 atoms have radius differences > 0.01 213s PASSED [ 98%] 213s tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] 213s -------------------------------- live log call --------------------------------- 213s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_neutra0/output.log 213s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 213s 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). 213s 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). 213s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 213s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 213s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 213s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 213s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 213s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 213s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 213s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 213s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 213s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 213s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 213s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 213s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 213s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 213s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 213s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 213s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 213s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 213s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 213s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 214s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 214s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 217s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 217s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 217s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 217s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 217s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 217s WARNING common:common.py:186 6 atoms have position differences > 0 217s INFO common:common.py:198 0 atoms have position differences > 0.01 217s INFO common:common.py:198 0 atoms have charge differences > 0 217s INFO common:common.py:198 0 atoms have charge differences > 0.01 217s INFO common:common.py:198 0 atoms have radius differences > 0 217s INFO common:common.py:198 0 atoms have radius differences > 0.01 217s PASSED [ 98%] 217s tests/regression_test.py::test_other_options[1AFS drop-water AMBER] 217s -------------------------------- live log call --------------------------------- 217s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_drop_w0/output.log 217s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 217s 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). 217s 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). 217s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 217s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 217s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 217s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 217s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 217s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms. 217s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 217s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 217s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 217s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 217s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 217s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 217s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 217s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 217s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 217s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 217s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 217s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 217s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 217s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 217s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 218s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 218s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 220s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 220s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 220s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 220s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 220s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 220s WARNING common:common.py:186 6 atoms have position differences > 0 220s INFO common:common.py:198 0 atoms have position differences > 0.01 220s INFO common:common.py:198 0 atoms have charge differences > 0 220s INFO common:common.py:198 0 atoms have charge differences > 0.01 220s INFO common:common.py:198 0 atoms have radius differences > 0 220s INFO common:common.py:198 0 atoms have radius differences > 0.01 220s PASSED [ 99%] 220s tests/regression_test.py::test_other_options[1AFS userff usernames whitespace] 220s -------------------------------- live log call --------------------------------- 220s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_userff0/output.log 220s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 220s 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). 220s 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). 220s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 220s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 220s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 220s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 220s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 220s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 220s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 220s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 220s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 220s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 220s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 220s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 220s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 220s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 220s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 220s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 220s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 220s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 220s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 220s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 221s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 222s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 224s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 224s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 224s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 224s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 224s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 224s WARNING common:common.py:186 6 atoms have position differences > 0 224s INFO common:common.py:198 0 atoms have position differences > 0.01 224s INFO common:common.py:198 0 atoms have charge differences > 0 224s INFO common:common.py:198 0 atoms have charge differences > 0.01 224s INFO common:common.py:198 0 atoms have radius differences > 0 224s INFO common:common.py:198 0 atoms have radius differences > 0.01 224s PASSED [ 99%] 224s tests/test_version.py::test_version_exists PASSED [ 99%] 224s tests/test_version.py::test_version PASSED [100%] 224s 224s =============================== warnings summary =============================== 224s ../../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37 224s /usr/lib/python3/dist-packages/dateutil/tz/tz.py:37: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC). 224s EPOCH = datetime.datetime.utcfromtimestamp(0) 224s 224s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 224s ============ 92 passed, 220 skipped, 4 xfailed, 1 warning in 57.47s ============ 225s autopkgtest [12:21:21]: test command1: -----------------------] 225s command1 PASS 225s autopkgtest [12:21:21]: test command1: - - - - - - - - - - results - - - - - - - - - - 226s autopkgtest [12:21:22]: @@@@@@@@@@@@@@@@@@@@ summary 226s installation-test PASS 226s pdb2pka-test PASS 226s command1 PASS 239s Creating nova instance adt-noble-s390x-pdb2pqr-20240322-121736-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240321.img (UUID f7ee8f0f-480f-4014-94f0-3be2a19e259d)...