0s autopkgtest [00:37:18]: starting date and time: 2025-10-22 00:37:18+0000 0s autopkgtest [00:37:18]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [00:37:18]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.wmbkz8ju/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:python-pluggy --apt-upgrade pdb2pqr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.4.2-1 python-pluggy/1.6.0-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-ppc64el-9.secgroup --name adt-resolute-ppc64el-pdb2pqr-20251022-003718-juju-7f2275-prod-proposed-migration-environment-20-f98faf19-23a6-4f10-af34-ab66ab21829f --image adt/ubuntu-resolute-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-ppc64el-pdb2pqr-20251022-003718-juju-7f2275-prod-proposed-migration-environment-20-f98faf19-23a6-4f10-af34-ab66ab21829f from image adt/ubuntu-resolute-ppc64el-server-20251021.img (UUID c177abc7-cbc1-4b1f-967f-196ea722a402)... 49s autopkgtest [00:38:07]: testbed dpkg architecture: ppc64el 49s autopkgtest [00:38:07]: testbed apt version: 3.1.8ubuntu1 50s autopkgtest [00:38:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 50s autopkgtest [00:38:08]: testbed release detected to be: None 51s autopkgtest [00:38:09]: updating testbed package index (apt update) 51s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 52s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 52s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 52s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 52s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [599 kB] 53s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [57.6 kB] 53s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 53s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.0 kB] 53s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main ppc64el Packages [121 kB] 53s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted ppc64el Packages [940 B] 53s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el Packages [397 kB] 54s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse ppc64el Packages [4596 B] 54s Fetched 1283 kB in 3s (421 kB/s) 54s Reading package lists... 55s Failed to check for VM: Permission denied 55s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 55s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 55s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 55s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 56s Reading package lists... 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 57s The following packages will be upgraded: 57s dracut-install 57s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 57s Need to get 49.5 kB of archives. 57s After this operation, 1024 B of additional disk space will be used. 57s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el dracut-install ppc64el 108-8ubuntu1 [49.5 kB] 57s dpkg-preconfigure: unable to re-open stdin: No such file or directory 57s Fetched 49.5 kB in 0s (171 kB/s) 58s (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 ... 76480 files and directories currently installed.) 58s Preparing to unpack .../dracut-install_108-8ubuntu1_ppc64el.deb ... 58s Unpacking dracut-install (108-8ubuntu1) over (108-3ubuntu3) ... 58s Setting up dracut-install (108-8ubuntu1) ... 58s autopkgtest [00:38:16]: upgrading testbed (apt dist-upgrade and autopurge) 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s Calculating upgrade... 58s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 58s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Solving dependencies... 59s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s autopkgtest [00:38:19]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:02:41 UTC 2025 61s autopkgtest [00:38:19]: @@@@@@@@@@@@@@@@@@@@ apt-source pdb2pqr 67s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (dsc) [1860 B] 67s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (tar) [7570 kB] 67s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (diff) [9876 B] 67s gpgv: Signature made Mon Jun 12 17:36:50 2023 UTC 67s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 67s gpgv: Can't check signature: No public key 67s dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found 68s autopkgtest [00:38:26]: testing package pdb2pqr version 3.6.1+dfsg-1 69s autopkgtest [00:38:27]: build not needed 71s autopkgtest [00:38:29]: test installation-test: preparing testbed 71s Reading package lists... 71s Building dependency tree... 71s Reading state information... 71s Solving dependencies... 71s The following NEW packages will be installed: 71s docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr python3-docutils 71s python3-numpy python3-numpy-dev python3-pdb2pqr python3-pdbx python3-propka 71s python3-roman sgml-base xml-core 72s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 72s Need to get 9734 kB of archives. 72s After this operation, 42.5 MB of additional disk space will be used. 72s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy-dev ppc64el 1:2.2.4+ds-1ubuntu1 [153 kB] 72s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el libblas3 ppc64el 3.12.1-6build1 [291 kB] 72s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libgfortran5 ppc64el 15.2.0-5ubuntu1 [620 kB] 72s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el liblapack3 ppc64el 3.12.1-6build1 [2960 kB] 73s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-numpy ppc64el 1:2.2.4+ds-1ubuntu1 [4887 kB] 74s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el sgml-base all 1.31+nmu1 [11.0 kB] 74s Get:7 http://ftpmaster.internal/ubuntu resolute/main ppc64el xml-core all 0.19 [20.3 kB] 74s Get:8 http://ftpmaster.internal/ubuntu resolute/main ppc64el docutils-common all 0.21.2+dfsg-2 [131 kB] 74s Get:9 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-roman all 5.1-1 [10.6 kB] 74s Get:10 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-docutils all 0.21.2+dfsg-2 [409 kB] 74s Get:11 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pdbx all 2.0.1-2 [16.5 kB] 74s Get:12 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-propka all 3.5.1-2 [70.1 kB] 74s Get:13 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pdb2pqr all 3.6.1+dfsg-1 [145 kB] 74s Get:14 http://ftpmaster.internal/ubuntu resolute/universe ppc64el pdb2pqr all 3.6.1+dfsg-1 [10.4 kB] 74s Fetched 9734 kB in 3s (3667 kB/s) 74s Selecting previously unselected package python3-numpy-dev:ppc64el. 74s (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 ... 76480 files and directories currently installed.) 74s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 74s Unpacking python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 74s Selecting previously unselected package libblas3:ppc64el. 74s Preparing to unpack .../01-libblas3_3.12.1-6build1_ppc64el.deb ... 74s Unpacking libblas3:ppc64el (3.12.1-6build1) ... 74s Selecting previously unselected package libgfortran5:ppc64el. 74s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_ppc64el.deb ... 74s Unpacking libgfortran5:ppc64el (15.2.0-5ubuntu1) ... 74s Selecting previously unselected package liblapack3:ppc64el. 74s Preparing to unpack .../03-liblapack3_3.12.1-6build1_ppc64el.deb ... 74s Unpacking liblapack3:ppc64el (3.12.1-6build1) ... 74s Selecting previously unselected package python3-numpy. 74s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_ppc64el.deb ... 75s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 75s Selecting previously unselected package sgml-base. 75s Preparing to unpack .../05-sgml-base_1.31+nmu1_all.deb ... 75s Unpacking sgml-base (1.31+nmu1) ... 75s Selecting previously unselected package xml-core. 75s Preparing to unpack .../06-xml-core_0.19_all.deb ... 75s Unpacking xml-core (0.19) ... 75s Selecting previously unselected package docutils-common. 75s Preparing to unpack .../07-docutils-common_0.21.2+dfsg-2_all.deb ... 75s Unpacking docutils-common (0.21.2+dfsg-2) ... 75s Selecting previously unselected package python3-roman. 75s Preparing to unpack .../08-python3-roman_5.1-1_all.deb ... 75s Unpacking python3-roman (5.1-1) ... 75s Selecting previously unselected package python3-docutils. 75s Preparing to unpack .../09-python3-docutils_0.21.2+dfsg-2_all.deb ... 75s Unpacking python3-docutils (0.21.2+dfsg-2) ... 75s Selecting previously unselected package python3-pdbx. 75s Preparing to unpack .../10-python3-pdbx_2.0.1-2_all.deb ... 75s Unpacking python3-pdbx (2.0.1-2) ... 75s Selecting previously unselected package python3-propka. 75s Preparing to unpack .../11-python3-propka_3.5.1-2_all.deb ... 75s Unpacking python3-propka (3.5.1-2) ... 75s Selecting previously unselected package python3-pdb2pqr. 75s Preparing to unpack .../12-python3-pdb2pqr_3.6.1+dfsg-1_all.deb ... 75s Unpacking python3-pdb2pqr (3.6.1+dfsg-1) ... 75s Selecting previously unselected package pdb2pqr. 75s Preparing to unpack .../13-pdb2pqr_3.6.1+dfsg-1_all.deb ... 75s Unpacking pdb2pqr (3.6.1+dfsg-1) ... 75s Setting up python3-propka (3.5.1-2) ... 75s Setting up python3-pdbx (2.0.1-2) ... 75s Setting up python3-roman (5.1-1) ... 75s Setting up libblas3:ppc64el (3.12.1-6build1) ... 75s 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 75s Setting up python3-numpy-dev:ppc64el (1:2.2.4+ds-1ubuntu1) ... 75s Setting up libgfortran5:ppc64el (15.2.0-5ubuntu1) ... 75s Setting up sgml-base (1.31+nmu1) ... 75s Setting up liblapack3:ppc64el (3.12.1-6build1) ... 75s 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 75s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 77s Setting up xml-core (0.19) ... 77s Processing triggers for libc-bin (2.42-0ubuntu3) ... 77s Processing triggers for man-db (2.13.1-1) ... 78s Processing triggers for sgml-base (1.31+nmu1) ... 78s Setting up docutils-common (0.21.2+dfsg-2) ... 79s Processing triggers for sgml-base (1.31+nmu1) ... 79s Setting up python3-docutils (0.21.2+dfsg-2) ... 79s Setting up python3-pdb2pqr (3.6.1+dfsg-1) ... 79s Setting up pdb2pqr (3.6.1+dfsg-1) ... 80s autopkgtest [00:38:38]: test installation-test: [----------------------- 80s Run pdb2pqr... 80s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 80s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 80s 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). 80s INFO:Checking and transforming input arguments. 80s INFO:Loading topology files. 80s INFO:Loading molecule: examples/1a1p/1a1p.pdb 80s INFO:Setting up molecule. 80s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 80s INFO:Created biomolecule object with 14 residues and 208 atoms. 80s INFO:Setting termini states for biomolecule chains. 80s INFO:Loading forcefield. 80s INFO:Loading hydrogen topology definitions. 80s INFO:This biomolecule is clean. No repair needed. 80s INFO:Updating disulfide bridges. 80s INFO:Debumping biomolecule. 80s INFO:Adding hydrogens to biomolecule. 80s INFO:Debumping biomolecule (again). 80s INFO:Optimizing hydrogen bonds 80s INFO:Applying force field to biomolecule states. 80s INFO:Regenerating headers. 80s INFO:Regenerating PDB lines. 80s WARNING:Ignoring 852 header lines in output. 80s WARNING:Ignoring 3 missing lines in output. 81s autopkgtest [00:38:39]: test installation-test: -----------------------] 81s installation-test PASS 81s autopkgtest [00:38:39]: test installation-test: - - - - - - - - - - results - - - - - - - - - - 82s autopkgtest [00:38:40]: test pdb2pka-test: preparing testbed 82s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s Solving dependencies... 82s The following NEW packages will be installed: 82s fonts-font-awesome fonts-lato libjs-jquery libjs-sphinxdoc libjs-underscore 82s pdb2pqr-doc sphinx-rtd-theme-common 82s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 82s Need to get 5041 kB of archives. 82s After this operation, 20.0 MB of additional disk space will be used. 82s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-lato all 2.015-1 [2781 kB] 83s Get:2 http://ftpmaster.internal/ubuntu resolute/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 83s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 84s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 84s Get:5 http://ftpmaster.internal/ubuntu resolute/main ppc64el libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 84s Get:6 http://ftpmaster.internal/ubuntu resolute/main ppc64el sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 84s Get:7 http://ftpmaster.internal/ubuntu resolute/universe ppc64el pdb2pqr-doc all 3.6.1+dfsg-1 [258 kB] 84s Fetched 5041 kB in 2s (2938 kB/s) 84s Selecting previously unselected package fonts-lato. 84s (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 ... 77981 files and directories currently installed.) 84s Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... 84s Unpacking fonts-lato (2.015-1) ... 84s Selecting previously unselected package fonts-font-awesome. 84s Preparing to unpack .../1-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 84s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 84s Selecting previously unselected package libjs-jquery. 84s Preparing to unpack .../2-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 84s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 84s Selecting previously unselected package libjs-underscore. 84s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 84s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 84s Selecting previously unselected package libjs-sphinxdoc. 84s Preparing to unpack .../4-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 84s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 84s Selecting previously unselected package sphinx-rtd-theme-common. 84s Preparing to unpack .../5-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 84s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 84s Selecting previously unselected package pdb2pqr-doc. 84s Preparing to unpack .../6-pdb2pqr-doc_3.6.1+dfsg-1_all.deb ... 84s Unpacking pdb2pqr-doc (3.6.1+dfsg-1) ... 84s Setting up fonts-lato (2.015-1) ... 84s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 84s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 84s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 85s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 85s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 85s Setting up pdb2pqr-doc (3.6.1+dfsg-1) ... 86s autopkgtest [00:38:44]: test pdb2pka-test: [----------------------- 86s Run pdb2pqr... 86s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 86s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 86s 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). 86s INFO:Checking and transforming input arguments. 86s INFO:Loading topology files. 86s INFO:Loading molecule: 1a1p/1a1p.pdb 86s INFO:Setting up molecule. 86s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 86s INFO:Created biomolecule object with 14 residues and 208 atoms. 86s INFO:Setting termini states for biomolecule chains. 86s INFO:Loading forcefield. 86s INFO:Loading hydrogen topology definitions. 86s INFO:This biomolecule is clean. No repair needed. 86s INFO:Updating disulfide bridges. 86s INFO:Debumping biomolecule. 86s INFO:Adding hydrogens to biomolecule. 86s INFO:Debumping biomolecule (again). 86s INFO:Optimizing hydrogen bonds 86s INFO:Applying force field to biomolecule states. 86s INFO:Regenerating headers. 86s INFO:Regenerating PDB lines. 86s WARNING:Ignoring 852 header lines in output. 86s WARNING:Ignoring 3 missing lines in output. 87s autopkgtest [00:38:45]: test pdb2pka-test: -----------------------] 87s autopkgtest [00:38:45]: test pdb2pka-test: - - - - - - - - - - results - - - - - - - - - - 87s pdb2pka-test PASS 87s autopkgtest [00:38:45]: test command1: preparing testbed 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 88s Solving dependencies... 88s The following NEW packages will be installed: 88s python3-dateutil python3-iniconfig python3-packaging python3-pandas 88s python3-pandas-lib python3-pluggy python3-pytest python3-pytz 88s python3-testfixtures 88s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 88s Need to get 8648 kB of archives. 88s After this operation, 54.2 MB of additional disk space will be used. 88s Get:1 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-dateutil all 2.9.0-4 [80.3 kB] 88s Get:2 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 88s Get:3 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-packaging all 25.0-1 [52.8 kB] 88s Get:4 http://ftpmaster.internal/ubuntu resolute/main ppc64el python3-pytz all 2025.2-3 [163 kB] 89s Get:5 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pandas-lib ppc64el 2.2.3+dfsg-9 [4865 kB] 90s Get:6 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pandas all 2.2.3+dfsg-9 [3112 kB] 90s Get:7 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-pluggy all 1.6.0-1 [21.0 kB] 90s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe ppc64el python3-pytest all 8.4.2-1 [268 kB] 90s Get:9 http://ftpmaster.internal/ubuntu resolute/universe ppc64el python3-testfixtures all 9.2.0-1 [79.2 kB] 90s Fetched 8648 kB in 2s (4302 kB/s) 90s Selecting previously unselected package python3-dateutil. 90s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 78316 files and directories currently installed.) 90s Preparing to unpack .../0-python3-dateutil_2.9.0-4_all.deb ... 90s Unpacking python3-dateutil (2.9.0-4) ... 90s Selecting previously unselected package python3-iniconfig. 90s Preparing to unpack .../1-python3-iniconfig_1.1.1-2_all.deb ... 90s Unpacking python3-iniconfig (1.1.1-2) ... 90s Selecting previously unselected package python3-packaging. 90s Preparing to unpack .../2-python3-packaging_25.0-1_all.deb ... 90s Unpacking python3-packaging (25.0-1) ... 90s Selecting previously unselected package python3-pytz. 90s Preparing to unpack .../3-python3-pytz_2025.2-3_all.deb ... 90s Unpacking python3-pytz (2025.2-3) ... 90s Selecting previously unselected package python3-pandas-lib:ppc64el. 91s Preparing to unpack .../4-python3-pandas-lib_2.2.3+dfsg-9_ppc64el.deb ... 91s Unpacking python3-pandas-lib:ppc64el (2.2.3+dfsg-9) ... 91s Selecting previously unselected package python3-pandas. 91s Preparing to unpack .../5-python3-pandas_2.2.3+dfsg-9_all.deb ... 91s Unpacking python3-pandas (2.2.3+dfsg-9) ... 91s Selecting previously unselected package python3-pluggy. 91s Preparing to unpack .../6-python3-pluggy_1.6.0-1_all.deb ... 91s Unpacking python3-pluggy (1.6.0-1) ... 91s Selecting previously unselected package python3-pytest. 91s Preparing to unpack .../7-python3-pytest_8.4.2-1_all.deb ... 91s Unpacking python3-pytest (8.4.2-1) ... 91s Selecting previously unselected package python3-testfixtures. 91s Preparing to unpack .../8-python3-testfixtures_9.2.0-1_all.deb ... 91s Unpacking python3-testfixtures (9.2.0-1) ... 91s Setting up python3-iniconfig (1.1.1-2) ... 91s Setting up python3-pandas-lib:ppc64el (2.2.3+dfsg-9) ... 91s Setting up python3-testfixtures (9.2.0-1) ... 91s Setting up python3-pytz (2025.2-3) ... 91s Setting up python3-packaging (25.0-1) ... 91s Setting up python3-pluggy (1.6.0-1) ... 92s Setting up python3-dateutil (2.9.0-4) ... 92s Setting up python3-pytest (8.4.2-1) ... 92s Setting up python3-pandas (2.2.3+dfsg-9) ... 96s Processing triggers for man-db (2.13.1-1) ... 98s autopkgtest [00:38:56]: test command1: pytest-3 98s autopkgtest [00:38:56]: test command1: [----------------------- 99s ============================= test session starts ============================== 99s platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 99s rootdir: /tmp/autopkgtest.vTCZ7i/build.kPr/src 99s configfile: pytest.ini 99s plugins: typeguard-4.4.2 99s 99s ----------------------------- live log collection ------------------------------ 99s WARNING py.warnings:warnings.py:110 /tmp/autopkgtest.vTCZ7i/build.kPr/src/tests/core_test.py:81: PytestUnknownMarkWarning: Unknown pytest.mark.long_test - is this a typo? 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[ 51%] 99s tests/core_test.py::test_long_pdb[1YQB] SKIPPED (not running tests r...) [ 52%] 99s tests/core_test.py::test_long_pdb[2NYC] SKIPPED (not running tests r...) [ 52%] 99s tests/core_test.py::test_long_pdb[3ZZP] SKIPPED (not running tests r...) [ 52%] 99s tests/core_test.py::test_long_pdb[5DV8] SKIPPED (not running tests r...) [ 53%] 99s tests/core_test.py::test_long_pdb[2D8E] SKIPPED (not running tests r...) [ 53%] 99s tests/core_test.py::test_long_pdb[1X6J] SKIPPED (not running tests r...) [ 53%] 99s tests/core_test.py::test_long_pdb[1ZVA] SKIPPED (not running tests r...) [ 54%] 99s tests/core_test.py::test_long_pdb[1AIL] SKIPPED (not running tests r...) [ 54%] 99s tests/core_test.py::test_long_pdb[3FH2] SKIPPED (not running tests r...) [ 54%] 99s tests/core_test.py::test_long_pdb[1OA4] SKIPPED (not running tests r...) [ 55%] 99s tests/core_test.py::test_long_pdb[1R7J] SKIPPED (not running tests r...) [ 55%] 99s tests/core_test.py::test_long_pdb[3IDW] SKIPPED (not running tests r...) [ 55%] 99s tests/core_test.py::test_long_pdb[2OP6] SKIPPED (not running tests r...) [ 56%] 99s tests/core_test.py::test_long_pdb[3HRO] SKIPPED (not running tests r...) [ 56%] 99s tests/core_test.py::test_long_pdb[2HDZ] SKIPPED (not running tests r...) [ 56%] 99s tests/core_test.py::test_long_pdb[4CVD] SKIPPED (not running tests r...) [ 56%] 99s tests/core_test.py::test_long_pdb[5V0O] SKIPPED (not running tests r...) [ 57%] 99s tests/core_test.py::test_long_pdb[1J2A] SKIPPED (not running tests r...) [ 57%] 99s tests/core_test.py::test_long_pdb[3H0X] SKIPPED (not running tests r...) [ 57%] 99s tests/core_test.py::test_long_pdb[4Q2Q] SKIPPED (not running tests r...) [ 58%] 99s tests/core_test.py::test_long_pdb[2SGA] SKIPPED (not running tests r...) [ 58%] 99s tests/core_test.py::test_long_pdb[1USM] SKIPPED (not running tests r...) [ 58%] 99s tests/core_test.py::test_long_pdb[4O7Q] SKIPPED (not running tests r...) [ 59%] 99s tests/core_test.py::test_long_pdb[2QR3] SKIPPED (not running tests r...) [ 59%] 99s tests/core_test.py::test_long_pdb[2FRG] SKIPPED (not running tests r...) [ 59%] 99s tests/core_test.py::test_long_pdb[1OPC] SKIPPED (not running tests r...) [ 60%] 99s tests/core_test.py::test_long_pdb[2IBL] SKIPPED (not running tests r...) [ 60%] 99s tests/core_test.py::test_long_pdb[3NGP] SKIPPED (not running tests r...) [ 60%] 99s tests/core_test.py::test_long_pdb[1NKD] SKIPPED (not running tests r...) [ 61%] 99s tests/core_test.py::test_long_pdb[4GS3] SKIPPED (not running tests r...) [ 61%] 99s tests/core_test.py::test_long_pdb[4S11] SKIPPED (not running tests r...) [ 61%] 99s tests/core_test.py::test_long_pdb[4G3O] SKIPPED (not running tests r...) [ 62%] 99s tests/core_test.py::test_long_pdb[4HTI] SKIPPED (not running tests r...) [ 62%] 99s tests/core_test.py::test_long_pdb[3LMO] SKIPPED (not running tests r...) [ 62%] 99s tests/core_test.py::test_long_pdb[2ERW] SKIPPED (not running tests r...) [ 62%] 99s tests/core_test.py::test_long_pdb[3RJS] SKIPPED (not running tests r...) [ 63%] 99s tests/core_test.py::test_long_pdb[4IL7] SKIPPED (not running tests r...) [ 63%] 99s tests/core_test.py::test_long_pdb[3B7H] SKIPPED (not running tests r...) [ 63%] 99s tests/core_test.py::test_long_pdb[3CSR] SKIPPED (not running tests r...) [ 64%] 99s tests/core_test.py::test_long_pdb[1SJV] SKIPPED (not running tests r...) [ 64%] 99s tests/core_test.py::test_long_pdb[3RVC] SKIPPED (not running tests r...) [ 64%] 99s tests/core_test.py::test_long_pdb[4NPN] SKIPPED (not running tests r...) [ 65%] 99s tests/core_test.py::test_long_pdb[2ERA] SKIPPED (not running tests r...) [ 65%] 99s tests/core_test.py::test_long_pdb[1HUF] SKIPPED (not running tests r...) [ 65%] 99s tests/core_test.py::test_long_pdb[3HRN] SKIPPED (not running tests r...) [ 66%] 99s tests/core_test.py::test_broken_backbone[2V75] 99s -------------------------------- live log call --------------------------------- 99s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_2V75_0/2V75.log 99s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 99s 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). 99s 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). 99s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 99s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 99s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 100s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 100s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 100s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 90 residues and 687 atoms. 100s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 100s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 100s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 100s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 100s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 100s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 100s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 101s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 8 missing atoms in biomolecule. 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 101s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 101s 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 101s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 101s XFAIL [ 66%] 101s tests/core_test.py::test_broken_backbone[3U7T] 101s -------------------------------- live log call --------------------------------- 101s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_3U7T_0/3U7T.log 101s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 101s 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). 101s 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). 101s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 101s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 101s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T 101s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 101s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 101s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 652 atoms. 101s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in PRO A 22. 101s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in PRO A 22. 101s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in PRO A 22. 101s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in PRO A 22. 101s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 22. 101s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in PRO A 22. 101s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in PRO A 22. 101s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 22. 101s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 22. 101s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in PRO A 22. 101s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 22. 101s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in PRO A 22. 101s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 22. 101s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 22. 101s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 22. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 22. 102s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 22. At least one of the instances is being ignored. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in LEU A 25. 102s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in LEU A 25. At least one of the instances is being ignored. 102s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 102s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 102s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 102s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 102s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 102s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 102s 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 102s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 102s XFAIL [ 66%] 102s tests/core_test.py::test_broken_backbone[4MGP] 102s -------------------------------- live log call --------------------------------- 102s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_4MGP_0/4MGP.log 102s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 102s 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). 102s 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). 102s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 102s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 102s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP 103s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 103s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 103s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 23 residues and 163 atoms. 103s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in MET A 21. 103s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in MET A 21. 103s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in MET A 21. 103s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: SD in MET A 21. 103s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE in MET A 21. 103s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in MET A 21. At least one of the instances is being ignored. 103s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 103s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 103s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 103s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 12 missing atoms in biomolecule. 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 103s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 11 at coordinates 1.430, -1.683, -11.529 103s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 11 at coordinates 1.940, -0.315, -11.800 103s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CG to residue LYS A 14 at coordinates -1.600, -8.819, -6.913 103s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CD to residue LYS A 14 at coordinates -2.056, -8.844, -8.361 103s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 14 at coordinates -3.548, -9.031, -8.498 103s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 14 at coordinates -3.947, -9.048, -9.928 103s 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 103s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 103s XFAIL [ 67%] 103s tests/core_test.py::test_broken_backbone[1EJG] 103s -------------------------------- live log call --------------------------------- 103s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_1EJG_0/1EJG.log 103s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 103s 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). 103s 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). 103s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 103s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 103s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG 105s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 105s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 105s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 650 atoms. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in THR A 1. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 1. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 1. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 1. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 1. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H1 in THR A 1. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H2 in THR A 1. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H3 in THR A 1. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 1. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 1. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 1. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 1. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 1. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 1. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 1. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 2. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 2. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 2. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 2. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 2. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 2. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 2. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 2. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 2. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 2. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 2. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 7. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 7. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in VAL A 8. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in VAL A 8. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in VAL A 8. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in VAL A 8. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in VAL A 8. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in VAL A 8. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in VAL A 8. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in VAL A 8. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG11 in VAL A 8. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in VAL A 8. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in VAL A 8. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in VAL A 8. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in VAL A 8. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in VAL A 8. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in VAL A 8. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NE in ARG A 10. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in ARG A 10. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH1 in ARG A 10. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH2 in ARG A 10. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE in ARG A 10. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH11 in ARG A 10. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH12 in ARG A 10. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH21 in ARG A 10. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH22 in ARG A 10. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ARG A 10. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ASN A 12. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASN A 12. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 12. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 12. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 12. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ASN A 12. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASN A 12. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASN A 12. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 12. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 12. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 12. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PHE A 13. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in PHE A 13. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in PHE A 13. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in PHE A 13. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in PHE A 13. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in PHE A 13. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in PHE A 13. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PHE A 13. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in PHE A 13. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in PHE A 13. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HZ in PHE A 13. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PHE A 13. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 19. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 19. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 19. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 19. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 19. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 19. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 19. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 19. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in SER A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in SER A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in SER A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in SER A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in SER A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in SER A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in SER A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in SER A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in SER A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in SER A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in SER A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in SER A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in SER A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in SER A 22. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in SER A 22. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in GLU A 23. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in GLU A 23. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE1 in GLU A 23. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE2 in GLU A 23. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in GLU A 23. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in GLU A 23. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in GLU A 23. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 25. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 25. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in TYR A 29. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in TYR A 29. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in TYR A 29. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in TYR A 29. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in TYR A 29. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in TYR A 29. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OH in TYR A 29. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in TYR A 29. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in TYR A 29. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in TYR A 29. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in TYR A 29. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH in TYR A 29. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in TYR A 29. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 34. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 34. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 34. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 34. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 34. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 34. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 34. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 34. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 34. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 34. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 34. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 34. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 34. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 34. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 36. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 36. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 36. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 36. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 36. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 36. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 36. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 39. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 39. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 39. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 39. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 39. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 39. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 39. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 39. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASP A 43. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASP A 43. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASP A 43. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD2 in ASP A 43. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASP A 43. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASP A 43. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASP A 43. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 46. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 46. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 46. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 46. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 46. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 46. At least one of the instances is being ignored. 105s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 105s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 105s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 105s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 105s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 105s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 105s 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 105s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 105s XFAIL [ 67%] 105s tests/core_test.py::test_protonated_terminals[C-terminal HID] 105s -------------------------------- live log call --------------------------------- 105s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log 105s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 105s 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). 105s 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). 105s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 105s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 105s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/cterm_hid.pdb 105s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 105s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms. 105s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 105s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 105s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 105s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 105s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 105s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule. 105s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 105s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402 105s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 105s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 105s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 105s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 105s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 105s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 105s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 105s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 105s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 105s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 105s INFO common:common.py:198 0 atoms have position differences > 0 105s INFO common:common.py:198 0 atoms have position differences > 0.01 105s INFO common:common.py:198 0 atoms have charge differences > 0 105s INFO common:common.py:198 0 atoms have charge differences > 0.01 105s INFO common:common.py:198 0 atoms have radius differences > 0 105s INFO common:common.py:198 0 atoms have radius differences > 0.01 105s PASSED [ 67%] 105s tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 105s -------------------------------- live log call --------------------------------- 105s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log 105s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 105s 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). 105s 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). 105s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 105s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 105s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/5vav_cyclic_peptide.pdb 105s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 105s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms. 105s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 105s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 105s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 105s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 105s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 105s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 105s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 105s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 105s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 105s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 105s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 105s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 105s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 105s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 105s INFO common:common.py:198 0 atoms have position differences > 0 105s INFO common:common.py:198 0 atoms have position differences > 0.01 105s INFO common:common.py:198 0 atoms have charge differences > 0 105s INFO common:common.py:198 0 atoms have charge differences > 0.01 105s INFO common:common.py:198 0 atoms have radius differences > 0 105s INFO common:common.py:198 0 atoms have radius differences > 0.01 105s PASSED [ 68%] 105s tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 68%] 105s tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 68%] 105s tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 68%] 105s tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 69%] 105s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 69%] 105s tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 69%] 105s tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 70%] 105s tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 70%] 105s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 70%] 105s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 71%] 105s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 71%] 105s tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 71%] 105s tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 72%] 105s 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%] 105s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 72%] 105s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 73%] 105s tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 73%] 105s tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 73%] 105s tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 74%] 105s tests/io_test.py::test_read_qcd PASSED [ 74%] 105s tests/io_test.py::test_dx2cube 105s -------------------------------- live log call --------------------------------- 105s INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... 105s INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... 106s INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 107s INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 107s INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... 107s INFO io_test:io_test.py:68 No differences found in output 107s PASSED [ 74%] 108s tests/ligand_test.py::test_peoe_charges 108s -------------------------------- live log call --------------------------------- 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s PASSED [ 75%] 108s tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 108s -------------------------------- live log call --------------------------------- 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 108s PASSED [ 75%] 109s tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 109s -------------------------------- live log call --------------------------------- 109s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 109s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 109s PASSED [ 75%] 109s tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 109s -------------------------------- live log call --------------------------------- 109s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 109s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 109s PASSED [ 75%] 109s tests/ligand_test.py::test_assign_parameters[acetate.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 109s PASSED [ 76%] 109s tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 109s PASSED [ 76%] 109s tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 109s -------------------------------- live log call --------------------------------- 109s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 109s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 109s PASSED [ 76%] 109s tests/ligand_test.py::test_assign_parameters[adp.mol2] 109s -------------------------------- live log call --------------------------------- 109s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 109s INFO ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00 109s PASSED [ 77%] 109s tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 109s PASSED [ 77%] 109s tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 109s PASSED [ 77%] 109s tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 109s PASSED [ 78%] 109s tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 109s PASSED [ 78%] 109s tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 109s PASSED [ 78%] 109s tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 109s PASSED [ 79%] 109s tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 109s PASSED [ 79%] 109s tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 109s -------------------------------- live log call --------------------------------- 109s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 109s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 109s PASSED [ 79%] 110s tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 110s -------------------------------- live log call --------------------------------- 110s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 110s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 110s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 110s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 110s PASSED [ 80%] 111s tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 111s -------------------------------- live log call --------------------------------- 111s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 111s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 111s PASSED [ 80%] 111s tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 111s -------------------------------- live log call --------------------------------- 111s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 111s PASSED [ 80%] 111s tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED [ 81%] 111s tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED [ 81%] 111s tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 111s -------------------------------- live log call --------------------------------- 111s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 111s PASSED [ 81%] 111s tests/ligand_test.py::test_formal_charge[adp.mol2] 111s -------------------------------- live log call --------------------------------- 111s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 111s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 111s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 111s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 111s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 111s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 111s PASSED [ 81%] 111s tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED [ 82%] 111s tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED [ 82%] 111s tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED [ 82%] 111s tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED [ 83%] 111s tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED [ 83%] 111s tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED [ 83%] 111s tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED [ 84%] 111s tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 111s -------------------------------- live log call --------------------------------- 111s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 111s PASSED [ 84%] 111s tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED [ 84%] 111s tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED [ 85%] 111s tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED [ 85%] 111s tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED [ 85%] 111s tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED [ 86%] 111s tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED [ 86%] 112s tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED [ 86%] 113s tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED [ 87%] 113s tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED [ 87%] 113s tests/ligand_test.py::test_rings[acetate.mol2] PASSED [ 87%] 113s tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED [ 87%] 113s tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED [ 88%] 113s tests/ligand_test.py::test_rings[adp.mol2] PASSED [ 88%] 113s tests/ligand_test.py::test_rings[anthracene.mol2] PASSED [ 88%] 113s tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED [ 89%] 113s tests/ligand_test.py::test_rings[ethanol.mol2] PASSED [ 89%] 113s tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED [ 89%] 113s tests/ligand_test.py::test_rings[glycerol.mol2] PASSED [ 90%] 113s tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED [ 90%] 113s tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED [ 90%] 113s tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED [ 91%] 113s tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%] 113s tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%] 113s tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%] 113s tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%] 113s tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%] 113s tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%] 113s tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%] 113s tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%] 113s tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%] 113s tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%] 113s tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%] 113s tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] 113s tests/regression_test.py::test_basic[1AFS basic local] 113s -------------------------------- live log call --------------------------------- 113s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_basic_1AFS_basic_local_0/output.log 113s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 113s 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). 113s 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). 113s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 113s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 113s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 113s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 113s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 113s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 113s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 113s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 113s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 113s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 113s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 113s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 113s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 113s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 113s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 113s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 113s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 113s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 113s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 113s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 113s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 113s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 113s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 113s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 114s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 115s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 116s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 116s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 116s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 116s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 116s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 116s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 116s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 116s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 116s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 116s WARNING pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages 119s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 119s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 119s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 119s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 119s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 120s WARNING common:common.py:186 6 atoms have position differences > 0 120s INFO common:common.py:198 0 atoms have position differences > 0.01 120s INFO common:common.py:198 0 atoms have charge differences > 0 120s INFO common:common.py:198 0 atoms have charge differences > 0.01 120s INFO common:common.py:198 0 atoms have radius differences > 0 120s INFO common:common.py:198 0 atoms have radius differences > 0.01 120s PASSED [ 95%] 120s tests/regression_test.py::test_forcefields[1AFS whitespace AMBER] 120s -------------------------------- live log call --------------------------------- 120s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa0/output.log 120s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 120s 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). 120s 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). 120s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 120s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 120s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 120s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 120s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 120s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 120s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 120s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 120s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 120s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 120s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 120s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 120s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 120s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 120s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 120s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 120s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 120s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 121s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 122s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 126s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 126s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 126s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 126s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 126s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 126s WARNING common:common.py:186 6 atoms have position differences > 0 126s INFO common:common.py:198 0 atoms have position differences > 0.01 126s INFO common:common.py:198 0 atoms have charge differences > 0 126s INFO common:common.py:198 0 atoms have charge differences > 0.01 126s INFO common:common.py:198 0 atoms have radius differences > 0 126s INFO common:common.py:198 0 atoms have radius differences > 0.01 126s PASSED [ 95%] 126s tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] 126s -------------------------------- live log call --------------------------------- 126s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa1/output.log 126s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 126s 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). 126s 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). 126s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 126s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 127s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 127s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 127s WARNING pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages 127s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 127s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 127s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 127s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 127s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 127s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 127s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 127s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 127s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 127s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 128s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 129s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 133s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 133s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 133s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 133s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 133s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 133s WARNING common:common.py:186 5 atoms have position differences > 0 133s INFO common:common.py:198 0 atoms have position differences > 0.01 133s INFO common:common.py:198 0 atoms have charge differences > 0 133s INFO common:common.py:198 0 atoms have charge differences > 0.01 133s INFO common:common.py:198 0 atoms have radius differences > 0 133s INFO common:common.py:198 0 atoms have radius differences > 0.01 133s PASSED [ 95%] 133s tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] 133s -------------------------------- live log call --------------------------------- 133s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa2/output.log 133s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 133s 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). 133s 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). 133s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 133s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 133s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 133s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 133s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 133s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 133s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 133s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 133s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 133s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 133s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 133s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 133s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 133s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 133s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 133s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 133s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 133s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 133s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 134s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 134s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 135s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 140s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 140s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 140s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 140s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 140s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 140s WARNING common:common.py:186 6 atoms have position differences > 0 140s INFO common:common.py:198 0 atoms have position differences > 0.01 140s INFO common:common.py:198 0 atoms have charge differences > 0 140s INFO common:common.py:198 0 atoms have charge differences > 0.01 140s INFO common:common.py:198 0 atoms have radius differences > 0 140s INFO common:common.py:198 0 atoms have radius differences > 0.01 140s PASSED [ 96%] 140s tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] 140s -------------------------------- live log call --------------------------------- 140s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa3/output.log 140s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 140s 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). 140s 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). 140s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 140s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 140s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 140s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 140s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 140s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 140s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 140s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 140s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 140s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 140s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 140s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 140s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 140s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 140s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 140s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 140s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 140s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 140s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 140s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 141s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 142s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 146s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 146s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 146s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 146s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 146s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 146s WARNING common:common.py:186 6 atoms have position differences > 0 146s INFO common:common.py:198 0 atoms have position differences > 0.01 146s INFO common:common.py:198 0 atoms have charge differences > 0 146s INFO common:common.py:198 0 atoms have charge differences > 0.01 146s INFO common:common.py:198 0 atoms have radius differences > 0 146s INFO common:common.py:198 0 atoms have radius differences > 0.01 146s PASSED [ 96%] 146s tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] 146s -------------------------------- live log call --------------------------------- 146s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa4/output.log 146s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 147s 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). 147s 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). 147s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 147s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 147s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 147s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 147s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 147s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 147s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 147s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 147s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 147s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 147s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 147s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 147s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 147s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 147s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 147s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 147s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 147s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 147s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 147s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 148s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 149s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 153s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 153s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 153s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 153s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output. 153s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 153s WARNING common:common.py:186 6 atoms have position differences > 0 153s INFO common:common.py:198 0 atoms have position differences > 0.01 153s INFO common:common.py:198 0 atoms have charge differences > 0 153s INFO common:common.py:198 0 atoms have charge differences > 0.01 153s INFO common:common.py:198 0 atoms have radius differences > 0 153s INFO common:common.py:198 0 atoms have radius differences > 0.01 153s PASSED [ 96%] 153s tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] 153s -------------------------------- live log call --------------------------------- 153s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa5/output.log 153s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 153s 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). 153s 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). 153s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 153s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 153s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 153s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 153s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 153s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 153s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 153s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 153s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 153s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 153s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 153s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 153s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 153s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 153s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 153s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 153s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 153s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 153s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 154s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 154s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 155s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 160s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 160s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 160s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 160s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 160s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 160s WARNING common:common.py:186 6 atoms have position differences > 0 160s INFO common:common.py:198 0 atoms have position differences > 0.01 160s INFO common:common.py:198 0 atoms have charge differences > 0 160s INFO common:common.py:198 0 atoms have charge differences > 0.01 160s INFO common:common.py:198 0 atoms have radius differences > 0 160s INFO common:common.py:198 0 atoms have radius differences > 0.01 160s PASSED [ 97%] 160s tests/regression_test.py::test_other_options[1AFS whitespace clean] 160s -------------------------------- live log call --------------------------------- 160s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_whites0/output.log 160s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 160s 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). 160s 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). 160s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 160s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 160s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 160s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 160s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 160s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 160s INFO PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps. 160s INFO common:common.py:198 0 atoms have position differences > 0 160s INFO common:common.py:198 0 atoms have position differences > 0.01 160s INFO common:common.py:198 0 atoms have charge differences > 0 160s INFO common:common.py:198 0 atoms have charge differences > 0.01 160s INFO common:common.py:198 0 atoms have radius differences > 0 160s INFO common:common.py:198 0 atoms have radius differences > 0.01 160s PASSED [ 97%] 160s tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] 160s -------------------------------- live log call --------------------------------- 160s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_assign0/output.log 160s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 160s 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). 160s 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). 160s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 160s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 160s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 160s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 160s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 160s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 160s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 160s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 160s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 160s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 160s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 160s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 160s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 160s INFO common:common.py:198 0 atoms have position differences > 0 160s INFO common:common.py:198 0 atoms have position differences > 0.01 160s INFO common:common.py:198 0 atoms have charge differences > 0 160s INFO common:common.py:198 0 atoms have charge differences > 0.01 160s INFO common:common.py:198 0 atoms have radius differences > 0 160s INFO common:common.py:198 0 atoms have radius differences > 0.01 160s PASSED [ 97%] 160s tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] 160s -------------------------------- live log call --------------------------------- 160s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_nodebu0/output.log 160s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 160s 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). 160s 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). 160s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 160s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 160s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 160s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 160s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 160s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 160s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 160s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 160s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 160s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 160s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 160s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 160s INFO pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization... 160s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 160s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 160s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 160s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 160s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 160s INFO common:common.py:198 0 atoms have position differences > 0 160s INFO common:common.py:198 0 atoms have position differences > 0.01 160s INFO common:common.py:198 0 atoms have charge differences > 0 160s INFO common:common.py:198 0 atoms have charge differences > 0.01 160s INFO common:common.py:198 0 atoms have radius differences > 0 160s INFO common:common.py:198 0 atoms have radius differences > 0.01 160s PASSED [ 98%] 160s tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] 160s -------------------------------- live log call --------------------------------- 160s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_chain_0/output.log 160s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 160s 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). 160s 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). 160s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 160s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 161s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 161s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 161s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 161s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 161s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 161s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 161s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 161s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 161s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 161s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 161s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 161s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 161s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 161s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 161s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 161s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 161s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 161s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 162s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 163s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 167s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 167s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 167s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 167s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 167s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 167s WARNING common:common.py:186 6 atoms have position differences > 0 167s INFO common:common.py:198 0 atoms have position differences > 0.01 167s INFO common:common.py:198 0 atoms have charge differences > 0 167s INFO common:common.py:198 0 atoms have charge differences > 0.01 167s INFO common:common.py:198 0 atoms have radius differences > 0 167s INFO common:common.py:198 0 atoms have radius differences > 0.01 167s PASSED [ 98%] 167s tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] 167s -------------------------------- live log call --------------------------------- 167s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_neutra0/output.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: tests/data/1AFS.pdb 167s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 167s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 167s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 167s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 167s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 167s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 167s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 167s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 167s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 167s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 167s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 167s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 167s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 167s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 167s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 167s 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). 169s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 173s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 174s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 174s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 174s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 174s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 174s WARNING common:common.py:186 6 atoms have position differences > 0 174s INFO common:common.py:198 0 atoms have position differences > 0.01 174s INFO common:common.py:198 0 atoms have charge differences > 0 174s INFO common:common.py:198 0 atoms have charge differences > 0.01 174s INFO common:common.py:198 0 atoms have radius differences > 0 174s INFO common:common.py:198 0 atoms have radius differences > 0.01 174s PASSED [ 98%] 174s tests/regression_test.py::test_other_options[1AFS drop-water AMBER] 174s -------------------------------- live log call --------------------------------- 174s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_drop_w0/output.log 174s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 174s 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). 174s 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). 174s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 174s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 174s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 174s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 174s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 174s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms. 174s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 174s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 174s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 174s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 174s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 174s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 174s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 174s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 174s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 174s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 174s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 174s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 174s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 174s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 174s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 175s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 176s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 178s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 178s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 178s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 179s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 179s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 179s WARNING common:common.py:186 6 atoms have position differences > 0 179s INFO common:common.py:198 0 atoms have position differences > 0.01 179s INFO common:common.py:198 0 atoms have charge differences > 0 179s INFO common:common.py:198 0 atoms have charge differences > 0.01 179s INFO common:common.py:198 0 atoms have radius differences > 0 179s INFO common:common.py:198 0 atoms have radius differences > 0.01 179s PASSED [ 99%] 179s tests/regression_test.py::test_other_options[1AFS userff usernames whitespace] 179s -------------------------------- live log call --------------------------------- 179s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_userff0/output.log 179s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 179s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 179s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 179s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 179s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 179s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 179s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 179s 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 185s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 185s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 185s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 185s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 185s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 185s WARNING common:common.py:186 6 atoms have position differences > 0 185s INFO common:common.py:198 0 atoms have position differences > 0.01 185s INFO common:common.py:198 0 atoms have charge differences > 0 185s INFO common:common.py:198 0 atoms have charge differences > 0.01 185s INFO common:common.py:198 0 atoms have radius differences > 0 185s INFO common:common.py:198 0 atoms have radius differences > 0.01 185s PASSED [ 99%] 185s tests/test_version.py::test_version_exists PASSED [ 99%] 185s tests/test_version.py::test_version PASSED [100%] 185s 185s ============ 92 passed, 220 skipped, 4 xfailed in 86.94s (0:01:26) ============= 186s autopkgtest [00:40:24]: test command1: -----------------------] 188s autopkgtest [00:40:25]: test command1: - - - - - - - - - - results - - - - - - - - - - 188s command1 PASS 189s autopkgtest [00:40:27]: @@@@@@@@@@@@@@@@@@@@ summary 189s installation-test PASS 189s pdb2pka-test PASS 189s command1 PASS