0s autopkgtest [04:27:51]: starting date and time: 2025-10-30 04:27:51+0000 0s autopkgtest [04:27:51]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [04:27:51]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.cmj0agmj/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:node-jquery --apt-upgrade pdb2pqr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=node-jquery/3.7.1+dfsg+~3.5.33-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-ppc64el-8.secgroup --name adt-resolute-ppc64el-pdb2pqr-20251030-042751-juju-7f2275-prod-proposed-migration-environment-2-de705d3f-969f-42b5-9c82-bd37a2d661ed --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-ppc64el-pdb2pqr-20251030-042751-juju-7f2275-prod-proposed-migration-environment-2-de705d3f-969f-42b5-9c82-bd37a2d661ed from image adt/ubuntu-resolute-ppc64el-server-20251029.img (UUID 27271d73-b679-46bf-826f-8c22ef3a1484)... 110s autopkgtest [04:29:41]: testbed dpkg architecture: ppc64el 110s autopkgtest [04:29:41]: testbed apt version: 3.1.11 111s autopkgtest [04:29:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 111s autopkgtest [04:29:42]: testbed release detected to be: None 112s autopkgtest [04:29:43]: updating testbed package index (apt update) 112s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 112s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 112s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 112s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 112s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5856 B] 112s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [70.5 kB] 113s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [3669 kB] 113s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [206 kB] 113s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [269 kB] 113s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted ppc64el Packages [940 B] 113s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [2494 kB] 114s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [38.5 kB] 114s Fetched 6843 kB in 3s (2543 kB/s) 115s Reading package lists... 116s Failed to check for VM: Permission denied 116s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 116s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 116s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 116s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 117s Reading package lists... 117s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Calculating upgrade... 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 118s autopkgtest [04:29:49]: upgrading testbed (apt dist-upgrade and autopurge) 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Calculating upgrade... 118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s Solving dependencies... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s autopkgtest [04:29:53]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:02:41 UTC 2025 122s autopkgtest [04:29:53]: @@@@@@@@@@@@@@@@@@@@ apt-source pdb2pqr 127s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (dsc) [1860 B] 127s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (tar) [7570 kB] 127s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (diff) [9876 B] 127s gpgv: Signature made Mon Jun 12 17:36:50 2023 UTC 127s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 127s gpgv: Can't check signature: No public key 127s dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found 128s autopkgtest [04:29:59]: testing package pdb2pqr version 3.6.1+dfsg-1 128s autopkgtest [04:29:59]: build not needed 131s autopkgtest [04:30:02]: test installation-test: preparing testbed 131s Reading package lists... 131s Building dependency tree... 131s Reading state information... 131s Solving dependencies... 132s The following NEW packages will be installed: 132s docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr python3-docutils 132s python3-numpy python3-numpy-dev python3-pdb2pqr python3-pdbx python3-propka 132s python3-roman sgml-base xml-core 132s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 132s Need to get 9734 kB of archives. 132s After this operation, 42.5 MB of additional disk space will be used. 132s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy-dev ppc64el 1:2.2.4+ds-1ubuntu1 [153 kB] 132s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-6build1 [291 kB] 132s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-5ubuntu1 [620 kB] 132s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-6build1 [2960 kB] 133s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy ppc64el 1:2.2.4+ds-1ubuntu1 [4887 kB] 133s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el sgml-base all 1.31+nmu1 [11.0 kB] 133s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el xml-core all 0.19 [20.3 kB] 133s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el docutils-common all 0.21.2+dfsg-2 [131 kB] 133s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-roman all 5.1-1 [10.6 kB] 133s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-docutils all 0.21.2+dfsg-2 [409 kB] 133s Get:11 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pdbx all 2.0.1-2 [16.5 kB] 133s Get:12 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-propka all 3.5.1-2 [70.1 kB] 133s Get:13 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pdb2pqr all 3.6.1+dfsg-1 [145 kB] 133s Get:14 http://ftpmaster.internal/ubuntu resolute/universe ppc64el pdb2pqr all 3.6.1+dfsg-1 [10.4 kB] 134s Fetched 9734 kB in 2s (5152 kB/s) 134s Selecting previously unselected package python3-numpy-dev:ppc64el. 134s (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 ... 76559 files and directories currently installed.) 134s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 134s Unpacking python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 134s Selecting previously unselected package libblas3:ppc64el. 134s Preparing to unpack .../01-libblas3_3.12.1-6build1_ppc64el.deb ... 134s Unpacking libblas3:ppc64el (3.12.1-6build1) ... 134s Selecting previously unselected package libgfortran5:ppc64el. 134s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_ppc64el.deb ... 134s Unpacking libgfortran5:ppc64el (15.2.0-5ubuntu1) ... 134s Selecting previously unselected package liblapack3:ppc64el. 134s Preparing to unpack .../03-liblapack3_3.12.1-6build1_ppc64el.deb ... 134s Unpacking liblapack3:ppc64el (3.12.1-6build1) ... 134s Selecting previously unselected package python3-numpy. 134s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 134s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 134s Selecting previously unselected package sgml-base. 134s Preparing to unpack .../05-sgml-base_1.31+nmu1_all.deb ... 134s Unpacking sgml-base (1.31+nmu1) ... 135s Selecting previously unselected package xml-core. 135s Preparing to unpack .../06-xml-core_0.19_all.deb ... 135s Unpacking xml-core (0.19) ... 135s Selecting previously unselected package docutils-common. 135s Preparing to unpack .../07-docutils-common_0.21.2+dfsg-2_all.deb ... 135s Unpacking docutils-common (0.21.2+dfsg-2) ... 135s Selecting previously unselected package python3-roman. 135s Preparing to unpack .../08-python3-roman_5.1-1_all.deb ... 135s Unpacking python3-roman (5.1-1) ... 135s Selecting previously unselected package python3-docutils. 135s Preparing to unpack .../09-python3-docutils_0.21.2+dfsg-2_all.deb ... 135s Unpacking python3-docutils (0.21.2+dfsg-2) ... 135s Selecting previously unselected package python3-pdbx. 135s Preparing to unpack .../10-python3-pdbx_2.0.1-2_all.deb ... 135s Unpacking python3-pdbx (2.0.1-2) ... 135s Selecting previously unselected package python3-propka. 135s Preparing to unpack .../11-python3-propka_3.5.1-2_all.deb ... 135s Unpacking python3-propka (3.5.1-2) ... 135s Selecting previously unselected package python3-pdb2pqr. 135s Preparing to unpack .../12-python3-pdb2pqr_3.6.1+dfsg-1_all.deb ... 135s Unpacking python3-pdb2pqr (3.6.1+dfsg-1) ... 135s Selecting previously unselected package pdb2pqr. 135s Preparing to unpack .../13-pdb2pqr_3.6.1+dfsg-1_all.deb ... 135s Unpacking pdb2pqr (3.6.1+dfsg-1) ... 135s Setting up python3-propka (3.5.1-2) ... 135s Setting up python3-pdbx (2.0.1-2) ... 135s Setting up python3-roman (5.1-1) ... 135s Setting up libblas3:ppc64el (3.12.1-6build1) ... 135s 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 135s Setting up python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 135s Setting up libgfortran5:ppc64el (15.2.0-5ubuntu1) ... 135s Setting up sgml-base (1.31+nmu1) ... 135s Setting up liblapack3:ppc64el (3.12.1-6build1) ... 135s 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 135s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 137s Setting up xml-core (0.19) ... 137s Processing triggers for libc-bin (2.42-0ubuntu3) ... 137s Processing triggers for man-db (2.13.1-1) ... 139s Processing triggers for sgml-base (1.31+nmu1) ... 139s Setting up docutils-common (0.21.2+dfsg-2) ... 139s Processing triggers for sgml-base (1.31+nmu1) ... 139s Setting up python3-docutils (0.21.2+dfsg-2) ... 140s Setting up python3-pdb2pqr (3.6.1+dfsg-1) ... 140s Setting up pdb2pqr (3.6.1+dfsg-1) ... 141s autopkgtest [04:30:12]: test installation-test: [----------------------- 141s Run pdb2pqr... 142s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 142s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 142s 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). 142s INFO:Checking and transforming input arguments. 142s INFO:Loading topology files. 142s INFO:Loading molecule: examples/1a1p/1a1p.pdb 142s INFO:Setting up molecule. 142s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 142s INFO:Created biomolecule object with 14 residues and 208 atoms. 142s INFO:Setting termini states for biomolecule chains. 142s INFO:Loading forcefield. 142s INFO:Loading hydrogen topology definitions. 142s INFO:This biomolecule is clean. No repair needed. 142s INFO:Updating disulfide bridges. 142s INFO:Debumping biomolecule. 142s INFO:Adding hydrogens to biomolecule. 142s INFO:Debumping biomolecule (again). 142s INFO:Optimizing hydrogen bonds 142s INFO:Applying force field to biomolecule states. 142s INFO:Regenerating headers. 142s INFO:Regenerating PDB lines. 142s WARNING:Ignoring 852 header lines in output. 142s WARNING:Ignoring 3 missing lines in output. 142s autopkgtest [04:30:13]: test installation-test: -----------------------] 143s autopkgtest [04:30:14]: test installation-test: - - - - - - - - - - results - - - - - - - - - - 143s installation-test PASS 143s autopkgtest [04:30:14]: test pdb2pka-test: preparing testbed 143s Reading package lists... 143s Building dependency tree... 143s Reading state information... 144s Solving dependencies... 144s The following NEW packages will be installed: 144s fonts-font-awesome fonts-lato libjs-jquery libjs-sphinxdoc libjs-underscore 144s pdb2pqr-doc sphinx-rtd-theme-common 144s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 144s Need to get 5035 kB of archives. 144s After this operation, 20.0 MB of additional disk space will be used. 144s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-lato all 2.015-1 [2781 kB] 145s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 145s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 145s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 145s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 145s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 145s Get:7 http://ftpmaster.internal/ubuntu resolute/universe ppc64el pdb2pqr-doc all 3.6.1+dfsg-1 [258 kB] 145s Fetched 5035 kB in 1s (4056 kB/s) 145s Selecting previously unselected package fonts-lato. 145s (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 ... 78060 files and directories currently installed.) 145s Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... 145s Unpacking fonts-lato (2.015-1) ... 146s Selecting previously unselected package fonts-font-awesome. 146s Preparing to unpack .../1-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 146s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 146s Selecting previously unselected package libjs-jquery. 146s Preparing to unpack .../2-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 146s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 146s Selecting previously unselected package libjs-underscore. 146s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 146s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 146s Selecting previously unselected package libjs-sphinxdoc. 146s Preparing to unpack .../4-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 146s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 146s Selecting previously unselected package sphinx-rtd-theme-common. 146s Preparing to unpack .../5-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 146s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 146s Selecting previously unselected package pdb2pqr-doc. 146s Preparing to unpack .../6-pdb2pqr-doc_3.6.1+dfsg-1_all.deb ... 146s Unpacking pdb2pqr-doc (3.6.1+dfsg-1) ... 146s Setting up fonts-lato (2.015-1) ... 146s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 146s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 146s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 146s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 146s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 146s Setting up pdb2pqr-doc (3.6.1+dfsg-1) ... 147s autopkgtest [04:30:18]: test pdb2pka-test: [----------------------- 147s Run pdb2pqr... 148s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 148s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 148s 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). 148s INFO:Checking and transforming input arguments. 148s INFO:Loading topology files. 148s INFO:Loading molecule: 1a1p/1a1p.pdb 148s INFO:Setting up molecule. 148s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 148s INFO:Created biomolecule object with 14 residues and 208 atoms. 148s INFO:Setting termini states for biomolecule chains. 148s INFO:Loading forcefield. 148s INFO:Loading hydrogen topology definitions. 148s INFO:This biomolecule is clean. No repair needed. 148s INFO:Updating disulfide bridges. 148s INFO:Debumping biomolecule. 148s INFO:Adding hydrogens to biomolecule. 148s INFO:Debumping biomolecule (again). 148s INFO:Optimizing hydrogen bonds 148s INFO:Applying force field to biomolecule states. 148s INFO:Regenerating headers. 148s INFO:Regenerating PDB lines. 148s WARNING:Ignoring 852 header lines in output. 148s WARNING:Ignoring 3 missing lines in output. 148s autopkgtest [04:30:19]: test pdb2pka-test: -----------------------] 149s autopkgtest [04:30:20]: test pdb2pka-test: - - - - - - - - - - results - - - - - - - - - - 149s pdb2pka-test PASS 149s autopkgtest [04:30:20]: test command1: preparing testbed 149s Reading package lists... 149s Building dependency tree... 149s Reading state information... 150s Solving dependencies... 150s The following NEW packages will be installed: 150s python3-dateutil python3-iniconfig python3-packaging python3-pandas 150s python3-pandas-lib python3-pluggy python3-pytest python3-pytz 150s python3-testfixtures 150s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 150s Need to get 11.1 MB of archives. 150s After this operation, 78.9 MB of additional disk space will be used. 150s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-dateutil all 2.9.0-4 [80.3 kB] 150s Get:2 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 150s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-packaging all 25.0-1 [52.8 kB] 150s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-pytz all 2025.2-4 [32.3 kB] 150s Get:5 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pandas-lib ppc64el 2.3.3+dfsg-1ubuntu1 [7666 kB] 152s Get:6 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 153s Get:7 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pluggy all 1.6.0-1 [21.0 kB] 153s Get:8 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pytest all 8.3.5-2 [252 kB] 153s Get:9 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-testfixtures all 9.2.0-1 [79.2 kB] 153s Fetched 11.1 MB in 3s (3594 kB/s) 153s Selecting previously unselected package python3-dateutil. 153s (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 ... 78395 files and directories currently installed.) 153s Preparing to unpack .../0-python3-dateutil_2.9.0-4_all.deb ... 153s Unpacking python3-dateutil (2.9.0-4) ... 153s Selecting previously unselected package python3-iniconfig. 153s Preparing to unpack .../1-python3-iniconfig_1.1.1-2_all.deb ... 153s Unpacking python3-iniconfig (1.1.1-2) ... 153s Selecting previously unselected package python3-packaging. 153s Preparing to unpack .../2-python3-packaging_25.0-1_all.deb ... 153s Unpacking python3-packaging (25.0-1) ... 153s Selecting previously unselected package python3-pytz. 153s Preparing to unpack .../3-python3-pytz_2025.2-4_all.deb ... 153s Unpacking python3-pytz (2025.2-4) ... 153s Selecting previously unselected package python3-pandas-lib:ppc64el. 153s Preparing to unpack .../4-python3-pandas-lib_2.3.3+dfsg-1ubuntu1_ppc64el.deb ... 153s Unpacking python3-pandas-lib:ppc64el (2.3.3+dfsg-1ubuntu1) ... 153s Selecting previously unselected package python3-pandas. 153s Preparing to unpack .../5-python3-pandas_2.3.3+dfsg-1ubuntu1_all.deb ... 153s Unpacking python3-pandas (2.3.3+dfsg-1ubuntu1) ... 154s Selecting previously unselected package python3-pluggy. 154s Preparing to unpack .../6-python3-pluggy_1.6.0-1_all.deb ... 154s Unpacking python3-pluggy (1.6.0-1) ... 154s Selecting previously unselected package python3-pytest. 154s Preparing to unpack .../7-python3-pytest_8.3.5-2_all.deb ... 154s Unpacking python3-pytest (8.3.5-2) ... 154s Selecting previously unselected package python3-testfixtures. 154s Preparing to unpack .../8-python3-testfixtures_9.2.0-1_all.deb ... 154s Unpacking python3-testfixtures (9.2.0-1) ... 154s Setting up python3-iniconfig (1.1.1-2) ... 154s Setting up python3-pandas-lib:ppc64el (2.3.3+dfsg-1ubuntu1) ... 154s Setting up python3-testfixtures (9.2.0-1) ... 154s Setting up python3-pytz (2025.2-4) ... 154s Setting up python3-packaging (25.0-1) ... 154s Setting up python3-pluggy (1.6.0-1) ... 154s Setting up python3-dateutil (2.9.0-4) ... 155s Setting up python3-pytest (8.3.5-2) ... 155s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 160s Processing triggers for man-db (2.13.1-1) ... 162s autopkgtest [04:30:33]: test command1: pytest-3 162s autopkgtest [04:30:33]: test command1: [----------------------- 163s ============================= test session starts ============================== 163s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 163s rootdir: /tmp/autopkgtest.D7wiF4/build.ETR/src 163s configfile: pytest.ini 163s plugins: typeguard-4.4.2 163s 163s ----------------------------- live log collection ------------------------------ 163s WARNING py.warnings:warnings.py:110 /tmp/autopkgtest.D7wiF4/build.ETR/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 163s @pytest.mark.long_test 163s 163s ERROR regression_test:regression_test.py:173 Need to reinstate the --apbs-input test with a temporary directory as path 163s collected 316 items 163s 163s tests/core_test.py::test_short_pdb[1NAJ] SKIPPED (not running tests ...) [ 0%] 163s tests/core_test.py::test_short_pdb[4UN3] SKIPPED (not running tests ...) [ 0%] 163s tests/core_test.py::test_short_pdb[1AQO] SKIPPED (not running tests ...) [ 0%] 164s tests/core_test.py::test_short_pdb[5D8V] SKIPPED (not running tests ...) [ 1%] 164s tests/core_test.py::test_short_pdb[1K1I] SKIPPED (not running tests ...) [ 1%] 164s tests/core_test.py::test_short_pdb[7BNA] SKIPPED (not running tests ...) [ 1%] 164s tests/core_test.py::test_short_pdb[1FAS] SKIPPED (not running tests ...) [ 2%] 164s tests/core_test.py::test_short_pdb[4E8M] SKIPPED (not running tests ...) 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[ 54%] 164s tests/core_test.py::test_long_pdb[2VWR] SKIPPED (not running tests r...) [ 55%] 164s tests/core_test.py::test_long_pdb[2PMR] SKIPPED (not running tests r...) [ 55%] 164s tests/core_test.py::test_long_pdb[3US6] SKIPPED (not running tests r...) [ 55%] 164s tests/core_test.py::test_long_pdb[2CGQ] SKIPPED (not running tests r...) [ 56%] 164s tests/core_test.py::test_long_pdb[3I1G] SKIPPED (not running tests r...) [ 56%] 164s tests/core_test.py::test_long_pdb[4RWU] SKIPPED (not running tests r...) [ 56%] 164s tests/core_test.py::test_long_pdb[2YXF] SKIPPED (not running tests r...) [ 56%] 164s tests/core_test.py::test_long_pdb[2GZV] SKIPPED (not running tests r...) [ 57%] 164s tests/core_test.py::test_long_pdb[1USM] SKIPPED (not running tests r...) [ 57%] 164s tests/core_test.py::test_long_pdb[2PND] SKIPPED (not running tests r...) [ 57%] 164s tests/core_test.py::test_long_pdb[2PTV] SKIPPED (not running tests r...) [ 58%] 164s tests/core_test.py::test_long_pdb[1R5Q] SKIPPED (not running tests r...) [ 58%] 164s tests/core_test.py::test_long_pdb[1KFN] SKIPPED (not running tests r...) [ 58%] 164s tests/core_test.py::test_long_pdb[1PZC] SKIPPED (not running tests r...) [ 59%] 164s tests/core_test.py::test_long_pdb[1UG4] SKIPPED (not running tests r...) [ 59%] 164s tests/core_test.py::test_long_pdb[1OPC] SKIPPED (not running tests r...) [ 59%] 164s tests/core_test.py::test_long_pdb[2H2C] SKIPPED (not running tests r...) [ 60%] 164s tests/core_test.py::test_long_pdb[2IGD] SKIPPED (not running tests r...) [ 60%] 164s tests/core_test.py::test_long_pdb[4CFI] SKIPPED (not running tests r...) [ 60%] 164s tests/core_test.py::test_long_pdb[2FRG] SKIPPED (not running tests r...) [ 61%] 164s tests/core_test.py::test_long_pdb[3H0X] SKIPPED (not running tests r...) [ 61%] 164s tests/core_test.py::test_long_pdb[1HOE] SKIPPED (not running tests r...) [ 61%] 164s tests/core_test.py::test_long_pdb[2XXC] SKIPPED (not running tests r...) [ 62%] 164s tests/core_test.py::test_long_pdb[1TGN] SKIPPED (not running tests r...) [ 62%] 164s tests/core_test.py::test_long_pdb[4CRH] SKIPPED (not running tests r...) [ 62%] 164s tests/core_test.py::test_long_pdb[2SFA] SKIPPED (not running tests r...) [ 62%] 164s tests/core_test.py::test_long_pdb[1AIL] SKIPPED (not running tests r...) [ 63%] 164s tests/core_test.py::test_long_pdb[3TSV] SKIPPED (not running tests r...) [ 63%] 164s tests/core_test.py::test_long_pdb[3ZSL] SKIPPED (not running tests r...) [ 63%] 164s tests/core_test.py::test_long_pdb[1DUP] SKIPPED (not running tests r...) [ 64%] 164s tests/core_test.py::test_long_pdb[2NSN] SKIPPED (not running tests r...) [ 64%] 164s tests/core_test.py::test_long_pdb[1BM8] SKIPPED (not running tests r...) [ 64%] 164s tests/core_test.py::test_long_pdb[4AXT] SKIPPED (not running tests r...) [ 65%] 164s tests/core_test.py::test_long_pdb[1IS5] SKIPPED (not running tests r...) [ 65%] 164s tests/core_test.py::test_long_pdb[3LMO] SKIPPED (not running tests r...) [ 65%] 164s tests/core_test.py::test_long_pdb[4L9E] SKIPPED (not running tests r...) [ 66%] 164s tests/core_test.py::test_broken_backbone[3U7T] 164s -------------------------------- live log call --------------------------------- 164s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_3U7T_0/3U7T.log 164s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 164s 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). 164s 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). 164s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 164s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 164s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T 164s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 164s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 164s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 652 atoms. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in PRO A 22. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in PRO A 22. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in PRO A 22. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in PRO A 22. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 22. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in PRO A 22. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in PRO A 22. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 22. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 22. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in PRO A 22. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 22. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in PRO A 22. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 22. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 22. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 22. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 22. 164s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 22. At least one of the instances is being ignored. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in LEU A 25. 164s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in LEU A 25. At least one of the instances is being ignored. 164s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 164s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 164s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 164s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 164s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 164s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 164s 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 164s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 165s XFAIL [ 66%] 165s tests/core_test.py::test_broken_backbone[4MGP] 165s -------------------------------- live log call --------------------------------- 165s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_4MGP_0/4MGP.log 165s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 165s 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). 165s 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). 165s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 165s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 165s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP 165s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 165s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 165s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 23 residues and 163 atoms. 165s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in MET A 21. 165s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in MET A 21. 165s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in MET A 21. 165s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: SD in MET A 21. 165s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE in MET A 21. 165s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in MET A 21. At least one of the instances is being ignored. 165s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 165s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 165s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 165s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 12 missing atoms in biomolecule. 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 165s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 165s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 11 at coordinates 1.430, -1.683, -11.529 165s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 11 at coordinates 1.940, -0.315, -11.800 165s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CG to residue LYS A 14 at coordinates -1.600, -8.819, -6.913 165s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CD to residue LYS A 14 at coordinates -2.056, -8.844, -8.361 165s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 14 at coordinates -3.548, -9.031, -8.498 165s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 14 at coordinates -3.947, -9.048, -9.928 165s 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 165s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 165s XFAIL [ 66%] 165s tests/core_test.py::test_broken_backbone[1EJG] 165s -------------------------------- live log call --------------------------------- 165s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_1EJG_0/1EJG.log 165s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 165s 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). 165s 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). 165s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 165s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 166s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG 166s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 166s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 166s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 650 atoms. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in THR A 1. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 1. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 1. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 1. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 1. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H1 in THR A 1. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H2 in THR A 1. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H3 in THR A 1. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 1. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 1. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 1. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 1. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 1. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 1. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 1. At least one of the instances is being ignored. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 2. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 2. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 2. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 2. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 2. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 2. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 2. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 2. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 2. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 2. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 2. At least one of the instances is being ignored. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 7. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 7. At least one of the instances is being ignored. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in VAL A 8. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in VAL A 8. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in VAL A 8. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in VAL A 8. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in VAL A 8. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in VAL A 8. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in VAL A 8. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in VAL A 8. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG11 in VAL A 8. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in VAL A 8. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in VAL A 8. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in VAL A 8. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in VAL A 8. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in VAL A 8. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in VAL A 8. At least one of the instances is being ignored. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NE in ARG A 10. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in ARG A 10. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH1 in ARG A 10. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH2 in ARG A 10. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE in ARG A 10. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH11 in ARG A 10. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH12 in ARG A 10. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH21 in ARG A 10. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH22 in ARG A 10. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ARG A 10. At least one of the instances is being ignored. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ASN A 12. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASN A 12. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 12. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 12. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 12. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ASN A 12. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASN A 12. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASN A 12. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 12. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 12. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 12. At least one of the instances is being ignored. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PHE A 13. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in PHE A 13. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in PHE A 13. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in PHE A 13. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in PHE A 13. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in PHE A 13. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in PHE A 13. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PHE A 13. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in PHE A 13. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in PHE A 13. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HZ in PHE A 13. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PHE A 13. At least one of the instances is being ignored. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 19. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 19. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 19. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 19. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 19. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 19. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 19. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 19. At least one of the instances is being ignored. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in SER A 22. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in SER A 22. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in SER A 22. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in SER A 22. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in SER A 22. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in SER A 22. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in SER A 22. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in SER A 22. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in SER A 22. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in SER A 22. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in SER A 22. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in SER A 22. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in SER A 22. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in SER A 22. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in SER A 22. At least one of the instances is being ignored. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in GLU A 23. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in GLU A 23. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE1 in GLU A 23. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE2 in GLU A 23. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in GLU A 23. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in GLU A 23. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in GLU A 23. At least one of the instances is being ignored. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 25. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 25. At least one of the instances is being ignored. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in TYR A 29. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in TYR A 29. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in TYR A 29. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in TYR A 29. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in TYR A 29. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in TYR A 29. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OH in TYR A 29. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in TYR A 29. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in TYR A 29. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in TYR A 29. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in TYR A 29. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH in TYR A 29. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in TYR A 29. At least one of the instances is being ignored. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 34. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 34. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 34. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 34. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 34. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 34. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 34. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 34. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 34. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 34. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 34. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 34. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 34. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 34. At least one of the instances is being ignored. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 36. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 36. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 36. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 36. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 36. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 36. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 36. At least one of the instances is being ignored. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 39. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 39. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 39. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 39. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 39. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 39. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 39. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 39. At least one of the instances is being ignored. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASP A 43. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASP A 43. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASP A 43. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD2 in ASP A 43. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASP A 43. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASP A 43. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASP A 43. At least one of the instances is being ignored. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 46. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 46. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 46. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 46. 166s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 46. 166s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 46. At least one of the instances is being ignored. 166s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 166s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 166s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 166s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 166s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 166s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 166s 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 166s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 167s XFAIL [ 67%] 167s tests/core_test.py::test_broken_backbone[2V75] 167s -------------------------------- live log call --------------------------------- 167s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_2V75_0/2V75.log 167s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 167s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 167s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 167s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 167s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 167s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 168s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 168s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 168s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 90 residues and 687 atoms. 168s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 168s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 168s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 168s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 8 missing atoms in biomolecule. 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 168s 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 168s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 168s XFAIL [ 67%] 168s tests/core_test.py::test_protonated_terminals[C-terminal HID] 168s -------------------------------- live log call --------------------------------- 168s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log 168s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 168s 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). 168s 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). 168s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 168s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 168s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/cterm_hid.pdb 168s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 168s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms. 168s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 168s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 168s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 168s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule. 168s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 168s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402 168s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 168s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 168s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 168s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 168s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 168s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 168s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 168s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 168s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 168s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 168s INFO common:common.py:198 0 atoms have position differences > 0 168s INFO common:common.py:198 0 atoms have position differences > 0.01 168s INFO common:common.py:198 0 atoms have charge differences > 0 168s INFO common:common.py:198 0 atoms have charge differences > 0.01 168s INFO common:common.py:198 0 atoms have radius differences > 0 168s INFO common:common.py:198 0 atoms have radius differences > 0.01 168s PASSED [ 67%] 168s tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 168s -------------------------------- live log call --------------------------------- 168s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log 168s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 168s 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). 168s 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). 168s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 168s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 168s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/5vav_cyclic_peptide.pdb 168s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 168s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms. 168s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 168s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 168s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 168s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 168s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 168s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 168s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 168s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 168s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 168s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 168s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 168s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 168s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 168s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 168s INFO common:common.py:198 0 atoms have position differences > 0 168s INFO common:common.py:198 0 atoms have position differences > 0.01 168s INFO common:common.py:198 0 atoms have charge differences > 0 168s INFO common:common.py:198 0 atoms have charge differences > 0.01 168s INFO common:common.py:198 0 atoms have radius differences > 0 168s INFO common:common.py:198 0 atoms have radius differences > 0.01 168s PASSED [ 68%] 168s tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 68%] 168s tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 68%] 168s tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 68%] 168s tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 69%] 169s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 69%] 169s tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 69%] 169s tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 70%] 169s tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 70%] 169s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 70%] 169s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 71%] 169s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 71%] 169s tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 71%] 169s tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 72%] 169s 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 [ 72%] 169s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 72%] 169s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 73%] 169s tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 73%] 169s tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 73%] 169s tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 74%] 169s tests/io_test.py::test_read_qcd PASSED [ 74%] 169s tests/io_test.py::test_dx2cube 169s -------------------------------- live log call --------------------------------- 169s INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... 169s INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... 170s INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 171s INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 171s INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... 171s INFO io_test:io_test.py:68 No differences found in output 171s PASSED [ 74%] 172s tests/ligand_test.py::test_peoe_charges 172s -------------------------------- live log call --------------------------------- 172s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 172s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 172s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 172s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 172s PASSED [ 75%] 173s tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 173s -------------------------------- live log call --------------------------------- 173s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 173s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 173s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 173s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 173s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 173s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 173s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 173s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 173s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 173s PASSED [ 75%] 174s tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 174s -------------------------------- live log call --------------------------------- 174s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 174s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 174s PASSED [ 75%] 174s tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 174s -------------------------------- live log call --------------------------------- 174s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 174s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 174s PASSED [ 75%] 174s tests/ligand_test.py::test_assign_parameters[acetate.mol2] 174s -------------------------------- live log call --------------------------------- 174s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 174s PASSED [ 76%] 174s tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 174s -------------------------------- live log call --------------------------------- 174s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 174s PASSED [ 76%] 174s tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 174s -------------------------------- live log call --------------------------------- 174s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 174s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 174s PASSED [ 76%] 174s tests/ligand_test.py::test_assign_parameters[adp.mol2] 174s -------------------------------- live log call --------------------------------- 174s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 174s INFO ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00 174s PASSED [ 77%] 174s tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 174s -------------------------------- live log call --------------------------------- 174s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 174s PASSED [ 77%] 174s tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 174s -------------------------------- live log call --------------------------------- 174s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 174s PASSED [ 77%] 174s tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 174s -------------------------------- live log call --------------------------------- 174s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 174s PASSED [ 78%] 174s tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 174s -------------------------------- live log call --------------------------------- 174s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 174s PASSED [ 78%] 174s tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 174s -------------------------------- live log call --------------------------------- 174s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 174s PASSED [ 78%] 174s tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 174s -------------------------------- live log call --------------------------------- 174s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 174s PASSED [ 79%] 174s tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 174s -------------------------------- live log call --------------------------------- 174s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 174s PASSED [ 79%] 174s tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 174s -------------------------------- live log call --------------------------------- 174s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 174s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 174s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 174s PASSED [ 79%] 175s tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 175s -------------------------------- live log call --------------------------------- 175s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 175s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 175s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 175s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 175s PASSED [ 80%] 176s tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 176s -------------------------------- live log call --------------------------------- 176s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 176s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 176s PASSED [ 80%] 176s tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 176s -------------------------------- live log call --------------------------------- 176s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 176s PASSED [ 80%] 176s tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED [ 81%] 176s tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED [ 81%] 176s tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 176s -------------------------------- live log call --------------------------------- 176s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 176s PASSED [ 81%] 176s tests/ligand_test.py::test_formal_charge[adp.mol2] 176s -------------------------------- live log call --------------------------------- 176s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 176s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 176s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 176s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 176s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 176s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 176s PASSED [ 81%] 176s tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED [ 82%] 176s tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED [ 82%] 176s tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED [ 82%] 176s tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED [ 83%] 176s tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED [ 83%] 176s tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED [ 83%] 176s tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED [ 84%] 176s tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 176s -------------------------------- live log call --------------------------------- 176s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 176s PASSED [ 84%] 176s tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED [ 84%] 176s tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED [ 85%] 176s tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED [ 85%] 176s tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED [ 85%] 176s tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED [ 86%] 176s tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED [ 86%] 177s tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED [ 86%] 178s tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED [ 87%] 178s tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED [ 87%] 178s tests/ligand_test.py::test_rings[acetate.mol2] PASSED [ 87%] 178s tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED [ 87%] 178s tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED [ 88%] 178s tests/ligand_test.py::test_rings[adp.mol2] PASSED [ 88%] 178s tests/ligand_test.py::test_rings[anthracene.mol2] PASSED [ 88%] 178s tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED [ 89%] 178s tests/ligand_test.py::test_rings[ethanol.mol2] PASSED [ 89%] 178s tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED [ 89%] 178s tests/ligand_test.py::test_rings[glycerol.mol2] PASSED [ 90%] 178s tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED [ 90%] 178s tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED [ 90%] 178s tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED [ 91%] 178s tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%] 178s tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%] 178s tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%] 178s tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%] 178s tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%] 178s tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%] 178s tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%] 178s tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%] 178s tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%] 178s tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%] 178s tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%] 178s tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] 178s tests/regression_test.py::test_basic[1AFS basic local] 178s -------------------------------- live log call --------------------------------- 178s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_basic_1AFS_basic_local_0/output.log 178s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 178s 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). 178s 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). 178s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 178s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 178s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 179s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 179s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 179s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 179s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 179s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 179s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 179s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 179s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 179s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 179s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 179s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 179s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 179s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 179s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 179s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 179s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 179s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 179s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 179s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 179s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 179s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 180s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 181s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 182s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 182s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 182s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 182s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 182s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 182s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 182s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 182s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 182s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 182s WARNING pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages 186s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 186s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 186s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 186s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 186s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 186s WARNING common:common.py:186 6 atoms have position differences > 0 186s INFO common:common.py:198 0 atoms have position differences > 0.01 186s INFO common:common.py:198 0 atoms have charge differences > 0 186s INFO common:common.py:198 0 atoms have charge differences > 0.01 186s INFO common:common.py:198 0 atoms have radius differences > 0 186s INFO common:common.py:198 0 atoms have radius differences > 0.01 186s PASSED [ 95%] 186s tests/regression_test.py::test_forcefields[1AFS whitespace AMBER] 186s -------------------------------- live log call --------------------------------- 186s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa0/output.log 186s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 186s 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). 186s 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). 186s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 186s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 186s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 186s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 186s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 186s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 186s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 186s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 186s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 186s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 186s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 186s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 186s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 186s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 186s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 186s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 186s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 186s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 186s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 186s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 186s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 186s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 186s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 187s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 187s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 189s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 193s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 193s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 193s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 193s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 193s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 194s WARNING common:common.py:186 6 atoms have position differences > 0 194s INFO common:common.py:198 0 atoms have position differences > 0.01 194s INFO common:common.py:198 0 atoms have charge differences > 0 194s INFO common:common.py:198 0 atoms have charge differences > 0.01 194s INFO common:common.py:198 0 atoms have radius differences > 0 194s INFO common:common.py:198 0 atoms have radius differences > 0.01 194s PASSED [ 95%] 194s tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] 194s -------------------------------- live log call --------------------------------- 194s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa1/output.log 194s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 194s 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). 194s 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). 194s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 194s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 194s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 194s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 194s WARNING pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages 194s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 194s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 194s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 194s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 194s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 194s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 194s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 194s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 194s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 194s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 194s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 194s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 194s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 194s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 194s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 194s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 195s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 196s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 201s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 201s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 201s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 201s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 201s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 202s WARNING common:common.py:186 5 atoms have position differences > 0 202s INFO common:common.py:198 0 atoms have position differences > 0.01 202s INFO common:common.py:198 0 atoms have charge differences > 0 202s INFO common:common.py:198 0 atoms have charge differences > 0.01 202s INFO common:common.py:198 0 atoms have radius differences > 0 202s INFO common:common.py:198 0 atoms have radius differences > 0.01 202s PASSED [ 95%] 202s tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] 202s -------------------------------- live log call --------------------------------- 202s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa2/output.log 202s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 202s 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). 202s 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). 202s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 202s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 202s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 202s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 202s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 202s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 202s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 202s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 202s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 202s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 202s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 202s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 202s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 202s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 202s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 202s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 202s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 202s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 202s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 202s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 203s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 204s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 209s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 209s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 209s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 209s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 209s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 209s WARNING common:common.py:186 6 atoms have position differences > 0 209s INFO common:common.py:198 0 atoms have position differences > 0.01 209s INFO common:common.py:198 0 atoms have charge differences > 0 209s INFO common:common.py:198 0 atoms have charge differences > 0.01 209s INFO common:common.py:198 0 atoms have radius differences > 0 209s INFO common:common.py:198 0 atoms have radius differences > 0.01 209s PASSED [ 96%] 209s tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] 209s -------------------------------- live log call --------------------------------- 209s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa3/output.log 209s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 209s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 209s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 209s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 209s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 209s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 209s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 209s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 209s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 209s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 209s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 209s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 209s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 209s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 209s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 209s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 209s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 209s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 209s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 209s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 209s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 209s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 210s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 210s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 212s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 216s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 217s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 217s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 217s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 217s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 217s WARNING common:common.py:186 6 atoms have position differences > 0 217s INFO common:common.py:198 0 atoms have position differences > 0.01 217s INFO common:common.py:198 0 atoms have charge differences > 0 217s INFO common:common.py:198 0 atoms have charge differences > 0.01 217s INFO common:common.py:198 0 atoms have radius differences > 0 217s INFO common:common.py:198 0 atoms have radius differences > 0.01 217s PASSED [ 96%] 217s tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] 217s -------------------------------- live log call --------------------------------- 217s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa4/output.log 217s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 217s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 217s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 217s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 217s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 217s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 217s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 217s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 217s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 217s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 217s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 217s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 217s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 217s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 217s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 217s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 217s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 217s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 217s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 217s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 217s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 217s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 217s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 218s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 219s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 224s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 224s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 224s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 224s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output. 224s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 225s WARNING common:common.py:186 6 atoms have position differences > 0 225s INFO common:common.py:198 0 atoms have position differences > 0.01 225s INFO common:common.py:198 0 atoms have charge differences > 0 225s INFO common:common.py:198 0 atoms have charge differences > 0.01 225s INFO common:common.py:198 0 atoms have radius differences > 0 225s INFO common:common.py:198 0 atoms have radius differences > 0.01 225s PASSED [ 96%] 225s tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] 225s -------------------------------- live log call --------------------------------- 225s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa5/output.log 225s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 225s 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). 225s 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). 225s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 225s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 225s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 225s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 225s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 225s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 225s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 225s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 225s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 225s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 225s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 225s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 225s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 225s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 225s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 225s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 225s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 225s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 225s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 225s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 226s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 227s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 232s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 232s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 232s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 232s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 232s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 232s WARNING common:common.py:186 6 atoms have position differences > 0 232s INFO common:common.py:198 0 atoms have position differences > 0.01 232s INFO common:common.py:198 0 atoms have charge differences > 0 232s INFO common:common.py:198 0 atoms have charge differences > 0.01 232s INFO common:common.py:198 0 atoms have radius differences > 0 232s INFO common:common.py:198 0 atoms have radius differences > 0.01 232s PASSED [ 97%] 232s tests/regression_test.py::test_other_options[1AFS whitespace clean] 232s -------------------------------- live log call --------------------------------- 232s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_whites0/output.log 232s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 232s 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). 232s 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). 232s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 232s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 232s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 232s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 232s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 232s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 232s INFO PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps. 233s INFO common:common.py:198 0 atoms have position differences > 0 233s INFO common:common.py:198 0 atoms have position differences > 0.01 233s INFO common:common.py:198 0 atoms have charge differences > 0 233s INFO common:common.py:198 0 atoms have charge differences > 0.01 233s INFO common:common.py:198 0 atoms have radius differences > 0 233s INFO common:common.py:198 0 atoms have radius differences > 0.01 233s PASSED [ 97%] 233s tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] 233s -------------------------------- live log call --------------------------------- 233s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_assign0/output.log 233s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 233s 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). 233s 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). 233s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 233s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 233s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 233s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 233s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 233s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 233s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 233s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 233s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 233s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 233s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 233s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 233s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 233s INFO common:common.py:198 0 atoms have position differences > 0 233s INFO common:common.py:198 0 atoms have position differences > 0.01 233s INFO common:common.py:198 0 atoms have charge differences > 0 233s INFO common:common.py:198 0 atoms have charge differences > 0.01 233s INFO common:common.py:198 0 atoms have radius differences > 0 233s INFO common:common.py:198 0 atoms have radius differences > 0.01 233s PASSED [ 97%] 233s tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] 233s -------------------------------- live log call --------------------------------- 233s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_nodebu0/output.log 233s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 233s 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). 233s 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). 233s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 233s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 233s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 233s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 233s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 233s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 233s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 233s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 233s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 233s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 233s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 233s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 233s INFO pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization... 233s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 233s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 233s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 233s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 233s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 233s INFO common:common.py:198 0 atoms have position differences > 0 233s INFO common:common.py:198 0 atoms have position differences > 0.01 233s INFO common:common.py:198 0 atoms have charge differences > 0 233s INFO common:common.py:198 0 atoms have charge differences > 0.01 233s INFO common:common.py:198 0 atoms have radius differences > 0 233s INFO common:common.py:198 0 atoms have radius differences > 0.01 233s PASSED [ 98%] 233s tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] 233s -------------------------------- live log call --------------------------------- 233s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_chain_0/output.log 233s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 233s 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). 233s 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). 233s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 233s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 233s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 233s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 233s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 233s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 233s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 233s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 233s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 233s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 233s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 233s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 233s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 233s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 233s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 233s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 233s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 233s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 233s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 234s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 234s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 236s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 241s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 241s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 241s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 241s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 241s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 241s WARNING common:common.py:186 6 atoms have position differences > 0 241s INFO common:common.py:198 0 atoms have position differences > 0.01 241s INFO common:common.py:198 0 atoms have charge differences > 0 241s INFO common:common.py:198 0 atoms have charge differences > 0.01 241s INFO common:common.py:198 0 atoms have radius differences > 0 241s INFO common:common.py:198 0 atoms have radius differences > 0.01 241s PASSED [ 98%] 241s tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] 241s -------------------------------- live log call --------------------------------- 241s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_neutra0/output.log 241s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 241s 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). 241s 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). 241s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 241s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 241s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 241s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 241s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 241s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 241s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 241s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 241s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 241s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 241s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 241s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 241s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 241s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 241s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 241s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 241s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 241s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 241s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 242s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 242s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 244s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 249s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 249s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 249s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 249s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 249s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 249s WARNING common:common.py:186 6 atoms have position differences > 0 249s INFO common:common.py:198 0 atoms have position differences > 0.01 249s INFO common:common.py:198 0 atoms have charge differences > 0 249s INFO common:common.py:198 0 atoms have charge differences > 0.01 249s INFO common:common.py:198 0 atoms have radius differences > 0 249s INFO common:common.py:198 0 atoms have radius differences > 0.01 249s PASSED [ 98%] 249s tests/regression_test.py::test_other_options[1AFS drop-water AMBER] 249s -------------------------------- live log call --------------------------------- 249s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_drop_w0/output.log 249s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 249s 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). 249s 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). 249s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 249s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 249s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 249s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 249s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 249s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms. 249s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 249s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 249s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 249s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 249s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 249s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 249s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 249s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 249s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 249s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 249s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 249s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 249s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 249s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 250s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 250s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 252s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 255s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 255s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 255s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 255s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 255s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 255s WARNING common:common.py:186 6 atoms have position differences > 0 255s INFO common:common.py:198 0 atoms have position differences > 0.01 255s INFO common:common.py:198 0 atoms have charge differences > 0 255s INFO common:common.py:198 0 atoms have charge differences > 0.01 255s INFO common:common.py:198 0 atoms have radius differences > 0 255s INFO common:common.py:198 0 atoms have radius differences > 0.01 255s PASSED [ 99%] 255s tests/regression_test.py::test_other_options[1AFS userff usernames whitespace] 255s -------------------------------- live log call --------------------------------- 255s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_userff0/output.log 255s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 255s 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). 255s 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). 255s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 255s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 255s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 255s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 255s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 255s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 255s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 255s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 255s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 255s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 255s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 255s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 255s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 255s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 255s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 255s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 255s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 255s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 255s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 256s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 256s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 258s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 262s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 263s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 263s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 263s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 263s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 263s WARNING common:common.py:186 6 atoms have position differences > 0 263s INFO common:common.py:198 0 atoms have position differences > 0.01 263s INFO common:common.py:198 0 atoms have charge differences > 0 263s INFO common:common.py:198 0 atoms have charge differences > 0.01 263s INFO common:common.py:198 0 atoms have radius differences > 0 263s INFO common:common.py:198 0 atoms have radius differences > 0.01 263s PASSED [ 99%] 263s tests/test_version.py::test_version_exists PASSED [ 99%] 263s tests/test_version.py::test_version PASSED [100%] 263s 263s ============ 92 passed, 220 skipped, 4 xfailed in 100.36s (0:01:40) ============ 263s autopkgtest [04:32:14]: test command1: -----------------------] 264s command1 PASS 264s autopkgtest [04:32:15]: test command1: - - - - - - - - - - results - - - - - - - - - - 264s autopkgtest [04:32:15]: @@@@@@@@@@@@@@@@@@@@ summary 264s installation-test PASS 264s pdb2pka-test PASS 264s command1 PASS