0s autopkgtest [20:27:11]: starting date and time: 2025-10-20 20:27:11+0000 0s autopkgtest [20:27:11]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [20:27:11]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6fxsxlx9/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-4.secgroup --name adt-resolute-arm64-pdb2pqr-20251020-202711-juju-7f2275-prod-proposed-migration-environment-20-575a2d12-6a4b-47a5-a58e-2a1ba6076bc0 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-arm64-pdb2pqr-20251020-202711-juju-7f2275-prod-proposed-migration-environment-20-575a2d12-6a4b-47a5-a58e-2a1ba6076bc0 from image adt/ubuntu-resolute-arm64-server-20251020.img (UUID 53f7e888-0b33-40b7-be7f-09b2db152d64)... 52s autopkgtest [20:28:03]: testbed dpkg architecture: arm64 53s autopkgtest [20:28:04]: testbed apt version: 3.1.8ubuntu1 53s autopkgtest [20:28:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 53s autopkgtest [20:28:04]: testbed release detected to be: None 54s autopkgtest [20:28:05]: updating testbed package index (apt update) 54s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 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 55s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [14.3 kB] 55s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 55s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [59.3 kB] 55s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [646 kB] 55s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [115 kB] 55s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [43.8 kB] 55s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [409 kB] 55s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [5672 B] 56s Fetched 1382 kB in 1s (1293 kB/s) 57s Reading package lists... 58s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 58s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 58s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 58s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 59s Reading package lists... 59s Reading package lists... 60s Building dependency tree... 60s Reading state information... 61s Calculating upgrade... 62s The following packages will be upgraded: 62s libbrotli1 libjson-c5 python3-inflect python3-oauthlib python3-zipp 62s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 62s Need to get 512 kB of archives. 62s After this operation, 31.7 kB of additional disk space will be used. 62s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 libjson-c5 arm64 0.18+ds-1.1 [37.5 kB] 62s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libbrotli1 arm64 1.1.0-2build6 [336 kB] 62s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-inflect all 7.5.0-1 [33.9 kB] 62s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-oauthlib all 3.3.1-1 [93.5 kB] 63s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-zipp all 3.23.0-1 [10.4 kB] 63s dpkg-preconfigure: unable to re-open stdin: No such file or directory 63s Fetched 512 kB in 1s (750 kB/s) 64s (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 ... 83364 files and directories currently installed.) 64s Preparing to unpack .../libjson-c5_0.18+ds-1.1_arm64.deb ... 64s Unpacking libjson-c5:arm64 (0.18+ds-1.1) over (0.18+ds-1) ... 64s Preparing to unpack .../libbrotli1_1.1.0-2build6_arm64.deb ... 64s Unpacking libbrotli1:arm64 (1.1.0-2build6) over (1.1.0-2build5) ... 64s Preparing to unpack .../python3-inflect_7.5.0-1_all.deb ... 64s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 64s Preparing to unpack .../python3-oauthlib_3.3.1-1_all.deb ... 64s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 64s Preparing to unpack .../python3-zipp_3.23.0-1_all.deb ... 65s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 65s Setting up libbrotli1:arm64 (1.1.0-2build6) ... 65s Setting up python3-zipp (3.23.0-1) ... 65s Setting up python3-inflect (7.5.0-1) ... 65s Setting up python3-oauthlib (3.3.1-1) ... 66s Setting up libjson-c5:arm64 (0.18+ds-1.1) ... 66s Processing triggers for libc-bin (2.42-0ubuntu3) ... 66s autopkgtest [20:28:17]: upgrading testbed (apt dist-upgrade and autopurge) 66s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Calculating upgrade... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s Reading package lists... 69s Building dependency tree... 69s Reading state information... 69s Solving dependencies... 70s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 73s autopkgtest [20:28:24]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 73s autopkgtest [20:28:24]: @@@@@@@@@@@@@@@@@@@@ apt-source pdb2pqr 78s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (dsc) [1860 B] 78s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (tar) [7570 kB] 78s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (diff) [9876 B] 78s gpgv: Signature made Mon Jun 12 17:36:50 2023 UTC 78s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 78s gpgv: Can't check signature: No public key 78s dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found 79s autopkgtest [20:28:30]: testing package pdb2pqr version 3.6.1+dfsg-1 80s autopkgtest [20:28:31]: build not needed 82s autopkgtest [20:28:33]: test installation-test: preparing testbed 82s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s Solving dependencies... 84s The following NEW packages will be installed: 84s docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr python3-docutils 84s python3-numpy python3-numpy-dev python3-pdb2pqr python3-pdbx python3-propka 84s python3-roman sgml-base xml-core 84s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 84s Need to get 7931 kB of archives. 84s After this operation, 34.3 MB of additional disk space will be used. 84s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 84s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 85s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-5ubuntu1 [450 kB] 85s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 85s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 86s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 sgml-base all 1.31+nmu1 [11.0 kB] 86s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 xml-core all 0.19 [20.3 kB] 86s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 docutils-common all 0.21.2+dfsg-2 [131 kB] 86s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-roman all 5.1-1 [10.6 kB] 86s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 86s Get:11 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pdbx all 2.0.1-2 [16.5 kB] 86s Get:12 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-propka all 3.5.1-2 [70.1 kB] 86s Get:13 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pdb2pqr all 3.6.1+dfsg-1 [145 kB] 86s Get:14 http://ftpmaster.internal/ubuntu resolute/universe arm64 pdb2pqr all 3.6.1+dfsg-1 [10.4 kB] 86s Fetched 7931 kB in 2s (4321 kB/s) 86s Selecting previously unselected package python3-numpy-dev:arm64. 86s (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 ... 83374 files and directories currently installed.) 86s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 86s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 86s Selecting previously unselected package libblas3:arm64. 86s Preparing to unpack .../01-libblas3_3.12.1-6build1_arm64.deb ... 86s Unpacking libblas3:arm64 (3.12.1-6build1) ... 87s Selecting previously unselected package libgfortran5:arm64. 87s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_arm64.deb ... 87s Unpacking libgfortran5:arm64 (15.2.0-5ubuntu1) ... 87s Selecting previously unselected package liblapack3:arm64. 87s Preparing to unpack .../03-liblapack3_3.12.1-6build1_arm64.deb ... 87s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 87s Selecting previously unselected package python3-numpy. 87s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 87s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 87s Selecting previously unselected package sgml-base. 87s Preparing to unpack .../05-sgml-base_1.31+nmu1_all.deb ... 87s Unpacking sgml-base (1.31+nmu1) ... 87s Selecting previously unselected package xml-core. 87s Preparing to unpack .../06-xml-core_0.19_all.deb ... 87s Unpacking xml-core (0.19) ... 87s Selecting previously unselected package docutils-common. 87s Preparing to unpack .../07-docutils-common_0.21.2+dfsg-2_all.deb ... 87s Unpacking docutils-common (0.21.2+dfsg-2) ... 87s Selecting previously unselected package python3-roman. 87s Preparing to unpack .../08-python3-roman_5.1-1_all.deb ... 87s Unpacking python3-roman (5.1-1) ... 87s Selecting previously unselected package python3-docutils. 87s Preparing to unpack .../09-python3-docutils_0.21.2+dfsg-2_all.deb ... 87s Unpacking python3-docutils (0.21.2+dfsg-2) ... 87s Selecting previously unselected package python3-pdbx. 87s Preparing to unpack .../10-python3-pdbx_2.0.1-2_all.deb ... 87s Unpacking python3-pdbx (2.0.1-2) ... 87s Selecting previously unselected package python3-propka. 87s Preparing to unpack .../11-python3-propka_3.5.1-2_all.deb ... 87s Unpacking python3-propka (3.5.1-2) ... 88s Selecting previously unselected package python3-pdb2pqr. 88s Preparing to unpack .../12-python3-pdb2pqr_3.6.1+dfsg-1_all.deb ... 88s Unpacking python3-pdb2pqr (3.6.1+dfsg-1) ... 88s Selecting previously unselected package pdb2pqr. 88s Preparing to unpack .../13-pdb2pqr_3.6.1+dfsg-1_all.deb ... 88s Unpacking pdb2pqr (3.6.1+dfsg-1) ... 88s Setting up python3-propka (3.5.1-2) ... 88s Setting up python3-pdbx (2.0.1-2) ... 88s Setting up python3-roman (5.1-1) ... 88s Setting up libblas3:arm64 (3.12.1-6build1) ... 88s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 88s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 88s Setting up libgfortran5:arm64 (15.2.0-5ubuntu1) ... 88s Setting up sgml-base (1.31+nmu1) ... 89s Setting up liblapack3:arm64 (3.12.1-6build1) ... 89s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 89s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 92s Setting up xml-core (0.19) ... 92s Processing triggers for libc-bin (2.42-0ubuntu3) ... 92s Processing triggers for man-db (2.13.1-1) ... 93s Processing triggers for sgml-base (1.31+nmu1) ... 93s Setting up docutils-common (0.21.2+dfsg-2) ... 93s Processing triggers for sgml-base (1.31+nmu1) ... 93s Setting up python3-docutils (0.21.2+dfsg-2) ... 94s Setting up python3-pdb2pqr (3.6.1+dfsg-1) ... 94s Setting up pdb2pqr (3.6.1+dfsg-1) ... 96s autopkgtest [20:28:47]: test installation-test: [----------------------- 96s Run pdb2pqr... 96s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 96s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 96s 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). 96s INFO:Checking and transforming input arguments. 96s INFO:Loading topology files. 96s INFO:Loading molecule: examples/1a1p/1a1p.pdb 96s INFO:Setting up molecule. 96s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 96s INFO:Created biomolecule object with 14 residues and 208 atoms. 96s INFO:Setting termini states for biomolecule chains. 96s INFO:Loading forcefield. 96s INFO:Loading hydrogen topology definitions. 96s INFO:This biomolecule is clean. No repair needed. 96s INFO:Updating disulfide bridges. 96s INFO:Debumping biomolecule. 96s INFO:Adding hydrogens to biomolecule. 96s INFO:Debumping biomolecule (again). 96s INFO:Optimizing hydrogen bonds 96s INFO:Applying force field to biomolecule states. 96s INFO:Regenerating headers. 96s INFO:Regenerating PDB lines. 96s WARNING:Ignoring 852 header lines in output. 96s WARNING:Ignoring 3 missing lines in output. 97s autopkgtest [20:28:48]: test installation-test: -----------------------] 97s installation-test PASS 97s autopkgtest [20:28:48]: test installation-test: - - - - - - - - - - results - - - - - - - - - - 98s autopkgtest [20:28:49]: test pdb2pka-test: preparing testbed 98s Reading package lists... 99s Building dependency tree... 99s Reading state information... 99s Solving dependencies... 99s The following NEW packages will be installed: 99s fonts-font-awesome fonts-lato libjs-jquery libjs-sphinxdoc libjs-underscore 99s pdb2pqr-doc sphinx-rtd-theme-common 100s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 100s Need to get 5041 kB of archives. 100s After this operation, 20.0 MB of additional disk space will be used. 100s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-lato all 2.015-1 [2781 kB] 101s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 101s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 101s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 101s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 101s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 101s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 pdb2pqr-doc all 3.6.1+dfsg-1 [258 kB] 102s Fetched 5041 kB in 2s (3354 kB/s) 102s Selecting previously unselected package fonts-lato. 102s (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 ... 84875 files and directories currently installed.) 102s Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... 102s Unpacking fonts-lato (2.015-1) ... 102s Selecting previously unselected package fonts-font-awesome. 102s Preparing to unpack .../1-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 102s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 102s Selecting previously unselected package libjs-jquery. 102s Preparing to unpack .../2-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 102s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 102s Selecting previously unselected package libjs-underscore. 102s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 102s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 102s Selecting previously unselected package libjs-sphinxdoc. 102s Preparing to unpack .../4-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 102s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 102s Selecting previously unselected package sphinx-rtd-theme-common. 102s Preparing to unpack .../5-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 102s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 102s Selecting previously unselected package pdb2pqr-doc. 102s Preparing to unpack .../6-pdb2pqr-doc_3.6.1+dfsg-1_all.deb ... 102s Unpacking pdb2pqr-doc (3.6.1+dfsg-1) ... 102s Setting up fonts-lato (2.015-1) ... 102s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 102s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 102s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 102s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 102s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 102s Setting up pdb2pqr-doc (3.6.1+dfsg-1) ... 104s autopkgtest [20:28:55]: test pdb2pka-test: [----------------------- 104s Run pdb2pqr... 106s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 106s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 106s 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). 106s INFO:Checking and transforming input arguments. 106s INFO:Loading topology files. 106s INFO:Loading molecule: 1a1p/1a1p.pdb 106s INFO:Setting up molecule. 106s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 106s INFO:Created biomolecule object with 14 residues and 208 atoms. 106s INFO:Setting termini states for biomolecule chains. 106s INFO:Loading forcefield. 106s INFO:Loading hydrogen topology definitions. 106s INFO:This biomolecule is clean. No repair needed. 106s INFO:Updating disulfide bridges. 106s INFO:Debumping biomolecule. 106s INFO:Adding hydrogens to biomolecule. 106s INFO:Debumping biomolecule (again). 106s INFO:Optimizing hydrogen bonds 106s INFO:Applying force field to biomolecule states. 106s INFO:Regenerating headers. 106s INFO:Regenerating PDB lines. 106s WARNING:Ignoring 852 header lines in output. 106s WARNING:Ignoring 3 missing lines in output. 106s autopkgtest [20:28:56]: test pdb2pka-test: -----------------------] 106s pdb2pka-test PASS 106s autopkgtest [20:28:57]: test pdb2pka-test: - - - - - - - - - - results - - - - - - - - - - 107s autopkgtest [20:28:58]: test command1: preparing testbed 107s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s Solving dependencies... 108s The following NEW packages will be installed: 108s python3-dateutil python3-iniconfig python3-packaging python3-pandas 108s python3-pandas-lib python3-pluggy python3-pytest python3-pytz 108s python3-testfixtures 109s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 109s Need to get 8359 kB of archives. 109s After this operation, 47.6 MB of additional disk space will be used. 109s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-dateutil all 2.9.0-4 [80.3 kB] 109s Get:2 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 109s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-packaging all 25.0-1 [52.8 kB] 109s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pytz all 2025.2-3 [163 kB] 109s Get:5 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-9 [4579 kB] 110s Get:6 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.2.3+dfsg-9 [3112 kB] 110s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-pluggy all 1.6.0-1 [21.0 kB] 110s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 python3-pytest all 8.4.2-1 [268 kB] 110s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-testfixtures all 8.3.0-2 [75.6 kB] 111s Fetched 8359 kB in 2s (4734 kB/s) 111s Selecting previously unselected package python3-dateutil. 111s (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 ... 85210 files and directories currently installed.) 111s Preparing to unpack .../0-python3-dateutil_2.9.0-4_all.deb ... 111s Unpacking python3-dateutil (2.9.0-4) ... 111s Selecting previously unselected package python3-iniconfig. 111s Preparing to unpack .../1-python3-iniconfig_1.1.1-2_all.deb ... 111s Unpacking python3-iniconfig (1.1.1-2) ... 111s Selecting previously unselected package python3-packaging. 111s Preparing to unpack .../2-python3-packaging_25.0-1_all.deb ... 111s Unpacking python3-packaging (25.0-1) ... 111s Selecting previously unselected package python3-pytz. 111s Preparing to unpack .../3-python3-pytz_2025.2-3_all.deb ... 111s Unpacking python3-pytz (2025.2-3) ... 111s Selecting previously unselected package python3-pandas-lib:arm64. 111s Preparing to unpack .../4-python3-pandas-lib_2.2.3+dfsg-9_arm64.deb ... 111s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-9) ... 111s Selecting previously unselected package python3-pandas. 111s Preparing to unpack .../5-python3-pandas_2.2.3+dfsg-9_all.deb ... 111s Unpacking python3-pandas (2.2.3+dfsg-9) ... 112s Selecting previously unselected package python3-pluggy. 112s Preparing to unpack .../6-python3-pluggy_1.6.0-1_all.deb ... 112s Unpacking python3-pluggy (1.6.0-1) ... 112s Selecting previously unselected package python3-pytest. 112s Preparing to unpack .../7-python3-pytest_8.4.2-1_all.deb ... 112s Unpacking python3-pytest (8.4.2-1) ... 112s Selecting previously unselected package python3-testfixtures. 112s Preparing to unpack .../8-python3-testfixtures_8.3.0-2_all.deb ... 112s Unpacking python3-testfixtures (8.3.0-2) ... 112s Setting up python3-iniconfig (1.1.1-2) ... 112s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-9) ... 112s Setting up python3-testfixtures (8.3.0-2) ... 113s Setting up python3-pytz (2025.2-3) ... 113s Setting up python3-packaging (25.0-1) ... 113s Setting up python3-pluggy (1.6.0-1) ... 114s Setting up python3-dateutil (2.9.0-4) ... 114s Setting up python3-pytest (8.4.2-1) ... 115s Setting up python3-pandas (2.2.3+dfsg-9) ... 122s Processing triggers for man-db (2.13.1-1) ... 124s autopkgtest [20:29:15]: test command1: pytest-3 124s autopkgtest [20:29:15]: test command1: [----------------------- 126s ============================= test session starts ============================== 126s platform linux -- Python 3.13.7, pytest-8.4.2, pluggy-1.6.0 126s rootdir: /tmp/autopkgtest.Ckm2Do/build.keN/src 126s configfile: pytest.ini 126s plugins: typeguard-4.4.2 126s 126s ----------------------------- live log collection ------------------------------ 126s WARNING py.warnings:warnings.py:110 /tmp/autopkgtest.Ckm2Do/build.keN/src/tests/core_test.py:81: PytestUnknownMarkWarning: Unknown pytest.mark.long_test - is this a typo? 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[ 51%] 126s tests/core_test.py::test_long_pdb[1RIS] SKIPPED (not running tests r...) [ 51%] 126s tests/core_test.py::test_long_pdb[1XAK] SKIPPED (not running tests r...) [ 51%] 126s tests/core_test.py::test_long_pdb[1DUP] SKIPPED (not running tests r...) [ 52%] 126s tests/core_test.py::test_long_pdb[1NOA] SKIPPED (not running tests r...) [ 52%] 126s tests/core_test.py::test_long_pdb[2PND] SKIPPED (not running tests r...) [ 52%] 126s tests/core_test.py::test_long_pdb[4YPC] SKIPPED (not running tests r...) [ 53%] 126s tests/core_test.py::test_long_pdb[1B0X] SKIPPED (not running tests r...) [ 53%] 126s tests/core_test.py::test_long_pdb[2PCY] SKIPPED (not running tests r...) [ 53%] 126s tests/core_test.py::test_long_pdb[4I2T] SKIPPED (not running tests r...) [ 54%] 126s tests/core_test.py::test_long_pdb[1YIB] SKIPPED (not running tests r...) [ 54%] 126s tests/core_test.py::test_long_pdb[3LS0] SKIPPED (not running tests r...) [ 54%] 126s tests/core_test.py::test_long_pdb[3US6] SKIPPED (not running tests r...) [ 55%] 126s tests/core_test.py::test_long_pdb[1IS5] SKIPPED (not running tests r...) [ 55%] 126s tests/core_test.py::test_long_pdb[1LN4] SKIPPED (not running tests r...) [ 55%] 126s tests/core_test.py::test_long_pdb[4RWU] SKIPPED (not running tests r...) [ 56%] 126s tests/core_test.py::test_long_pdb[3CE7] SKIPPED (not running tests r...) [ 56%] 126s tests/core_test.py::test_long_pdb[4O7Q] SKIPPED (not running tests r...) [ 56%] 126s tests/core_test.py::test_long_pdb[4LJ1] SKIPPED (not running tests r...) [ 56%] 126s tests/core_test.py::test_long_pdb[1OPS] SKIPPED (not running tests r...) [ 57%] 126s tests/core_test.py::test_long_pdb[1TVQ] SKIPPED (not running tests r...) [ 57%] 126s tests/core_test.py::test_long_pdb[1NH9] SKIPPED (not running tests r...) [ 57%] 126s tests/core_test.py::test_long_pdb[4CRH] SKIPPED (not running tests r...) [ 58%] 126s tests/core_test.py::test_long_pdb[4N6T] SKIPPED (not running tests r...) [ 58%] 126s tests/core_test.py::test_long_pdb[2FRG] SKIPPED (not running tests r...) [ 58%] 126s tests/core_test.py::test_long_pdb[3QC7] SKIPPED (not running tests r...) [ 59%] 126s tests/core_test.py::test_long_pdb[3ZHI] SKIPPED (not running tests r...) [ 59%] 126s tests/core_test.py::test_long_pdb[2P5K] SKIPPED (not running tests r...) [ 59%] 126s tests/core_test.py::test_long_pdb[1ZLM] SKIPPED (not running tests r...) [ 60%] 126s tests/core_test.py::test_long_pdb[3IDW] SKIPPED (not running tests r...) [ 60%] 126s tests/core_test.py::test_long_pdb[4ZMK] SKIPPED (not running tests r...) [ 60%] 126s tests/core_test.py::test_long_pdb[2GZV] SKIPPED (not running tests r...) [ 61%] 126s tests/core_test.py::test_long_pdb[1JQ0] SKIPPED (not running tests r...) [ 61%] 126s tests/core_test.py::test_long_pdb[3RJS] SKIPPED (not running tests r...) [ 61%] 126s tests/core_test.py::test_long_pdb[2REY] SKIPPED (not running tests r...) [ 62%] 126s tests/core_test.py::test_long_pdb[2ZQE] SKIPPED (not running tests r...) [ 62%] 126s tests/core_test.py::test_long_pdb[1AIL] SKIPPED (not running tests r...) [ 62%] 126s tests/core_test.py::test_long_pdb[1USM] SKIPPED (not running tests r...) [ 62%] 126s tests/core_test.py::test_long_pdb[3LLB] SKIPPED (not running tests r...) [ 63%] 126s tests/core_test.py::test_long_pdb[2ERW] SKIPPED (not running tests r...) [ 63%] 126s tests/core_test.py::test_long_pdb[2IGD] SKIPPED (not running tests r...) [ 63%] 126s tests/core_test.py::test_long_pdb[1J27] SKIPPED (not running tests r...) [ 64%] 126s tests/core_test.py::test_long_pdb[2QVO] SKIPPED (not running tests r...) [ 64%] 126s tests/core_test.py::test_long_pdb[4GS3] SKIPPED (not running tests r...) [ 64%] 126s tests/core_test.py::test_long_pdb[2OCH] SKIPPED (not running tests r...) [ 65%] 126s tests/core_test.py::test_long_pdb[2IVY] SKIPPED (not running tests r...) [ 65%] 126s tests/core_test.py::test_long_pdb[3QE1] SKIPPED (not running tests r...) [ 65%] 126s tests/core_test.py::test_long_pdb[4TTW] SKIPPED (not running tests r...) [ 66%] 126s tests/core_test.py::test_broken_backbone[4MGP] 126s -------------------------------- live log call --------------------------------- 126s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_4MGP_0/4MGP.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: 4MGP 127s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 127s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 127s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 23 residues and 163 atoms. 127s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in MET A 21. 127s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in MET A 21. 127s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in MET A 21. 127s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: SD in MET A 21. 127s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE in MET A 21. 127s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in MET A 21. At least one of the instances is being ignored. 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 CE in residue LYS A 11 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 127s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 12 missing atoms in biomolecule. 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 127s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 11 at coordinates 1.430, -1.683, -11.529 127s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 11 at coordinates 1.940, -0.315, -11.800 127s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CG to residue LYS A 14 at coordinates -1.600, -8.819, -6.913 127s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CD to residue LYS A 14 at coordinates -2.056, -8.844, -8.361 127s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 14 at coordinates -3.548, -9.031, -8.498 127s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 14 at coordinates -3.947, -9.048, -9.928 127s 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 127s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 127s XFAIL [ 66%] 127s tests/core_test.py::test_broken_backbone[3U7T] 127s -------------------------------- live log call --------------------------------- 127s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_3U7T_0/3U7T.log 127s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 127s 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). 127s 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). 127s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 127s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 127s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T 128s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 128s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 128s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 652 atoms. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in PRO A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in PRO A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in PRO A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in PRO A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in PRO A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in PRO A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in PRO A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in PRO A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 22. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 22. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in LEU A 25. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in LEU A 25. At least one of the instances is being ignored. 128s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 128s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 128s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 128s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 128s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 128s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 128s 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 128s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 128s XFAIL [ 66%] 128s tests/core_test.py::test_broken_backbone[1EJG] 128s -------------------------------- live log call --------------------------------- 128s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_1EJG_0/1EJG.log 128s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 128s 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). 128s 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). 128s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 128s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 128s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG 128s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 128s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 128s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 650 atoms. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in THR A 1. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 1. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 1. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 1. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 1. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H1 in THR A 1. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H2 in THR A 1. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H3 in THR A 1. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 1. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 1. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 1. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 1. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 1. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 1. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 1. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 2. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 2. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 2. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 2. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 2. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 2. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 2. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 2. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 2. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 2. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 2. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 7. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 7. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in VAL A 8. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in VAL A 8. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in VAL A 8. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in VAL A 8. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in VAL A 8. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in VAL A 8. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in VAL A 8. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in VAL A 8. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG11 in VAL A 8. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in VAL A 8. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in VAL A 8. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in VAL A 8. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in VAL A 8. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in VAL A 8. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in VAL A 8. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NE in ARG A 10. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in ARG A 10. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH1 in ARG A 10. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH2 in ARG A 10. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE in ARG A 10. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH11 in ARG A 10. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH12 in ARG A 10. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH21 in ARG A 10. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH22 in ARG A 10. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ARG A 10. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ASN A 12. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASN A 12. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 12. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 12. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 12. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ASN A 12. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASN A 12. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASN A 12. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 12. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 12. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 12. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PHE A 13. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in PHE A 13. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in PHE A 13. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in PHE A 13. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in PHE A 13. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in PHE A 13. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in PHE A 13. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PHE A 13. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in PHE A 13. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in PHE A 13. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HZ in PHE A 13. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PHE A 13. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 19. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 19. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 19. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 19. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 19. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 19. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 19. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 19. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in SER A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in SER A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in SER A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in SER A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in SER A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in SER A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in SER A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in SER A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in SER A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in SER A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in SER A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in SER A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in SER A 22. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in SER A 22. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in SER A 22. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in GLU A 23. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in GLU A 23. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE1 in GLU A 23. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE2 in GLU A 23. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in GLU A 23. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in GLU A 23. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in GLU A 23. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 25. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 25. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in TYR A 29. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in TYR A 29. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in TYR A 29. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in TYR A 29. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in TYR A 29. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in TYR A 29. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OH in TYR A 29. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in TYR A 29. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in TYR A 29. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in TYR A 29. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in TYR A 29. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH in TYR A 29. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in TYR A 29. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 34. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 34. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 34. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 34. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 34. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 34. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 34. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 34. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 34. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 34. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 34. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 34. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 34. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 34. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 36. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 36. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 36. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 36. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 36. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 36. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 36. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 39. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 39. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 39. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 39. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 39. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 39. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 39. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 39. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASP A 43. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASP A 43. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASP A 43. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD2 in ASP A 43. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASP A 43. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASP A 43. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASP A 43. At least one of the instances is being ignored. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 46. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 46. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 46. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 46. 128s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 46. 128s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 46. At least one of the instances is being ignored. 128s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 128s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 128s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 128s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 128s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 128s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 128s 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 128s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 128s XFAIL [ 67%] 128s tests/core_test.py::test_broken_backbone[2V75] 128s -------------------------------- live log call --------------------------------- 128s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_2V75_0/2V75.log 128s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 128s 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). 128s 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). 128s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 128s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 129s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 129s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 129s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 129s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 90 residues and 687 atoms. 129s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 129s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 129s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 129s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 8 missing atoms in biomolecule. 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 129s 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 129s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 129s XFAIL [ 67%] 129s tests/core_test.py::test_protonated_terminals[C-terminal HID] 129s -------------------------------- live log call --------------------------------- 129s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log 129s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 129s 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). 129s 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). 129s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 129s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 129s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/cterm_hid.pdb 129s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 129s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms. 129s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 129s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 129s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 129s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule. 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 129s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402 129s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 129s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 129s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 129s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 129s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 129s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 129s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 129s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 129s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 129s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 129s INFO common:common.py:198 0 atoms have position differences > 0 129s INFO common:common.py:198 0 atoms have position differences > 0.01 129s INFO common:common.py:198 0 atoms have charge differences > 0 129s INFO common:common.py:198 0 atoms have charge differences > 0.01 129s INFO common:common.py:198 0 atoms have radius differences > 0 129s INFO common:common.py:198 0 atoms have radius differences > 0.01 129s PASSED [ 67%] 129s tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 129s -------------------------------- live log call --------------------------------- 129s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log 129s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 129s 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). 129s 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). 129s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 129s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 129s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/5vav_cyclic_peptide.pdb 129s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 129s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms. 129s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 129s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 129s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 129s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 129s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 129s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 129s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 129s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 129s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 129s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 129s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 129s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 129s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 129s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 129s INFO common:common.py:198 0 atoms have position differences > 0 129s INFO common:common.py:198 0 atoms have position differences > 0.01 129s INFO common:common.py:198 0 atoms have charge differences > 0 129s INFO common:common.py:198 0 atoms have charge differences > 0.01 129s INFO common:common.py:198 0 atoms have radius differences > 0 129s INFO common:common.py:198 0 atoms have radius differences > 0.01 130s PASSED [ 68%] 130s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 68%] 130s tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 68%] 130s tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 68%] 130s tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 69%] 130s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 69%] 130s 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 [ 69%] 130s tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 70%] 130s tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 70%] 130s tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 70%] 130s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 71%] 130s tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 71%] 130s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 71%] 130s tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 72%] 130s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 72%] 130s tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 72%] 130s tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 73%] 130s tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 73%] 130s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 73%] 130s tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 74%] 130s tests/io_test.py::test_read_qcd PASSED [ 74%] 130s tests/io_test.py::test_dx2cube 130s -------------------------------- live log call --------------------------------- 130s INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... 130s INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... 131s INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 132s INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 132s INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... 132s INFO io_test:io_test.py:68 No differences found in output 132s PASSED [ 74%] 133s tests/ligand_test.py::test_peoe_charges 133s -------------------------------- live log call --------------------------------- 133s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 133s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 133s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 133s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 133s PASSED [ 75%] 133s tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 133s -------------------------------- live log call --------------------------------- 133s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 133s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 133s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 133s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 133s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 133s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 133s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 133s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 133s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 133s PASSED [ 75%] 134s tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 134s -------------------------------- live log call --------------------------------- 134s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 134s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 134s PASSED [ 75%] 134s tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 134s -------------------------------- live log call --------------------------------- 134s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 134s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 134s PASSED [ 75%] 134s tests/ligand_test.py::test_assign_parameters[acetate.mol2] 134s -------------------------------- live log call --------------------------------- 134s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 134s PASSED [ 76%] 134s tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 134s -------------------------------- live log call --------------------------------- 134s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 134s PASSED [ 76%] 134s tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 134s -------------------------------- live log call --------------------------------- 134s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 134s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 134s PASSED [ 76%] 134s tests/ligand_test.py::test_assign_parameters[adp.mol2] 134s -------------------------------- live log call --------------------------------- 134s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 134s INFO ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00 134s PASSED [ 77%] 134s tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 134s -------------------------------- live log call --------------------------------- 134s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 134s PASSED [ 77%] 134s tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 134s -------------------------------- live log call --------------------------------- 134s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 134s PASSED [ 77%] 134s tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 134s -------------------------------- live log call --------------------------------- 134s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 134s PASSED [ 78%] 134s tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 134s -------------------------------- live log call --------------------------------- 134s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 134s PASSED [ 78%] 134s tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 134s -------------------------------- live log call --------------------------------- 134s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 134s PASSED [ 78%] 134s tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 134s -------------------------------- live log call --------------------------------- 134s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 134s PASSED [ 79%] 134s tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 134s -------------------------------- live log call --------------------------------- 134s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 134s PASSED [ 79%] 134s tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 134s -------------------------------- live log call --------------------------------- 134s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 134s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 134s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 134s PASSED [ 79%] 135s tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 135s -------------------------------- live log call --------------------------------- 135s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 135s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 135s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 135s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 135s PASSED [ 80%] 135s tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 135s -------------------------------- live log call --------------------------------- 135s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 135s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 135s PASSED [ 80%] 135s tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 135s -------------------------------- live log call --------------------------------- 135s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 135s PASSED [ 80%] 135s tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED [ 81%] 135s tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED [ 81%] 135s tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 135s -------------------------------- live log call --------------------------------- 135s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 135s PASSED [ 81%] 135s tests/ligand_test.py::test_formal_charge[adp.mol2] 135s -------------------------------- live log call --------------------------------- 135s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 135s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 135s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 135s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 135s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 135s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 135s PASSED [ 81%] 135s tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED [ 82%] 135s tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED [ 82%] 135s tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED [ 82%] 135s tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED [ 83%] 135s tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED [ 83%] 135s tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED [ 83%] 135s tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED [ 84%] 135s tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 135s -------------------------------- live log call --------------------------------- 135s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 135s PASSED [ 84%] 135s tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED [ 84%] 135s tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED [ 85%] 135s tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED [ 85%] 135s tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED [ 85%] 135s tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED [ 86%] 135s tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED [ 86%] 136s tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED [ 86%] 136s tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED [ 87%] 136s tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED [ 87%] 136s tests/ligand_test.py::test_rings[acetate.mol2] PASSED [ 87%] 136s tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED [ 87%] 136s tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED [ 88%] 136s tests/ligand_test.py::test_rings[adp.mol2] PASSED [ 88%] 136s tests/ligand_test.py::test_rings[anthracene.mol2] PASSED [ 88%] 136s tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED [ 89%] 136s tests/ligand_test.py::test_rings[ethanol.mol2] PASSED [ 89%] 136s tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED [ 89%] 136s tests/ligand_test.py::test_rings[glycerol.mol2] PASSED [ 90%] 136s tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED [ 90%] 137s tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED [ 90%] 137s tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED [ 91%] 137s tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%] 137s tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%] 137s tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%] 137s tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%] 137s tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%] 137s tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%] 137s tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%] 137s tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%] 137s tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%] 137s tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%] 137s tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%] 137s tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] 137s tests/regression_test.py::test_basic[1AFS basic local] 137s -------------------------------- live log call --------------------------------- 137s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_basic_1AFS_basic_local_0/output.log 137s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 137s 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). 137s 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). 137s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 137s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 137s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 137s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 137s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 137s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 137s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 137s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 137s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 137s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 137s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 137s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 137s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 137s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 137s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 137s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 137s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 137s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 137s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 137s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 137s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 137s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 137s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 137s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 138s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 138s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 139s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 139s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 139s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 139s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 139s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 139s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 139s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 139s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 139s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 139s WARNING pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages 141s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 141s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 141s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 142s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 142s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 142s WARNING common:common.py:186 6 atoms have position differences > 0 142s INFO common:common.py:198 0 atoms have position differences > 0.01 142s INFO common:common.py:198 0 atoms have charge differences > 0 142s INFO common:common.py:198 0 atoms have charge differences > 0.01 142s INFO common:common.py:198 0 atoms have radius differences > 0 142s INFO common:common.py:198 0 atoms have radius differences > 0.01 142s PASSED [ 95%] 142s tests/regression_test.py::test_forcefields[1AFS whitespace AMBER] 142s -------------------------------- live log call --------------------------------- 142s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa0/output.log 142s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 142s 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). 142s 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). 142s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 142s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 142s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 142s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 142s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 142s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 142s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 142s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 142s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 142s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 142s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 142s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 142s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 142s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 142s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 142s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 142s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 142s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 142s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 142s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 142s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 142s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 142s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 142s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 143s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 144s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 147s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 147s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 147s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 147s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 147s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 147s WARNING common:common.py:186 6 atoms have position differences > 0 147s INFO common:common.py:198 0 atoms have position differences > 0.01 147s INFO common:common.py:198 0 atoms have charge differences > 0 147s INFO common:common.py:198 0 atoms have charge differences > 0.01 147s INFO common:common.py:198 0 atoms have radius differences > 0 147s INFO common:common.py:198 0 atoms have radius differences > 0.01 147s PASSED [ 95%] 147s tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] 147s -------------------------------- live log call --------------------------------- 147s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa1/output.log 147s 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 WARNING pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages 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). 148s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 151s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 151s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 151s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 151s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 151s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 151s WARNING common:common.py:186 5 atoms have position differences > 0 151s INFO common:common.py:198 0 atoms have position differences > 0.01 151s INFO common:common.py:198 0 atoms have charge differences > 0 151s INFO common:common.py:198 0 atoms have charge differences > 0.01 151s INFO common:common.py:198 0 atoms have radius differences > 0 151s INFO common:common.py:198 0 atoms have radius differences > 0.01 151s PASSED [ 95%] 151s tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] 151s -------------------------------- live log call --------------------------------- 151s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa2/output.log 151s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 151s 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). 151s 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). 151s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 151s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 151s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 152s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 152s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 152s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 152s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 152s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 152s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 152s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 152s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 152s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 152s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 152s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 152s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 152s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 152s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 152s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 152s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 152s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 152s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 153s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 156s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 156s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 156s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 156s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 156s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 156s WARNING common:common.py:186 6 atoms have position differences > 0 156s INFO common:common.py:198 0 atoms have position differences > 0.01 156s INFO common:common.py:198 0 atoms have charge differences > 0 156s INFO common:common.py:198 0 atoms have charge differences > 0.01 156s INFO common:common.py:198 0 atoms have radius differences > 0 156s INFO common:common.py:198 0 atoms have radius differences > 0.01 156s PASSED [ 96%] 156s tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] 156s -------------------------------- live log call --------------------------------- 156s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa3/output.log 156s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 156s 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). 156s 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). 156s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 156s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 156s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 156s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 156s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 156s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 156s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 156s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 156s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 156s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 156s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 156s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 156s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 156s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 156s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 156s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 156s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 156s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 156s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 156s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 157s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 158s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 161s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 161s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 161s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 161s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 161s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 161s WARNING common:common.py:186 6 atoms have position differences > 0 161s INFO common:common.py:198 0 atoms have position differences > 0.01 161s INFO common:common.py:198 0 atoms have charge differences > 0 161s INFO common:common.py:198 0 atoms have charge differences > 0.01 161s INFO common:common.py:198 0 atoms have radius differences > 0 161s INFO common:common.py:198 0 atoms have radius differences > 0.01 161s PASSED [ 96%] 161s tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] 161s -------------------------------- live log call --------------------------------- 161s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa4/output.log 161s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 161s 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). 161s 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). 161s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 161s 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 166s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 166s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 166s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 166s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output. 166s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 166s WARNING common:common.py:186 6 atoms have position differences > 0 166s INFO common:common.py:198 0 atoms have position differences > 0.01 166s INFO common:common.py:198 0 atoms have charge differences > 0 166s INFO common:common.py:198 0 atoms have charge differences > 0.01 166s INFO common:common.py:198 0 atoms have radius differences > 0 166s INFO common:common.py:198 0 atoms have radius differences > 0.01 166s PASSED [ 96%] 166s tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] 166s -------------------------------- live log call --------------------------------- 166s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa5/output.log 166s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 166s 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). 166s 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). 166s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 166s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 166s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 166s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 166s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 166s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 166s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 166s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 166s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 166s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 166s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 166s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 166s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 166s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 166s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 166s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 166s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 166s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 166s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 167s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 167s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 168s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 171s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 171s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 171s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 171s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 171s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 171s WARNING common:common.py:186 6 atoms have position differences > 0 171s INFO common:common.py:198 0 atoms have position differences > 0.01 171s INFO common:common.py:198 0 atoms have charge differences > 0 171s INFO common:common.py:198 0 atoms have charge differences > 0.01 171s INFO common:common.py:198 0 atoms have radius differences > 0 171s INFO common:common.py:198 0 atoms have radius differences > 0.01 171s PASSED [ 97%] 171s tests/regression_test.py::test_other_options[1AFS whitespace clean] 171s -------------------------------- live log call --------------------------------- 171s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_whites0/output.log 171s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 171s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 171s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 171s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 171s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 171s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 171s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 172s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 172s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 172s INFO PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps. 172s INFO common:common.py:198 0 atoms have position differences > 0 172s INFO common:common.py:198 0 atoms have position differences > 0.01 172s INFO common:common.py:198 0 atoms have charge differences > 0 172s INFO common:common.py:198 0 atoms have charge differences > 0.01 172s INFO common:common.py:198 0 atoms have radius differences > 0 172s INFO common:common.py:198 0 atoms have radius differences > 0.01 172s PASSED [ 97%] 172s tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] 172s -------------------------------- live log call --------------------------------- 172s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_assign0/output.log 172s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 172s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 172s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 172s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 172s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 172s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 172s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 172s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 172s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 172s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 172s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 172s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 172s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 172s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 172s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 172s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 172s INFO common:common.py:198 0 atoms have position differences > 0 172s INFO common:common.py:198 0 atoms have position differences > 0.01 172s INFO common:common.py:198 0 atoms have charge differences > 0 172s INFO common:common.py:198 0 atoms have charge differences > 0.01 172s INFO common:common.py:198 0 atoms have radius differences > 0 172s INFO common:common.py:198 0 atoms have radius differences > 0.01 172s PASSED [ 97%] 172s tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] 172s -------------------------------- live log call --------------------------------- 172s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_nodebu0/output.log 172s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 172s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 172s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 172s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 172s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 172s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 172s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 172s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 172s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 172s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 172s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 172s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 172s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 172s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 172s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 172s INFO pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization... 172s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 172s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 172s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 172s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 172s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 172s INFO common:common.py:198 0 atoms have position differences > 0 172s INFO common:common.py:198 0 atoms have position differences > 0.01 172s INFO common:common.py:198 0 atoms have charge differences > 0 172s INFO common:common.py:198 0 atoms have charge differences > 0.01 172s INFO common:common.py:198 0 atoms have radius differences > 0 172s INFO common:common.py:198 0 atoms have radius differences > 0.01 172s PASSED [ 98%] 172s tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] 172s -------------------------------- live log call --------------------------------- 172s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_chain_0/output.log 172s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 172s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 172s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 172s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 172s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 172s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 172s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 172s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 172s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 172s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 172s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 172s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 172s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 172s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 172s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 172s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 172s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 172s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 172s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 172s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 172s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 172s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 173s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 173s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 174s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 176s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 176s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 176s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 176s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 176s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 177s WARNING common:common.py:186 6 atoms have position differences > 0 177s INFO common:common.py:198 0 atoms have position differences > 0.01 177s INFO common:common.py:198 0 atoms have charge differences > 0 177s INFO common:common.py:198 0 atoms have charge differences > 0.01 177s INFO common:common.py:198 0 atoms have radius differences > 0 177s INFO common:common.py:198 0 atoms have radius differences > 0.01 177s PASSED [ 98%] 177s tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] 177s -------------------------------- live log call --------------------------------- 177s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_neutra0/output.log 177s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 177s 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). 177s 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). 177s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 177s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 177s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 177s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 177s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 177s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 177s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 177s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 177s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 177s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 177s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 177s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 177s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 177s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 177s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 177s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 177s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 177s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 177s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 177s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 178s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 178s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 181s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 181s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 181s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 181s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 181s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 181s WARNING common:common.py:186 6 atoms have position differences > 0 181s INFO common:common.py:198 0 atoms have position differences > 0.01 181s INFO common:common.py:198 0 atoms have charge differences > 0 181s INFO common:common.py:198 0 atoms have charge differences > 0.01 181s INFO common:common.py:198 0 atoms have radius differences > 0 181s INFO common:common.py:198 0 atoms have radius differences > 0.01 181s PASSED [ 98%] 181s tests/regression_test.py::test_other_options[1AFS drop-water AMBER] 181s -------------------------------- live log call --------------------------------- 181s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_drop_w0/output.log 181s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 181s 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). 181s 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). 181s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 181s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 181s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 181s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 181s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 182s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms. 182s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 182s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 182s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 182s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 182s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 182s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 182s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 182s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 182s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 182s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 182s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 182s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 182s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 182s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 182s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 182s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 183s 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/regression_test.py::test_other_options[1AFS userff usernames whitespace] 185s -------------------------------- live log call --------------------------------- 185s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_userff0/output.log 185s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 185s 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). 185s 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). 185s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 185s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 185s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 185s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 185s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 185s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 185s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 185s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 185s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 185s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 185s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 185s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 185s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 185s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 185s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 185s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 185s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 185s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 185s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 185s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 186s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 187s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 189s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 189s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 189s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 189s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 189s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 190s WARNING common:common.py:186 6 atoms have position differences > 0 190s INFO common:common.py:198 0 atoms have position differences > 0.01 190s INFO common:common.py:198 0 atoms have charge differences > 0 190s INFO common:common.py:198 0 atoms have charge differences > 0.01 190s INFO common:common.py:198 0 atoms have radius differences > 0 190s INFO common:common.py:198 0 atoms have radius differences > 0.01 190s PASSED [ 99%] 190s tests/test_version.py::test_version_exists PASSED [ 99%] 190s tests/test_version.py::test_version PASSED [100%] 190s 190s ============ 92 passed, 220 skipped, 4 xfailed in 64.67s (0:01:04) ============= 191s autopkgtest [20:30:22]: test command1: -----------------------] 192s command1 PASS 192s autopkgtest [20:30:23]: test command1: - - - - - - - - - - results - - - - - - - - - - 192s autopkgtest [20:30:23]: @@@@@@@@@@@@@@@@@@@@ summary 192s installation-test PASS 192s pdb2pka-test PASS 192s command1 PASS