0s autopkgtest [15:08:50]: starting date and time: 2024-03-22 15:08:50+0000 0s autopkgtest [15:08:50]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [15:08:50]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ongtjjdm/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-2@bos02-ppc64el-1.secgroup --name adt-noble-ppc64el-pdb2pqr-20240322-150849-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 123s autopkgtest [15:10:53]: testbed dpkg architecture: ppc64el 123s autopkgtest [15:10:53]: testbed apt version: 2.7.12 123s autopkgtest [15:10:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 124s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 124s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3809 kB] 125s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 125s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [54.0 kB] 125s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [498 kB] 126s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [672 kB] 126s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 126s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 126s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 126s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4130 kB] 127s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 127s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [58.3 kB] 127s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 129s Fetched 9358 kB in 4s (2409 kB/s) 130s Reading package lists... 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 133s Calculating upgrade... 133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s Reading package lists... 134s Building dependency tree... 134s Reading state information... 134s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s sh: Attempting to set up Debian/Ubuntu apt sources automatically 135s sh: Distribution appears to be Ubuntu 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s eatmydata is already the newest version (131-1). 136s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 137s dbus is already the newest version (1.14.10-4ubuntu1). 137s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s rng-tools-debian is already the newest version (2.4). 137s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 137s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s The following packages will be REMOVED: 137s cloud-init* python3-configobj* python3-debconf* 138s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 138s After this operation, 3256 kB disk space will be freed. 138s (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 ... 70156 files and directories currently installed.) 138s Removing cloud-init (24.1.2-0ubuntu1) ... 138s Removing python3-configobj (5.0.8-3) ... 138s Removing python3-debconf (1.5.86) ... 138s Processing triggers for man-db (2.12.0-3) ... 139s (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 ... 69767 files and directories currently installed.) 139s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 140s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 140s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 140s invoke-rc.d: policy-rc.d denied execution of try-restart. 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s linux-generic is already the newest version (6.8.0-11.11+1). 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 141s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 141s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 143s Reading package lists... 143s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Calculating upgrade... 144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 145s autopkgtest [15:11:15]: rebooting testbed after setup commands that affected boot 309s autopkgtest [15:13:59]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 312s autopkgtest [15:14:02]: @@@@@@@@@@@@@@@@@@@@ apt-source pdb2pqr 316s Get:1 http://ftpmaster.internal/ubuntu noble/universe pdb2pqr 3.6.1+dfsg-1 (dsc) [1860 B] 316s Get:2 http://ftpmaster.internal/ubuntu noble/universe pdb2pqr 3.6.1+dfsg-1 (tar) [7570 kB] 316s Get:3 http://ftpmaster.internal/ubuntu noble/universe pdb2pqr 3.6.1+dfsg-1 (diff) [9876 B] 316s gpgv: Signature made Mon Jun 12 17:36:50 2023 UTC 316s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 316s gpgv: Can't check signature: No public key 316s dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found 317s autopkgtest [15:14:07]: testing package pdb2pqr version 3.6.1+dfsg-1 317s autopkgtest [15:14:07]: build not needed 331s autopkgtest [15:14:21]: test installation-test: preparing testbed 332s Reading package lists... 332s Building dependency tree... 332s Reading state information... 333s Starting pkgProblemResolver with broken count: 0 333s Starting 2 pkgProblemResolver with broken count: 0 333s Done 333s The following additional packages will be installed: 333s docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr python3-docutils 333s python3-numpy python3-pdb2pqr python3-pdbx python3-propka python3-roman 333s sgml-base xml-core 333s Suggested packages: 333s apbs docutils-doc fonts-linuxlibertine | ttf-linux-libertine 333s texlive-lang-french texlive-latex-base texlive-latex-recommended gcc 333s gfortran python3-dev python3-pytest python-pdbx-doc python-propka-doc 333s sgml-base-doc debhelper 333s Recommended packages: 333s libpaper-utils python3-pil 333s The following NEW packages will be installed: 333s autopkgtest-satdep docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr 333s python3-docutils python3-numpy python3-pdb2pqr python3-pdbx python3-propka 333s python3-roman sgml-base xml-core 333s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 333s Need to get 10.0 MB/10.0 MB of archives. 333s After this operation, 50.8 MB of additional disk space will be used. 333s Get:1 /tmp/autopkgtest.RB36Ap/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [704 B] 333s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el sgml-base all 1.31 [11.4 kB] 333s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el xml-core all 0.19 [20.3 kB] 333s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el docutils-common all 0.20.1+dfsg-3 [132 kB] 334s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 334s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 335s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 337s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB] 340s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-roman all 3.3-3 [9632 B] 340s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-docutils all 0.20.1+dfsg-3 [393 kB] 341s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pdbx all 2.0.1-2 [16.5 kB] 341s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-propka all 3.5.1-1 [85.5 kB] 341s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pdb2pqr all 3.6.1+dfsg-1 [145 kB] 341s Get:14 http://ftpmaster.internal/ubuntu noble/universe ppc64el pdb2pqr all 3.6.1+dfsg-1 [10.4 kB] 341s Fetched 10.0 MB in 8s (1276 kB/s) 341s Selecting previously unselected package sgml-base. 341s (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 ... 69712 files and directories currently installed.) 341s Preparing to unpack .../00-sgml-base_1.31_all.deb ... 341s Unpacking sgml-base (1.31) ... 341s Selecting previously unselected package xml-core. 341s Preparing to unpack .../01-xml-core_0.19_all.deb ... 341s Unpacking xml-core (0.19) ... 341s Selecting previously unselected package docutils-common. 341s Preparing to unpack .../02-docutils-common_0.20.1+dfsg-3_all.deb ... 341s Unpacking docutils-common (0.20.1+dfsg-3) ... 341s Selecting previously unselected package libblas3:ppc64el. 341s Preparing to unpack .../03-libblas3_3.12.0-3_ppc64el.deb ... 341s Unpacking libblas3:ppc64el (3.12.0-3) ... 341s Selecting previously unselected package libgfortran5:ppc64el. 341s Preparing to unpack .../04-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 341s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 341s Selecting previously unselected package liblapack3:ppc64el. 341s Preparing to unpack .../05-liblapack3_3.12.0-3_ppc64el.deb ... 341s Unpacking liblapack3:ppc64el (3.12.0-3) ... 341s Selecting previously unselected package python3-numpy. 341s Preparing to unpack .../06-python3-numpy_1%3a1.24.2-2_ppc64el.deb ... 341s Unpacking python3-numpy (1:1.24.2-2) ... 342s Selecting previously unselected package python3-roman. 342s Preparing to unpack .../07-python3-roman_3.3-3_all.deb ... 342s Unpacking python3-roman (3.3-3) ... 342s Selecting previously unselected package python3-docutils. 342s Preparing to unpack .../08-python3-docutils_0.20.1+dfsg-3_all.deb ... 342s Unpacking python3-docutils (0.20.1+dfsg-3) ... 342s Selecting previously unselected package python3-pdbx. 342s Preparing to unpack .../09-python3-pdbx_2.0.1-2_all.deb ... 342s Unpacking python3-pdbx (2.0.1-2) ... 342s Selecting previously unselected package python3-propka. 342s Preparing to unpack .../10-python3-propka_3.5.1-1_all.deb ... 342s Unpacking python3-propka (3.5.1-1) ... 342s Selecting previously unselected package python3-pdb2pqr. 342s Preparing to unpack .../11-python3-pdb2pqr_3.6.1+dfsg-1_all.deb ... 342s Unpacking python3-pdb2pqr (3.6.1+dfsg-1) ... 342s Selecting previously unselected package pdb2pqr. 342s Preparing to unpack .../12-pdb2pqr_3.6.1+dfsg-1_all.deb ... 342s Unpacking pdb2pqr (3.6.1+dfsg-1) ... 342s Selecting previously unselected package autopkgtest-satdep. 342s Preparing to unpack .../13-1-autopkgtest-satdep.deb ... 342s Unpacking autopkgtest-satdep (0) ... 342s Setting up python3-propka (3.5.1-1) ... 342s Setting up python3-pdbx (2.0.1-2) ... 342s Setting up python3-roman (3.3-3) ... 342s Setting up libblas3:ppc64el (3.12.0-3) ... 342s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 342s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 342s Setting up sgml-base (1.31) ... 342s Setting up liblapack3:ppc64el (3.12.0-3) ... 342s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 342s Setting up python3-numpy (1:1.24.2-2) ... 344s Setting up xml-core (0.19) ... 344s Processing triggers for libc-bin (2.39-0ubuntu2) ... 345s Processing triggers for man-db (2.12.0-3) ... 345s Processing triggers for sgml-base (1.31) ... 345s Setting up docutils-common (0.20.1+dfsg-3) ... 345s Processing triggers for sgml-base (1.31) ... 345s Setting up python3-docutils (0.20.1+dfsg-3) ... 346s Setting up python3-pdb2pqr (3.6.1+dfsg-1) ... 346s Setting up pdb2pqr (3.6.1+dfsg-1) ... 346s Setting up autopkgtest-satdep (0) ... 348s (Reading database ... 71226 files and directories currently installed.) 348s Removing autopkgtest-satdep (0) ... 349s autopkgtest [15:14:39]: test installation-test: [----------------------- 349s Run pdb2pqr... 349s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 349s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 349s 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). 349s INFO:Checking and transforming input arguments. 349s INFO:Loading topology files. 349s INFO:Loading molecule: examples/1a1p/1a1p.pdb 349s INFO:Setting up molecule. 350s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 350s INFO:Created biomolecule object with 14 residues and 208 atoms. 350s INFO:Setting termini states for biomolecule chains. 350s INFO:Loading forcefield. 350s INFO:Loading hydrogen topology definitions. 350s INFO:This biomolecule is clean. No repair needed. 350s INFO:Updating disulfide bridges. 350s INFO:Debumping biomolecule. 350s INFO:Adding hydrogens to biomolecule. 350s INFO:Debumping biomolecule (again). 350s INFO:Optimizing hydrogen bonds 350s INFO:Applying force field to biomolecule states. 350s INFO:Regenerating headers. 350s INFO:Regenerating PDB lines. 350s WARNING:Ignoring 852 header lines in output. 350s WARNING:Ignoring 3 missing lines in output. 350s autopkgtest [15:14:40]: test installation-test: -----------------------] 350s autopkgtest [15:14:40]: test installation-test: - - - - - - - - - - results - - - - - - - - - - 350s installation-test PASS 351s autopkgtest [15:14:41]: test pdb2pka-test: preparing testbed 353s Reading package lists... 353s Building dependency tree... 353s Reading state information... 353s Starting pkgProblemResolver with broken count: 0 353s Starting 2 pkgProblemResolver with broken count: 0 353s Done 353s The following additional packages will be installed: 353s fonts-font-awesome fonts-lato libjs-jquery libjs-sphinxdoc libjs-underscore 353s pdb2pqr-doc sphinx-rtd-theme-common 353s Recommended packages: 353s javascript-common 353s The following NEW packages will be installed: 353s autopkgtest-satdep fonts-font-awesome fonts-lato libjs-jquery 353s libjs-sphinxdoc libjs-underscore pdb2pqr-doc sphinx-rtd-theme-common 353s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 353s Need to get 5162 kB/5162 kB of archives. 353s After this operation, 20.1 MB of additional disk space will be used. 353s Get:1 /tmp/autopkgtest.RB36Ap/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B] 354s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-lato all 2.015-1 [2781 kB] 355s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 355s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 355s Get:5 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 355s Get:6 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-sphinxdoc all 7.2.6-4 [149 kB] 355s Get:7 http://ftpmaster.internal/ubuntu noble/main ppc64el sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB] 356s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el pdb2pqr-doc all 3.6.1+dfsg-1 [258 kB] 356s Fetched 5162 kB in 2s (2374 kB/s) 356s Selecting previously unselected package fonts-lato. 356s (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 ... 71226 files and directories currently installed.) 356s Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... 356s Unpacking fonts-lato (2.015-1) ... 356s Selecting previously unselected package fonts-font-awesome. 356s Preparing to unpack .../1-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 356s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 356s Selecting previously unselected package libjs-jquery. 356s Preparing to unpack .../2-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 356s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 356s Selecting previously unselected package libjs-underscore. 356s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 356s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 356s Selecting previously unselected package libjs-sphinxdoc. 356s Preparing to unpack .../4-libjs-sphinxdoc_7.2.6-4_all.deb ... 356s Unpacking libjs-sphinxdoc (7.2.6-4) ... 356s Selecting previously unselected package sphinx-rtd-theme-common. 356s Preparing to unpack .../5-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... 356s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 356s Selecting previously unselected package pdb2pqr-doc. 356s Preparing to unpack .../6-pdb2pqr-doc_3.6.1+dfsg-1_all.deb ... 356s Unpacking pdb2pqr-doc (3.6.1+dfsg-1) ... 356s Selecting previously unselected package autopkgtest-satdep. 356s Preparing to unpack .../7-2-autopkgtest-satdep.deb ... 356s Unpacking autopkgtest-satdep (0) ... 356s Setting up fonts-lato (2.015-1) ... 356s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 356s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 356s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 356s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 356s Setting up libjs-sphinxdoc (7.2.6-4) ... 356s Setting up pdb2pqr-doc (3.6.1+dfsg-1) ... 356s Setting up autopkgtest-satdep (0) ... 359s (Reading database ... 71560 files and directories currently installed.) 359s Removing autopkgtest-satdep (0) ... 359s autopkgtest [15:14:49]: test pdb2pka-test: [----------------------- 360s Run pdb2pqr... 360s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 360s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 360s 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). 360s INFO:Checking and transforming input arguments. 360s INFO:Loading topology files. 360s INFO:Loading molecule: 1a1p/1a1p.pdb 360s INFO:Setting up molecule. 360s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 360s INFO:Created biomolecule object with 14 residues and 208 atoms. 360s INFO:Setting termini states for biomolecule chains. 360s INFO:Loading forcefield. 360s INFO:Loading hydrogen topology definitions. 360s INFO:This biomolecule is clean. No repair needed. 360s INFO:Updating disulfide bridges. 360s INFO:Debumping biomolecule. 360s INFO:Adding hydrogens to biomolecule. 360s INFO:Debumping biomolecule (again). 360s INFO:Optimizing hydrogen bonds 360s INFO:Applying force field to biomolecule states. 360s INFO:Regenerating headers. 360s INFO:Regenerating PDB lines. 360s WARNING:Ignoring 852 header lines in output. 360s WARNING:Ignoring 3 missing lines in output. 360s autopkgtest [15:14:50]: test pdb2pka-test: -----------------------] 361s autopkgtest [15:14:51]: test pdb2pka-test: - - - - - - - - - - results - - - - - - - - - - 361s pdb2pka-test PASS 361s autopkgtest [15:14:51]: test command1: preparing testbed 364s Reading package lists... 364s Building dependency tree... 364s Reading state information... 364s Starting pkgProblemResolver with broken count: 0 364s Starting 2 pkgProblemResolver with broken count: 0 364s Done 365s The following additional packages will be installed: 365s python3-dateutil python3-iniconfig python3-packaging python3-pandas 365s python3-pandas-lib python3-pluggy python3-pytest python3-testfixtures 365s Suggested packages: 365s python-pandas-doc python3-statsmodels python-testfixtures-doc 365s Recommended packages: 365s python3-scipy python3-matplotlib python3-bottleneck python3-numexpr 365s python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml 365s python3-tables 365s The following NEW packages will be installed: 365s autopkgtest-satdep python3-dateutil python3-iniconfig python3-packaging 365s python3-pandas python3-pandas-lib python3-pluggy python3-pytest 365s python3-testfixtures 365s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 365s Need to get 12.4 MB/12.4 MB of archives. 365s After this operation, 78.7 MB of additional disk space will be used. 365s Get:1 /tmp/autopkgtest.RB36Ap/3-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [744 B] 365s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-dateutil all 2.8.2-3 [79.2 kB] 365s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 365s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-packaging all 23.2-1 [40.6 kB] 365s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pandas-lib ppc64el 2.1.4+dfsg-4ubuntu2 [8837 kB] 368s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 368s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pluggy all 1.4.0-1 [20.4 kB] 368s Get:8 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pytest all 7.4.4-1 [305 kB] 369s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-testfixtures all 8.1.0-1 [73.5 kB] 369s Fetched 12.4 MB in 4s (3283 kB/s) 369s Selecting previously unselected package python3-dateutil. 369s (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 ... 71560 files and directories currently installed.) 369s Preparing to unpack .../0-python3-dateutil_2.8.2-3_all.deb ... 369s Unpacking python3-dateutil (2.8.2-3) ... 369s Selecting previously unselected package python3-iniconfig. 369s Preparing to unpack .../1-python3-iniconfig_1.1.1-2_all.deb ... 369s Unpacking python3-iniconfig (1.1.1-2) ... 369s Selecting previously unselected package python3-packaging. 369s Preparing to unpack .../2-python3-packaging_23.2-1_all.deb ... 369s Unpacking python3-packaging (23.2-1) ... 369s Selecting previously unselected package python3-pandas-lib:ppc64el. 369s Preparing to unpack .../3-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_ppc64el.deb ... 369s Unpacking python3-pandas-lib:ppc64el (2.1.4+dfsg-4ubuntu2) ... 369s Selecting previously unselected package python3-pandas. 369s Preparing to unpack .../4-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 369s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 370s Selecting previously unselected package python3-pluggy. 370s Preparing to unpack .../5-python3-pluggy_1.4.0-1_all.deb ... 370s Unpacking python3-pluggy (1.4.0-1) ... 370s Selecting previously unselected package python3-pytest. 370s Preparing to unpack .../6-python3-pytest_7.4.4-1_all.deb ... 370s Unpacking python3-pytest (7.4.4-1) ... 370s Selecting previously unselected package python3-testfixtures. 370s Preparing to unpack .../7-python3-testfixtures_8.1.0-1_all.deb ... 370s Unpacking python3-testfixtures (8.1.0-1) ... 370s Selecting previously unselected package autopkgtest-satdep. 370s Preparing to unpack .../8-3-autopkgtest-satdep.deb ... 370s Unpacking autopkgtest-satdep (0) ... 370s Setting up python3-iniconfig (1.1.1-2) ... 370s Setting up python3-pandas-lib:ppc64el (2.1.4+dfsg-4ubuntu2) ... 370s Setting up python3-testfixtures (8.1.0-1) ... 370s Setting up python3-packaging (23.2-1) ... 370s Setting up python3-pluggy (1.4.0-1) ... 370s Setting up python3-dateutil (2.8.2-3) ... 370s Setting up python3-pytest (7.4.4-1) ... 371s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 375s Setting up autopkgtest-satdep (0) ... 375s Processing triggers for man-db (2.12.0-3) ... 378s (Reading database ... 73573 files and directories currently installed.) 378s Removing autopkgtest-satdep (0) ... 379s autopkgtest [15:15:09]: test command1: pytest-3 379s autopkgtest [15:15:09]: test command1: [----------------------- 380s ============================= test session starts ============================== 380s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 380s rootdir: /tmp/autopkgtest.RB36Ap/build.sMY/src 380s configfile: pytest.ini 380s 380s ----------------------------- live log collection ------------------------------ 380s WARNING py.warnings:warnings.py:110 /tmp/autopkgtest.RB36Ap/build.sMY/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 380s @pytest.mark.long_test 380s 380s ERROR regression_test:regression_test.py:173 Need to reinstate the --apbs-input test with a temporary directory as path 380s collected 316 items 380s 380s tests/core_test.py::test_short_pdb[1K1I] SKIPPED (not running tests ...) [ 0%] 380s tests/core_test.py::test_short_pdb[4E8M] SKIPPED (not running tests ...) [ 0%] 380s tests/core_test.py::test_short_pdb[5D8V] SKIPPED (not running tests ...) [ 0%] 380s tests/core_test.py::test_short_pdb[1NAJ] SKIPPED (not running tests ...) [ 1%] 380s tests/core_test.py::test_short_pdb[1AQO] SKIPPED (not running tests ...) [ 1%] 380s tests/core_test.py::test_short_pdb[1FAS] SKIPPED (not running tests ...) [ 1%] 380s tests/core_test.py::test_short_pdb[4UN3] SKIPPED (not running tests ...) [ 2%] 380s tests/core_test.py::test_short_pdb[7BNA] SKIPPED (not running tests ...) [ 2%] 380s tests/core_test.py::test_basic_cif[1K1I] SKIPPED (not running tests ...) [ 2%] 380s tests/core_test.py::test_basic_cif[4E8M] SKIPPED (not running tests ...) [ 3%] 380s tests/core_test.py::test_basic_cif[5D8V] SKIPPED (not running tests ...) [ 3%] 380s tests/core_test.py::test_basic_cif[1NAJ] SKIPPED (not running tests ...) [ 3%] 380s tests/core_test.py::test_basic_cif[1AQO] SKIPPED (not running tests ...) [ 4%] 380s tests/core_test.py::test_basic_cif[1FAS] SKIPPED (not running tests ...) [ 4%] 380s tests/core_test.py::test_basic_cif[4UN3] SKIPPED (not running tests ...) [ 4%] 380s tests/core_test.py::test_basic_cif[7BNA] SKIPPED (not running tests ...) [ 5%] 380s tests/core_test.py::test_long_pdb[2PII] SKIPPED (not running tests r...) [ 5%] 380s tests/core_test.py::test_long_pdb[2XXC] SKIPPED (not running tests r...) [ 5%] 380s tests/core_test.py::test_long_pdb[2HC8] SKIPPED (not running tests r...) [ 6%] 380s tests/core_test.py::test_long_pdb[3LS0] SKIPPED (not running tests r...) [ 6%] 380s tests/core_test.py::test_long_pdb[2HP7] SKIPPED (not running tests r...) [ 6%] 380s tests/core_test.py::test_long_pdb[4G3O] SKIPPED (not running tests r...) [ 6%] 380s tests/core_test.py::test_long_pdb[3RFI] SKIPPED (not running tests r...) [ 7%] 380s tests/core_test.py::test_long_pdb[4CRH] SKIPPED (not running tests r...) [ 7%] 380s tests/core_test.py::test_long_pdb[1NH9] SKIPPED (not running tests r...) [ 7%] 380s tests/core_test.py::test_long_pdb[1SJV] SKIPPED (not running tests r...) [ 8%] 380s tests/core_test.py::test_long_pdb[2PMR] SKIPPED (not running tests r...) [ 8%] 380s tests/core_test.py::test_long_pdb[2OO2] SKIPPED (not running tests r...) [ 8%] 380s tests/core_test.py::test_long_pdb[3HRN] SKIPPED (not running tests r...) [ 9%] 380s tests/core_test.py::test_long_pdb[2SFA] SKIPPED (not running tests r...) [ 9%] 380s tests/core_test.py::test_long_pdb[1HUF] SKIPPED (not running tests r...) [ 9%] 380s tests/core_test.py::test_long_pdb[2ESK] SKIPPED (not running tests r...) [ 10%] 380s tests/core_test.py::test_long_pdb[3HRO] SKIPPED (not running tests r...) [ 10%] 380s tests/core_test.py::test_long_pdb[4O7Q] SKIPPED (not running tests r...) [ 10%] 380s tests/core_test.py::test_long_pdb[1IS5] SKIPPED (not running tests r...) [ 11%] 380s tests/core_test.py::test_long_pdb[2OCH] SKIPPED (not running tests r...) [ 11%] 380s tests/core_test.py::test_long_pdb[2IBL] SKIPPED (not running tests r...) [ 11%] 380s tests/core_test.py::test_long_pdb[3I35] SKIPPED (not running tests r...) [ 12%] 380s tests/core_test.py::test_long_pdb[4CFI] SKIPPED (not running tests r...) [ 12%] 380s tests/core_test.py::test_long_pdb[1TEN] SKIPPED (not running tests r...) [ 12%] 380s tests/core_test.py::test_long_pdb[2IWN] SKIPPED (not running tests r...) [ 12%] 380s tests/core_test.py::test_long_pdb[1PZC] SKIPPED (not running tests r...) [ 13%] 380s tests/core_test.py::test_long_pdb[1OX3] SKIPPED (not running tests r...) [ 13%] 380s tests/core_test.py::test_long_pdb[3LLB] SKIPPED (not running tests r...) [ 13%] 380s tests/core_test.py::test_long_pdb[5EE2] SKIPPED (not running tests r...) [ 14%] 380s tests/core_test.py::test_long_pdb[1TGN] SKIPPED (not running tests r...) [ 14%] 380s tests/core_test.py::test_long_pdb[1L2P] SKIPPED (not running tests r...) [ 14%] 380s tests/core_test.py::test_long_pdb[4EO0] SKIPPED (not running tests r...) [ 15%] 380s tests/core_test.py::test_long_pdb[4CVD] SKIPPED (not running tests r...) [ 15%] 380s tests/core_test.py::test_long_pdb[2EBB] SKIPPED (not running tests r...) [ 15%] 380s tests/core_test.py::test_long_pdb[4YPC] SKIPPED (not running tests r...) [ 16%] 380s tests/core_test.py::test_long_pdb[2PTV] SKIPPED (not running tests r...) [ 16%] 380s tests/core_test.py::test_long_pdb[1FAS] SKIPPED (not running tests r...) [ 16%] 380s tests/core_test.py::test_long_pdb[2CKX] SKIPPED (not running tests r...) [ 17%] 380s tests/core_test.py::test_long_pdb[2J70] SKIPPED (not running tests r...) [ 17%] 380s tests/core_test.py::test_long_pdb[2NWD] SKIPPED (not running tests r...) [ 17%] 380s tests/core_test.py::test_long_pdb[5V0O] SKIPPED (not running tests r...) [ 18%] 380s tests/core_test.py::test_long_pdb[2G7O] SKIPPED (not running tests r...) [ 18%] 380s tests/core_test.py::test_long_pdb[2CJJ] SKIPPED (not running tests r...) [ 18%] 380s tests/core_test.py::test_long_pdb[2NYC] SKIPPED (not running tests r...) [ 18%] 380s tests/core_test.py::test_long_pdb[4OSN] SKIPPED (not running tests r...) [ 19%] 380s tests/core_test.py::test_long_pdb[3V1A] SKIPPED (not running tests r...) [ 19%] 380s tests/core_test.py::test_long_pdb[3KT2] SKIPPED (not running tests r...) [ 19%] 380s tests/core_test.py::test_long_pdb[3TSV] SKIPPED (not running tests r...) [ 20%] 380s tests/core_test.py::test_long_pdb[1ZLM] SKIPPED (not running tests r...) [ 20%] 380s tests/core_test.py::test_long_pdb[1YQB] SKIPPED (not running tests r...) [ 20%] 380s tests/core_test.py::test_long_pdb[3ZZP] SKIPPED (not running tests r...) [ 21%] 380s tests/core_test.py::test_long_pdb[3I1G] SKIPPED (not running tests r...) [ 21%] 380s tests/core_test.py::test_long_pdb[3ISU] SKIPPED (not running tests r...) [ 21%] 380s tests/core_test.py::test_long_pdb[2ERW] SKIPPED (not running tests r...) [ 22%] 380s tests/core_test.py::test_long_pdb[3CP1] SKIPPED (not running tests r...) [ 22%] 380s tests/core_test.py::test_long_pdb[1PHT] SKIPPED (not running tests r...) [ 22%] 380s tests/core_test.py::test_long_pdb[4GQM] SKIPPED (not running tests r...) [ 23%] 380s tests/core_test.py::test_long_pdb[1NOA] SKIPPED (not running tests r...) [ 23%] 380s tests/core_test.py::test_long_pdb[1X91] SKIPPED (not running tests r...) [ 23%] 380s tests/core_test.py::test_long_pdb[3QE1] SKIPPED (not running tests r...) [ 24%] 380s tests/core_test.py::test_long_pdb[3SO2] SKIPPED (not running tests r...) [ 24%] 380s tests/core_test.py::test_long_pdb[4ZQA] SKIPPED (not running tests r...) [ 24%] 380s tests/core_test.py::test_long_pdb[1TUD] SKIPPED (not running tests r...) [ 25%] 380s tests/core_test.py::test_long_pdb[4S11] SKIPPED (not running tests r...) [ 25%] 380s tests/core_test.py::test_long_pdb[2J6B] SKIPPED (not running tests r...) [ 25%] 380s tests/core_test.py::test_long_pdb[3LMO] SKIPPED (not running tests r...) [ 25%] 380s tests/core_test.py::test_long_pdb[3C97] SKIPPED (not running tests r...) [ 26%] 380s tests/core_test.py::test_long_pdb[3JTE] SKIPPED (not running tests r...) [ 26%] 380s tests/core_test.py::test_long_pdb[1Z0P] SKIPPED (not running tests r...) [ 26%] 380s tests/core_test.py::test_long_pdb[5DV8] SKIPPED (not running tests r...) [ 27%] 380s tests/core_test.py::test_long_pdb[1R7J] SKIPPED (not running tests r...) [ 27%] 380s tests/core_test.py::test_long_pdb[1OA4] SKIPPED (not running tests r...) [ 27%] 380s tests/core_test.py::test_long_pdb[3T8R] SKIPPED (not running tests r...) [ 28%] 380s tests/core_test.py::test_long_pdb[3LAA] SKIPPED (not running tests r...) [ 28%] 380s tests/core_test.py::test_long_pdb[3NGP] SKIPPED (not running tests r...) [ 28%] 380s tests/core_test.py::test_long_pdb[2QVO] SKIPPED (not running tests r...) [ 29%] 380s tests/core_test.py::test_long_pdb[1RJ1] SKIPPED (not running tests r...) [ 29%] 380s tests/core_test.py::test_long_pdb[3CE7] SKIPPED (not running tests r...) [ 29%] 380s tests/core_test.py::test_long_pdb[4HTI] SKIPPED (not running tests r...) [ 30%] 380s tests/core_test.py::test_long_pdb[1J2A] SKIPPED (not running tests r...) [ 30%] 380s tests/core_test.py::test_long_pdb[1E7G] SKIPPED (not running tests r...) [ 30%] 380s tests/core_test.py::test_long_pdb[4GS3] SKIPPED (not running tests r...) [ 31%] 380s tests/core_test.py::test_long_pdb[1ZZK] SKIPPED (not running tests r...) [ 31%] 380s tests/core_test.py::test_long_pdb[4GMQ] SKIPPED (not running tests r...) [ 31%] 380s tests/core_test.py::test_long_pdb[2X4J] SKIPPED (not running tests r...) [ 31%] 380s tests/core_test.py::test_long_pdb[1DUP] SKIPPED (not running tests r...) [ 32%] 380s tests/core_test.py::test_long_pdb[3B7H] SKIPPED (not running tests r...) [ 32%] 380s tests/core_test.py::test_long_pdb[3RVC] SKIPPED (not running tests r...) [ 32%] 380s tests/core_test.py::test_long_pdb[3CSR] SKIPPED (not running tests r...) [ 33%] 380s tests/core_test.py::test_long_pdb[3FH2] SKIPPED (not running tests r...) [ 33%] 380s tests/core_test.py::test_long_pdb[4L9E] SKIPPED (not running tests r...) [ 33%] 380s tests/core_test.py::test_long_pdb[2R6Q] SKIPPED (not running tests r...) [ 34%] 380s tests/core_test.py::test_long_pdb[3CQT] SKIPPED (not running tests r...) [ 34%] 380s tests/core_test.py::test_long_pdb[1RIS] SKIPPED (not running tests r...) [ 34%] 380s tests/core_test.py::test_long_pdb[1USM] SKIPPED (not running tests r...) [ 35%] 380s tests/core_test.py::test_long_pdb[2D8E] SKIPPED (not running tests r...) [ 35%] 380s tests/core_test.py::test_long_pdb[1PGX] SKIPPED (not running tests r...) [ 35%] 380s tests/core_test.py::test_long_pdb[1R5Q] SKIPPED (not running tests r...) [ 36%] 380s tests/core_test.py::test_long_pdb[2QBV] SKIPPED (not running tests r...) [ 36%] 380s tests/core_test.py::test_long_pdb[2CMP] SKIPPED (not running tests r...) [ 36%] 380s tests/core_test.py::test_long_pdb[2SGA] SKIPPED (not running tests r...) [ 37%] 380s tests/core_test.py::test_long_pdb[1NKD] SKIPPED (not running tests r...) [ 37%] 380s tests/core_test.py::test_long_pdb[1YZM] SKIPPED (not running tests r...) [ 37%] 380s tests/core_test.py::test_long_pdb[4IL7] SKIPPED (not running tests r...) [ 37%] 380s tests/core_test.py::test_long_pdb[2VWR] SKIPPED (not running tests r...) [ 38%] 380s tests/core_test.py::test_long_pdb[1KFN] SKIPPED (not running tests r...) [ 38%] 380s tests/core_test.py::test_long_pdb[2TGI] SKIPPED (not running tests r...) [ 38%] 380s tests/core_test.py::test_long_pdb[1HOE] SKIPPED (not running tests r...) [ 39%] 380s tests/core_test.py::test_long_pdb[1USE] SKIPPED (not running tests r...) [ 39%] 380s tests/core_test.py::test_long_pdb[3US6] SKIPPED (not running tests r...) [ 39%] 380s tests/core_test.py::test_long_pdb[3KZD] SKIPPED (not running tests r...) [ 40%] 380s tests/core_test.py::test_long_pdb[1DF4] SKIPPED (not running tests r...) [ 40%] 380s tests/core_test.py::test_long_pdb[3T1S] SKIPPED (not running tests r...) [ 40%] 380s tests/core_test.py::test_long_pdb[1B0X] SKIPPED (not running tests r...) [ 41%] 380s tests/core_test.py::test_long_pdb[1TQG] SKIPPED (not running tests r...) [ 41%] 380s tests/core_test.py::test_long_pdb[1P9I] SKIPPED (not running tests r...) [ 41%] 380s tests/core_test.py::test_long_pdb[1JQ0] SKIPPED (not running tests r...) [ 42%] 380s tests/core_test.py::test_long_pdb[4PGR] SKIPPED (not running tests r...) [ 42%] 380s tests/core_test.py::test_long_pdb[1BM8] SKIPPED (not running tests r...) [ 42%] 380s tests/core_test.py::test_long_pdb[1P1L] SKIPPED (not running tests r...) [ 43%] 380s tests/core_test.py::test_long_pdb[4LJ1] SKIPPED (not running tests r...) [ 43%] 380s tests/core_test.py::test_long_pdb[1UG4] SKIPPED (not running tests r...) [ 43%] 380s tests/core_test.py::test_long_pdb[2GZV] SKIPPED (not running tests r...) [ 43%] 380s tests/core_test.py::test_long_pdb[2ZQE] SKIPPED (not running tests r...) [ 44%] 380s tests/core_test.py::test_long_pdb[1LN4] SKIPPED (not running tests r...) [ 44%] 380s tests/core_test.py::test_long_pdb[4I2T] SKIPPED (not running tests r...) [ 44%] 380s tests/core_test.py::test_long_pdb[1J27] SKIPPED (not running tests r...) [ 45%] 380s tests/core_test.py::test_long_pdb[1PDO] SKIPPED (not running tests r...) [ 45%] 380s tests/core_test.py::test_long_pdb[4RWU] SKIPPED (not running tests r...) [ 45%] 380s tests/core_test.py::test_long_pdb[3IDW] SKIPPED (not running tests r...) [ 46%] 380s tests/core_test.py::test_long_pdb[2HDZ] SKIPPED (not running tests r...) [ 46%] 380s tests/core_test.py::test_long_pdb[2CGQ] SKIPPED (not running tests r...) [ 46%] 380s tests/core_test.py::test_long_pdb[3WFV] SKIPPED (not running tests r...) [ 47%] 380s tests/core_test.py::test_long_pdb[2PND] SKIPPED (not running tests r...) [ 47%] 380s tests/core_test.py::test_long_pdb[1TG0] SKIPPED (not running tests r...) [ 47%] 380s tests/core_test.py::test_long_pdb[3NX6] SKIPPED (not running tests r...) [ 48%] 380s tests/core_test.py::test_long_pdb[4POY] SKIPPED (not running tests r...) [ 48%] 380s tests/core_test.py::test_long_pdb[4N6T] SKIPPED (not running tests r...) [ 48%] 380s tests/core_test.py::test_long_pdb[2FRG] SKIPPED (not running tests r...) [ 49%] 380s tests/core_test.py::test_long_pdb[2NSN] SKIPPED (not running tests r...) [ 49%] 380s tests/core_test.py::test_long_pdb[2JCP] SKIPPED (not running tests r...) [ 49%] 380s tests/core_test.py::test_long_pdb[4HS2] SKIPPED (not running tests r...) [ 50%] 380s tests/core_test.py::test_long_pdb[2CWR] SKIPPED (not running tests r...) [ 50%] 380s tests/core_test.py::test_long_pdb[2REY] SKIPPED (not running tests r...) [ 50%] 380s tests/core_test.py::test_long_pdb[4NPN] SKIPPED (not running tests r...) [ 50%] 380s tests/core_test.py::test_long_pdb[1X6J] SKIPPED (not running tests r...) [ 51%] 380s tests/core_test.py::test_long_pdb[1AIL] SKIPPED (not running tests r...) [ 51%] 380s tests/core_test.py::test_long_pdb[3ONJ] SKIPPED (not running tests r...) [ 51%] 380s tests/core_test.py::test_long_pdb[2H2C] SKIPPED (not running tests r...) [ 52%] 380s tests/core_test.py::test_long_pdb[1OPS] SKIPPED (not running tests r...) [ 52%] 380s tests/core_test.py::test_long_pdb[2J9V] SKIPPED (not running tests r...) [ 52%] 380s tests/core_test.py::test_long_pdb[4TTW] SKIPPED (not running tests r...) [ 53%] 380s tests/core_test.py::test_long_pdb[2FI9] SKIPPED (not running tests r...) [ 53%] 380s tests/core_test.py::test_long_pdb[1YIB] SKIPPED (not running tests r...) [ 53%] 380s tests/core_test.py::test_long_pdb[4YKD] SKIPPED (not running tests r...) [ 54%] 380s tests/core_test.py::test_long_pdb[1NXO] SKIPPED (not running tests r...) [ 54%] 380s tests/core_test.py::test_long_pdb[1TIG] SKIPPED (not running tests r...) [ 54%] 380s tests/core_test.py::test_long_pdb[2YXF] SKIPPED (not running tests r...) [ 55%] 380s tests/core_test.py::test_long_pdb[4AXT] SKIPPED (not running tests r...) [ 55%] 380s tests/core_test.py::test_long_pdb[3H0X] SKIPPED (not running tests r...) [ 55%] 380s tests/core_test.py::test_long_pdb[1ZX6] SKIPPED (not running tests r...) [ 56%] 380s tests/core_test.py::test_long_pdb[1I2T] SKIPPED (not running tests r...) [ 56%] 380s tests/core_test.py::test_long_pdb[2P5K] SKIPPED (not running tests r...) [ 56%] 380s tests/core_test.py::test_long_pdb[2YGS] SKIPPED (not running tests r...) [ 56%] 380s tests/core_test.py::test_long_pdb[3RJS] SKIPPED (not running tests r...) [ 57%] 380s tests/core_test.py::test_long_pdb[1ZVA] SKIPPED (not running tests r...) [ 57%] 380s tests/core_test.py::test_long_pdb[1TVQ] SKIPPED (not running tests r...) [ 57%] 380s tests/core_test.py::test_long_pdb[3ZHI] SKIPPED (not running tests r...) [ 58%] 380s tests/core_test.py::test_long_pdb[1V2Z] SKIPPED (not running tests r...) [ 58%] 380s tests/core_test.py::test_long_pdb[2BYG] SKIPPED (not running tests r...) [ 58%] 380s tests/core_test.py::test_long_pdb[2QR3] SKIPPED (not running tests r...) [ 59%] 380s tests/core_test.py::test_long_pdb[3QC7] SKIPPED (not running tests r...) [ 59%] 380s tests/core_test.py::test_long_pdb[2GUS] SKIPPED (not running tests r...) [ 59%] 380s tests/core_test.py::test_long_pdb[4Q2Q] SKIPPED (not running tests r...) [ 60%] 380s tests/core_test.py::test_long_pdb[1XAK] SKIPPED (not running tests r...) [ 60%] 380s tests/core_test.py::test_long_pdb[3DVI] SKIPPED (not running tests r...) [ 60%] 380s tests/core_test.py::test_long_pdb[2JIC] SKIPPED (not running tests r...) [ 61%] 380s tests/core_test.py::test_long_pdb[2IGD] SKIPPED (not running tests r...) [ 61%] 380s tests/core_test.py::test_long_pdb[1X3O] SKIPPED (not running tests r...) [ 61%] 380s tests/core_test.py::test_long_pdb[3RFF] SKIPPED (not running tests r...) [ 62%] 380s tests/core_test.py::test_long_pdb[2OP6] SKIPPED (not running tests r...) [ 62%] 380s tests/core_test.py::test_long_pdb[2IVY] SKIPPED (not running tests r...) [ 62%] 380s tests/core_test.py::test_long_pdb[1AFS] SKIPPED (not running tests r...) [ 62%] 380s tests/core_test.py::test_long_pdb[1H75] SKIPPED (not running tests r...) [ 63%] 380s tests/core_test.py::test_long_pdb[2FD4] SKIPPED (not running tests r...) [ 63%] 380s tests/core_test.py::test_long_pdb[3ZSL] SKIPPED (not running tests r...) [ 63%] 380s tests/core_test.py::test_long_pdb[2PCY] SKIPPED (not running tests r...) [ 64%] 380s tests/core_test.py::test_long_pdb[1OPC] SKIPPED (not running tests r...) [ 64%] 380s tests/core_test.py::test_long_pdb[4ZMK] SKIPPED (not running tests r...) [ 64%] 380s tests/core_test.py::test_long_pdb[1WOU] SKIPPED (not running tests r...) [ 65%] 380s tests/core_test.py::test_long_pdb[2FWG] SKIPPED (not running tests r...) [ 65%] 380s tests/core_test.py::test_long_pdb[3S0A] SKIPPED (not running tests r...) [ 65%] 380s tests/core_test.py::test_long_pdb[2ERA] SKIPPED (not running tests r...) [ 66%] 380s tests/core_test.py::test_broken_backbone[3U7T] 380s -------------------------------- live log call --------------------------------- 380s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_3U7T_0/3U7T.log 380s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 380s 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). 380s 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). 380s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 380s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 380s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T 381s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 381s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 381s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 652 atoms. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in PRO A 22. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in PRO A 22. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in PRO A 22. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in PRO A 22. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 22. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in PRO A 22. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in PRO A 22. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 22. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 22. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in PRO A 22. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 22. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in PRO A 22. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 22. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 22. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 22. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 22. 381s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 22. At least one of the instances is being ignored. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in LEU A 25. 381s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in LEU A 25. At least one of the instances is being ignored. 381s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 381s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 381s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 381s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 381s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 381s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 381s 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 381s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 381s XFAIL [ 66%] 381s tests/core_test.py::test_broken_backbone[4MGP] 381s -------------------------------- live log call --------------------------------- 381s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_4MGP_0/4MGP.log 381s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 381s 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). 381s 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). 381s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 381s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 382s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP 382s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 382s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 382s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 23 residues and 163 atoms. 382s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in MET A 21. 382s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in MET A 21. 382s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in MET A 21. 382s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: SD in MET A 21. 382s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE in MET A 21. 382s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in MET A 21. At least one of the instances is being ignored. 382s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 382s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 382s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 382s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 12 missing atoms in biomolecule. 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 382s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 382s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 11 at coordinates 1.430, -1.683, -11.529 382s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 11 at coordinates 1.940, -0.315, -11.800 382s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CG to residue LYS A 14 at coordinates -1.600, -8.819, -6.913 382s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CD to residue LYS A 14 at coordinates -2.056, -8.844, -8.361 382s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 14 at coordinates -3.548, -9.031, -8.498 382s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 14 at coordinates -3.947, -9.048, -9.928 382s 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 382s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 382s XFAIL [ 66%] 382s tests/core_test.py::test_broken_backbone[1EJG] 382s -------------------------------- live log call --------------------------------- 382s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_1EJG_0/1EJG.log 382s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 382s 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). 382s 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). 382s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 382s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 382s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG 383s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 383s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 383s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 650 atoms. 383s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in THR A 1. 383s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 1. 383s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 1. 383s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 1. 383s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 1. 383s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H1 in THR A 1. 383s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H2 in THR A 1. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H3 in THR A 1. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 1. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 1. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 1. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 1. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 1. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 1. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 1. At least one of the instances is being ignored. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 2. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 2. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 2. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 2. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 2. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 2. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 2. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 2. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 2. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 2. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 2. At least one of the instances is being ignored. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 7. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 7. At least one of the instances is being ignored. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in VAL A 8. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in VAL A 8. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in VAL A 8. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in VAL A 8. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in VAL A 8. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in VAL A 8. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in VAL A 8. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in VAL A 8. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG11 in VAL A 8. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in VAL A 8. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in VAL A 8. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in VAL A 8. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in VAL A 8. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in VAL A 8. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in VAL A 8. At least one of the instances is being ignored. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NE in ARG A 10. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in ARG A 10. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH1 in ARG A 10. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH2 in ARG A 10. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE in ARG A 10. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH11 in ARG A 10. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH12 in ARG A 10. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH21 in ARG A 10. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH22 in ARG A 10. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ARG A 10. At least one of the instances is being ignored. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ASN A 12. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASN A 12. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 12. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 12. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 12. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ASN A 12. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASN A 12. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASN A 12. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 12. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 12. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 12. At least one of the instances is being ignored. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PHE A 13. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in PHE A 13. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in PHE A 13. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in PHE A 13. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in PHE A 13. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in PHE A 13. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in PHE A 13. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PHE A 13. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in PHE A 13. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in PHE A 13. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HZ in PHE A 13. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PHE A 13. At least one of the instances is being ignored. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 19. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 19. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 19. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 19. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 19. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 19. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 19. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 19. At least one of the instances is being ignored. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in SER A 22. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in SER A 22. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in SER A 22. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in SER A 22. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in SER A 22. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in SER A 22. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in SER A 22. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in SER A 22. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in SER A 22. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in SER A 22. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in SER A 22. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in SER A 22. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in SER A 22. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in SER A 22. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in SER A 22. At least one of the instances is being ignored. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in GLU A 23. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in GLU A 23. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE1 in GLU A 23. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE2 in GLU A 23. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in GLU A 23. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in GLU A 23. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in GLU A 23. At least one of the instances is being ignored. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 25. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 25. At least one of the instances is being ignored. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in TYR A 29. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in TYR A 29. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in TYR A 29. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in TYR A 29. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in TYR A 29. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in TYR A 29. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OH in TYR A 29. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in TYR A 29. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in TYR A 29. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in TYR A 29. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in TYR A 29. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH in TYR A 29. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in TYR A 29. At least one of the instances is being ignored. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 34. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 34. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 34. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 34. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 34. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 34. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 34. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 34. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 34. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 34. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 34. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 34. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 34. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 34. At least one of the instances is being ignored. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 36. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 36. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 36. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 36. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 36. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 36. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 36. At least one of the instances is being ignored. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 39. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 39. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 39. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 39. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 39. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 39. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 39. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 39. At least one of the instances is being ignored. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASP A 43. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASP A 43. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASP A 43. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD2 in ASP A 43. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASP A 43. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASP A 43. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASP A 43. At least one of the instances is being ignored. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 46. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 46. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 46. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 46. 384s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 46. 384s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 46. At least one of the instances is being ignored. 384s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 384s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 384s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 384s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 384s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 384s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 384s 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 384s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 384s XFAIL [ 67%] 384s tests/core_test.py::test_broken_backbone[2V75] 384s -------------------------------- live log call --------------------------------- 384s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_2V75_0/2V75.log 384s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 384s 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). 384s 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). 384s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 384s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 384s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 385s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 385s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 385s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 90 residues and 687 atoms. 385s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 385s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 385s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 385s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 8 missing atoms in biomolecule. 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 385s 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 385s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 385s XFAIL [ 67%] 385s tests/core_test.py::test_protonated_terminals[C-terminal HID] 385s -------------------------------- live log call --------------------------------- 385s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log 385s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 385s 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). 385s 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). 385s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 385s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 385s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/cterm_hid.pdb 385s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 385s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms. 385s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 385s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 385s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 385s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule. 385s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 385s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402 385s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 385s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 385s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 385s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 385s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 385s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 385s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 385s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 385s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 385s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 385s INFO common:common.py:198 0 atoms have position differences > 0 385s INFO common:common.py:198 0 atoms have position differences > 0.01 385s INFO common:common.py:198 0 atoms have charge differences > 0 385s INFO common:common.py:198 0 atoms have charge differences > 0.01 385s INFO common:common.py:198 0 atoms have radius differences > 0 385s INFO common:common.py:198 0 atoms have radius differences > 0.01 385s PASSED [ 67%] 385s tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 385s -------------------------------- live log call --------------------------------- 385s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log 385s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 385s 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). 385s 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). 385s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 385s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 385s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/5vav_cyclic_peptide.pdb 385s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 385s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms. 385s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 385s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 385s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 385s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 385s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 385s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 385s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 385s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 385s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 385s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 385s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 385s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 385s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 385s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 385s INFO common:common.py:198 0 atoms have position differences > 0 385s INFO common:common.py:198 0 atoms have position differences > 0.01 385s INFO common:common.py:198 0 atoms have charge differences > 0 385s INFO common:common.py:198 0 atoms have charge differences > 0.01 385s INFO common:common.py:198 0 atoms have radius differences > 0 385s INFO common:common.py:198 0 atoms have radius differences > 0.01 385s PASSED [ 68%] 385s 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 [ 68%] 385s tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 68%] 385s tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 68%] 385s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 69%] 385s tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 69%] 385s tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 69%] 385s tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 70%] 385s tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 70%] 385s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 70%] 385s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 71%] 386s tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 71%] 386s tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 71%] 386s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 72%] 386s tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 72%] 386s tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 72%] 386s tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 73%] 386s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 73%] 386s tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 73%] 386s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 74%] 386s tests/io_test.py::test_read_qcd PASSED [ 74%] 386s tests/io_test.py::test_dx2cube 386s -------------------------------- live log call --------------------------------- 386s INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... 386s INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... 386s INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 388s INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 388s INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... 388s INFO io_test:io_test.py:68 No differences found in output 388s PASSED [ 74%] 389s tests/ligand_test.py::test_peoe_charges 389s -------------------------------- live log call --------------------------------- 389s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 389s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 389s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 389s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 389s PASSED [ 75%] 389s tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 389s -------------------------------- live log call --------------------------------- 389s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 389s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 389s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 389s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 389s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 389s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 389s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 389s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 389s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 389s PASSED [ 75%] 390s tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 390s -------------------------------- live log call --------------------------------- 390s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 390s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 390s PASSED [ 75%] 390s tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 390s -------------------------------- live log call --------------------------------- 390s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 390s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 390s PASSED [ 75%] 390s tests/ligand_test.py::test_assign_parameters[acetate.mol2] 390s -------------------------------- live log call --------------------------------- 390s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 390s PASSED [ 76%] 390s tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 390s -------------------------------- live log call --------------------------------- 390s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 390s PASSED [ 76%] 390s tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 390s -------------------------------- live log call --------------------------------- 390s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 390s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 390s PASSED [ 76%] 390s tests/ligand_test.py::test_assign_parameters[adp.mol2] 390s -------------------------------- live log call --------------------------------- 390s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 390s INFO ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00 390s PASSED [ 77%] 390s tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 390s -------------------------------- live log call --------------------------------- 390s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 390s PASSED [ 77%] 390s tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 390s -------------------------------- live log call --------------------------------- 390s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 390s PASSED [ 77%] 390s tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 390s -------------------------------- live log call --------------------------------- 390s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 390s PASSED [ 78%] 390s tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 390s -------------------------------- live log call --------------------------------- 390s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 390s PASSED [ 78%] 390s tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 390s -------------------------------- live log call --------------------------------- 390s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 390s PASSED [ 78%] 390s tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 390s -------------------------------- live log call --------------------------------- 390s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 390s PASSED [ 79%] 390s tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 390s -------------------------------- live log call --------------------------------- 390s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 390s PASSED [ 79%] 390s tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 390s -------------------------------- live log call --------------------------------- 390s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 390s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 390s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 390s PASSED [ 79%] 391s tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 391s -------------------------------- live log call --------------------------------- 391s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 391s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 391s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 391s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 391s PASSED [ 80%] 392s tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 392s -------------------------------- live log call --------------------------------- 392s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 392s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 392s PASSED [ 80%] 392s tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 392s -------------------------------- live log call --------------------------------- 392s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 392s PASSED [ 80%] 392s tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED [ 81%] 392s tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED [ 81%] 392s tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 392s -------------------------------- live log call --------------------------------- 392s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 392s PASSED [ 81%] 392s tests/ligand_test.py::test_formal_charge[adp.mol2] 392s -------------------------------- live log call --------------------------------- 392s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 392s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 392s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 392s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 392s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 392s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 392s PASSED [ 81%] 392s tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED [ 82%] 392s tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED [ 82%] 392s tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED [ 82%] 392s tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED [ 83%] 392s tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED [ 83%] 392s tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED [ 83%] 392s tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED [ 84%] 392s tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 392s -------------------------------- live log call --------------------------------- 392s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 392s PASSED [ 84%] 392s tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED [ 84%] 392s tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED [ 85%] 392s tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED [ 85%] 392s tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED [ 85%] 392s tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED [ 86%] 392s tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED [ 86%] 392s tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED [ 86%] 393s tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED [ 87%] 393s tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED [ 87%] 393s tests/ligand_test.py::test_rings[acetate.mol2] PASSED [ 87%] 393s tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED [ 87%] 393s tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED [ 88%] 393s tests/ligand_test.py::test_rings[adp.mol2] PASSED [ 88%] 393s tests/ligand_test.py::test_rings[anthracene.mol2] PASSED [ 88%] 393s tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED [ 89%] 393s tests/ligand_test.py::test_rings[ethanol.mol2] PASSED [ 89%] 393s tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED [ 89%] 393s tests/ligand_test.py::test_rings[glycerol.mol2] PASSED [ 90%] 393s tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED [ 90%] 393s tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED [ 90%] 393s tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED [ 91%] 393s tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%] 394s tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%] 394s tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%] 394s tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%] 394s tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%] 394s tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%] 394s tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%] 394s tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%] 394s tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%] 394s tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%] 394s tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%] 394s tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] 394s tests/regression_test.py::test_basic[1AFS basic local] 394s -------------------------------- live log call --------------------------------- 394s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_basic_1AFS_basic_local_0/output.log 394s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 394s 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). 394s 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). 394s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 394s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 394s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 394s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 394s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 394s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 394s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 394s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 394s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 394s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 394s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 394s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 394s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 394s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 394s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 394s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 394s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 394s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 394s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 394s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 394s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 394s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 394s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 394s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 395s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 396s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 397s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 397s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 397s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 397s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 397s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 397s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 397s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 397s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 397s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 397s WARNING pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages 400s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 400s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 400s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 400s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 400s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 401s WARNING common:common.py:186 6 atoms have position differences > 0 401s INFO common:common.py:198 0 atoms have position differences > 0.01 401s INFO common:common.py:198 0 atoms have charge differences > 0 401s INFO common:common.py:198 0 atoms have charge differences > 0.01 401s INFO common:common.py:198 0 atoms have radius differences > 0 401s INFO common:common.py:198 0 atoms have radius differences > 0.01 401s PASSED [ 95%] 401s tests/regression_test.py::test_forcefields[1AFS whitespace AMBER] 401s -------------------------------- live log call --------------------------------- 401s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa0/output.log 401s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 401s 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). 401s 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). 401s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 401s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 401s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 401s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 401s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 401s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 401s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 401s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 401s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 401s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 401s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 401s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 401s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 401s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 401s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 401s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 401s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 401s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 401s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 401s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 401s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 401s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 401s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 401s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 402s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 403s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 408s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 408s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 408s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 408s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 408s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 408s WARNING common:common.py:186 6 atoms have position differences > 0 408s INFO common:common.py:198 0 atoms have position differences > 0.01 408s INFO common:common.py:198 0 atoms have charge differences > 0 408s INFO common:common.py:198 0 atoms have charge differences > 0.01 408s INFO common:common.py:198 0 atoms have radius differences > 0 408s INFO common:common.py:198 0 atoms have radius differences > 0.01 408s PASSED [ 95%] 408s tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] 408s -------------------------------- live log call --------------------------------- 408s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa1/output.log 408s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 408s 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). 408s 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). 408s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 408s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 408s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 408s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 408s WARNING pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages 408s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 408s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 408s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 408s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 408s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 408s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 408s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 408s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 408s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 408s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 408s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 408s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 408s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 408s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 408s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 408s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 409s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 410s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 415s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 415s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 415s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 415s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 415s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 415s WARNING common:common.py:186 5 atoms have position differences > 0 415s INFO common:common.py:198 0 atoms have position differences > 0.01 415s INFO common:common.py:198 0 atoms have charge differences > 0 415s INFO common:common.py:198 0 atoms have charge differences > 0.01 415s INFO common:common.py:198 0 atoms have radius differences > 0 415s INFO common:common.py:198 0 atoms have radius differences > 0.01 415s PASSED [ 95%] 415s tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] 415s -------------------------------- live log call --------------------------------- 415s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa2/output.log 415s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 415s 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). 415s 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). 415s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 415s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 415s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 415s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 415s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 415s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 415s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 415s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 415s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 415s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 415s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 415s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 415s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 415s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 415s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 415s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 415s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 415s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 415s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 415s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 416s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 417s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 422s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 422s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 422s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 422s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 422s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 423s WARNING common:common.py:186 6 atoms have position differences > 0 423s INFO common:common.py:198 0 atoms have position differences > 0.01 423s INFO common:common.py:198 0 atoms have charge differences > 0 423s INFO common:common.py:198 0 atoms have charge differences > 0.01 423s INFO common:common.py:198 0 atoms have radius differences > 0 423s INFO common:common.py:198 0 atoms have radius differences > 0.01 423s PASSED [ 96%] 423s tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] 423s -------------------------------- live log call --------------------------------- 423s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa3/output.log 423s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 423s 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). 423s 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). 423s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 423s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 423s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 423s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 423s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 423s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 423s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 423s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 423s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 423s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 423s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 423s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 423s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 423s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 423s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 423s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 423s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 423s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 423s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 423s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 424s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 425s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 430s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 430s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 430s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 430s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 430s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 430s WARNING common:common.py:186 6 atoms have position differences > 0 430s INFO common:common.py:198 0 atoms have position differences > 0.01 430s INFO common:common.py:198 0 atoms have charge differences > 0 430s INFO common:common.py:198 0 atoms have charge differences > 0.01 430s INFO common:common.py:198 0 atoms have radius differences > 0 430s INFO common:common.py:198 0 atoms have radius differences > 0.01 430s PASSED [ 96%] 430s tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] 430s -------------------------------- live log call --------------------------------- 430s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa4/output.log 430s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 430s 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). 430s 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). 430s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 430s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 430s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 430s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 430s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 430s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 430s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 430s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 430s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 430s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 430s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 430s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 430s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 430s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 430s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 430s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 430s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 430s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 430s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 430s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 431s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 432s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 437s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 437s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 437s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 437s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output. 437s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 437s WARNING common:common.py:186 6 atoms have position differences > 0 437s INFO common:common.py:198 0 atoms have position differences > 0.01 437s INFO common:common.py:198 0 atoms have charge differences > 0 437s INFO common:common.py:198 0 atoms have charge differences > 0.01 437s INFO common:common.py:198 0 atoms have radius differences > 0 437s INFO common:common.py:198 0 atoms have radius differences > 0.01 437s PASSED [ 96%] 437s tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] 437s -------------------------------- live log call --------------------------------- 437s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa5/output.log 437s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 437s 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). 437s 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). 437s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 437s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 437s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 437s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 437s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 437s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 437s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 437s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 437s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 437s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 437s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 437s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 437s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 437s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 437s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 437s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 437s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 437s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 437s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 438s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 438s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 440s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 444s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 444s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 444s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 444s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 444s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 444s WARNING common:common.py:186 6 atoms have position differences > 0 444s INFO common:common.py:198 0 atoms have position differences > 0.01 444s INFO common:common.py:198 0 atoms have charge differences > 0 444s INFO common:common.py:198 0 atoms have charge differences > 0.01 444s INFO common:common.py:198 0 atoms have radius differences > 0 444s INFO common:common.py:198 0 atoms have radius differences > 0.01 444s PASSED [ 97%] 444s tests/regression_test.py::test_other_options[1AFS whitespace clean] 444s -------------------------------- live log call --------------------------------- 444s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_whites0/output.log 444s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 444s 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). 444s 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). 444s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 444s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 444s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 444s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 444s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 444s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 444s INFO PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps. 445s INFO common:common.py:198 0 atoms have position differences > 0 445s INFO common:common.py:198 0 atoms have position differences > 0.01 445s INFO common:common.py:198 0 atoms have charge differences > 0 445s INFO common:common.py:198 0 atoms have charge differences > 0.01 445s INFO common:common.py:198 0 atoms have radius differences > 0 445s INFO common:common.py:198 0 atoms have radius differences > 0.01 445s PASSED [ 97%] 445s tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] 445s -------------------------------- live log call --------------------------------- 445s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_assign0/output.log 445s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 445s 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). 445s 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). 445s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 445s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 445s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 445s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 445s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 445s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 445s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 445s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 445s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 445s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 445s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 445s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 445s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 445s INFO common:common.py:198 0 atoms have position differences > 0 445s INFO common:common.py:198 0 atoms have position differences > 0.01 445s INFO common:common.py:198 0 atoms have charge differences > 0 445s INFO common:common.py:198 0 atoms have charge differences > 0.01 445s INFO common:common.py:198 0 atoms have radius differences > 0 445s INFO common:common.py:198 0 atoms have radius differences > 0.01 445s PASSED [ 97%] 445s tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] 445s -------------------------------- live log call --------------------------------- 445s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_nodebu0/output.log 445s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 445s 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). 445s 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). 445s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 445s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 445s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 445s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 445s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 445s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 445s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 445s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 445s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 445s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 445s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 445s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 445s INFO pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization... 445s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 445s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 445s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 445s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 445s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 445s INFO common:common.py:198 0 atoms have position differences > 0 445s INFO common:common.py:198 0 atoms have position differences > 0.01 445s INFO common:common.py:198 0 atoms have charge differences > 0 445s INFO common:common.py:198 0 atoms have charge differences > 0.01 445s INFO common:common.py:198 0 atoms have radius differences > 0 445s INFO common:common.py:198 0 atoms have radius differences > 0.01 445s PASSED [ 98%] 445s tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] 445s -------------------------------- live log call --------------------------------- 445s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_chain_0/output.log 445s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 445s 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). 445s 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). 445s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 445s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 445s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 445s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 445s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 445s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 445s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 445s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 445s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 445s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 445s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 445s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 445s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 445s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 445s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 445s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 445s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 445s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 445s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 445s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 446s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 447s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 452s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 452s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 452s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 452s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 452s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 452s WARNING common:common.py:186 6 atoms have position differences > 0 452s INFO common:common.py:198 0 atoms have position differences > 0.01 452s INFO common:common.py:198 0 atoms have charge differences > 0 452s INFO common:common.py:198 0 atoms have charge differences > 0.01 452s INFO common:common.py:198 0 atoms have radius differences > 0 452s INFO common:common.py:198 0 atoms have radius differences > 0.01 452s PASSED [ 98%] 452s tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] 452s -------------------------------- live log call --------------------------------- 452s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_neutra0/output.log 452s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 452s 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). 452s 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). 452s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 452s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 452s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 452s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 452s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 452s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 452s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 453s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 453s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 453s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 453s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 453s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 453s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 453s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 453s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 453s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 453s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 453s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 453s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 453s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 453s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 455s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 459s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 459s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 459s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 459s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 459s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 460s WARNING common:common.py:186 6 atoms have position differences > 0 460s INFO common:common.py:198 0 atoms have position differences > 0.01 460s INFO common:common.py:198 0 atoms have charge differences > 0 460s INFO common:common.py:198 0 atoms have charge differences > 0.01 460s INFO common:common.py:198 0 atoms have radius differences > 0 460s INFO common:common.py:198 0 atoms have radius differences > 0.01 460s PASSED [ 98%] 460s tests/regression_test.py::test_other_options[1AFS drop-water AMBER] 460s -------------------------------- live log call --------------------------------- 460s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_drop_w0/output.log 460s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 460s 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). 460s 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). 460s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 460s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 460s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 460s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 460s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 460s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms. 460s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 460s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 460s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 460s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 460s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 460s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 460s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 460s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 460s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 460s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 460s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 460s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 460s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 460s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 460s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 461s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 462s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 465s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 465s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 465s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 465s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 465s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 465s WARNING common:common.py:186 6 atoms have position differences > 0 465s INFO common:common.py:198 0 atoms have position differences > 0.01 465s INFO common:common.py:198 0 atoms have charge differences > 0 465s INFO common:common.py:198 0 atoms have charge differences > 0.01 465s INFO common:common.py:198 0 atoms have radius differences > 0 465s INFO common:common.py:198 0 atoms have radius differences > 0.01 465s PASSED [ 99%] 465s tests/regression_test.py::test_other_options[1AFS userff usernames whitespace] 465s -------------------------------- live log call --------------------------------- 465s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_userff0/output.log 465s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 465s 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). 465s 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). 465s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 465s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 465s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 465s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 465s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 465s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 465s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 465s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 465s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 465s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 465s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 465s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 465s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 465s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 465s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 465s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 465s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 465s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 465s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 465s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 466s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 467s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 472s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 472s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 472s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 472s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 472s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 472s WARNING common:common.py:186 6 atoms have position differences > 0 472s INFO common:common.py:198 0 atoms have position differences > 0.01 472s INFO common:common.py:198 0 atoms have charge differences > 0 472s INFO common:common.py:198 0 atoms have charge differences > 0.01 472s INFO common:common.py:198 0 atoms have radius differences > 0 472s INFO common:common.py:198 0 atoms have radius differences > 0.01 472s PASSED [ 99%] 472s tests/test_version.py::test_version_exists PASSED [ 99%] 472s tests/test_version.py::test_version PASSED [100%] 472s 472s =============================== warnings summary =============================== 472s ../../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37 472s /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). 472s EPOCH = datetime.datetime.utcfromtimestamp(0) 472s 472s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 472s ======= 92 passed, 220 skipped, 4 xfailed, 1 warning in 92.59s (0:01:32) ======= 472s autopkgtest [15:16:42]: test command1: -----------------------] 473s autopkgtest [15:16:43]: test command1: - - - - - - - - - - results - - - - - - - - - - 473s command1 PASS 474s autopkgtest [15:16:44]: @@@@@@@@@@@@@@@@@@@@ summary 474s installation-test PASS 474s pdb2pka-test PASS 474s command1 PASS 486s Creating nova instance adt-noble-ppc64el-pdb2pqr-20240322-150849-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240322.img (UUID 8499323f-6fcd-4f77-8a53-77410adea6d3)...