0s autopkgtest [14:49:27]: starting date and time: 2025-10-30 14:49:27+0000 0s autopkgtest [14:49:27]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [14:49:27]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.o855xr0d/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:node-jquery --apt-upgrade pdb2pqr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=node-jquery/3.7.1+dfsg+~3.5.33-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-1.secgroup --name adt-resolute-amd64-pdb2pqr-20251030-144927-juju-7f2275-prod-proposed-migration-environment-20-7280cb93-1047-4aee-b937-e821aad43f91 --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-pdb2pqr-20251030-144927-juju-7f2275-prod-proposed-migration-environment-20-7280cb93-1047-4aee-b937-e821aad43f91 from image adt/ubuntu-resolute-amd64-server-20251029.img (UUID 5761d511-8185-4ff5-8689-0f6c7cb11ec6)... 46s autopkgtest [14:50:13]: testbed dpkg architecture: amd64 46s autopkgtest [14:50:13]: testbed apt version: 3.1.11 47s autopkgtest [14:50:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 47s autopkgtest [14:50:14]: testbed release detected to be: None 48s autopkgtest [14:50:15]: updating testbed package index (apt update) 48s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 48s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 48s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 48s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 48s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [70.5 kB] 48s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [206 kB] 49s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [3669 kB] 50s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5856 B] 50s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [188 kB] 50s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [290 kB] 50s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [5760 B] 50s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.6 kB] 50s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [4212 B] 50s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 50s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [1142 kB] 51s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [2594 kB] 51s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [72.3 kB] 51s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [47.3 kB] 51s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [19.9 kB] 51s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [2068 B] 53s Fetched 8434 kB in 4s (2399 kB/s) 53s Reading package lists... 54s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 54s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 54s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 54s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 55s Reading package lists... 55s Reading package lists... 55s Building dependency tree... 55s Reading state information... 55s Calculating upgrade... 55s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s autopkgtest [14:50:22]: upgrading testbed (apt dist-upgrade and autopurge) 55s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 57s Solving dependencies... 57s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 59s autopkgtest [14:50:26]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 59s autopkgtest [14:50:26]: @@@@@@@@@@@@@@@@@@@@ apt-source pdb2pqr 63s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (dsc) [1860 B] 63s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (tar) [7570 kB] 63s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (diff) [9876 B] 63s gpgv: Signature made Mon Jun 12 17:36:50 2023 UTC 63s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 63s gpgv: Can't check signature: No public key 63s dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found 64s autopkgtest [14:50:31]: testing package pdb2pqr version 3.6.1+dfsg-1 64s autopkgtest [14:50:31]: build not needed 66s autopkgtest [14:50:33]: test installation-test: preparing testbed 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Solving dependencies... 67s The following NEW packages will be installed: 67s docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr python3-docutils 67s python3-numpy python3-numpy-dev python3-pdb2pqr python3-pdbx python3-propka 67s python3-roman sgml-base xml-core 67s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 67s Need to get 10.3 MB of archives. 67s After this operation, 45.1 MB of additional disk space will be used. 67s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 67s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-6build1 [263 kB] 68s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-5ubuntu1 [939 kB] 68s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-6build1 [2762 kB] 68s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 69s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 69s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19 [20.3 kB] 69s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 docutils-common all 0.21.2+dfsg-2 [131 kB] 69s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-roman all 5.1-1 [10.6 kB] 69s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 69s Get:11 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pdbx all 2.0.1-2 [16.5 kB] 69s Get:12 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-propka all 3.5.1-2 [70.1 kB] 69s Get:13 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pdb2pqr all 3.6.1+dfsg-1 [145 kB] 69s Get:14 http://ftpmaster.internal/ubuntu resolute/universe amd64 pdb2pqr all 3.6.1+dfsg-1 [10.4 kB] 69s Fetched 10.3 MB in 2s (4929 kB/s) 69s Selecting previously unselected package python3-numpy-dev:amd64. 69s (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 ... 78531 files and directories currently installed.) 69s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 69s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 69s Selecting previously unselected package libblas3:amd64. 69s Preparing to unpack .../01-libblas3_3.12.1-6build1_amd64.deb ... 69s Unpacking libblas3:amd64 (3.12.1-6build1) ... 69s Selecting previously unselected package libgfortran5:amd64. 69s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_amd64.deb ... 69s Unpacking libgfortran5:amd64 (15.2.0-5ubuntu1) ... 69s Selecting previously unselected package liblapack3:amd64. 69s Preparing to unpack .../03-liblapack3_3.12.1-6build1_amd64.deb ... 69s Unpacking liblapack3:amd64 (3.12.1-6build1) ... 70s Selecting previously unselected package python3-numpy. 70s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 70s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 70s Selecting previously unselected package sgml-base. 70s Preparing to unpack .../05-sgml-base_1.31+nmu1_all.deb ... 70s Unpacking sgml-base (1.31+nmu1) ... 70s Selecting previously unselected package xml-core. 70s Preparing to unpack .../06-xml-core_0.19_all.deb ... 70s Unpacking xml-core (0.19) ... 70s Selecting previously unselected package docutils-common. 70s Preparing to unpack .../07-docutils-common_0.21.2+dfsg-2_all.deb ... 70s Unpacking docutils-common (0.21.2+dfsg-2) ... 70s Selecting previously unselected package python3-roman. 70s Preparing to unpack .../08-python3-roman_5.1-1_all.deb ... 70s Unpacking python3-roman (5.1-1) ... 70s Selecting previously unselected package python3-docutils. 70s Preparing to unpack .../09-python3-docutils_0.21.2+dfsg-2_all.deb ... 70s Unpacking python3-docutils (0.21.2+dfsg-2) ... 70s Selecting previously unselected package python3-pdbx. 70s Preparing to unpack .../10-python3-pdbx_2.0.1-2_all.deb ... 70s Unpacking python3-pdbx (2.0.1-2) ... 70s Selecting previously unselected package python3-propka. 70s Preparing to unpack .../11-python3-propka_3.5.1-2_all.deb ... 70s Unpacking python3-propka (3.5.1-2) ... 70s Selecting previously unselected package python3-pdb2pqr. 70s Preparing to unpack .../12-python3-pdb2pqr_3.6.1+dfsg-1_all.deb ... 70s Unpacking python3-pdb2pqr (3.6.1+dfsg-1) ... 70s Selecting previously unselected package pdb2pqr. 70s Preparing to unpack .../13-pdb2pqr_3.6.1+dfsg-1_all.deb ... 70s Unpacking pdb2pqr (3.6.1+dfsg-1) ... 70s Setting up python3-propka (3.5.1-2) ... 70s Setting up python3-pdbx (2.0.1-2) ... 70s Setting up python3-roman (5.1-1) ... 70s Setting up libblas3:amd64 (3.12.1-6build1) ... 70s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 70s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 70s Setting up libgfortran5:amd64 (15.2.0-5ubuntu1) ... 70s Setting up sgml-base (1.31+nmu1) ... 70s Setting up liblapack3:amd64 (3.12.1-6build1) ... 70s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 70s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 72s Setting up xml-core (0.19) ... 72s Processing triggers for libc-bin (2.42-0ubuntu3) ... 72s Processing triggers for man-db (2.13.1-1) ... 73s Processing triggers for sgml-base (1.31+nmu1) ... 73s Setting up docutils-common (0.21.2+dfsg-2) ... 73s Processing triggers for sgml-base (1.31+nmu1) ... 73s Setting up python3-docutils (0.21.2+dfsg-2) ... 73s Setting up python3-pdb2pqr (3.6.1+dfsg-1) ... 73s Setting up pdb2pqr (3.6.1+dfsg-1) ... 74s autopkgtest [14:50:41]: test installation-test: [----------------------- 74s Run pdb2pqr... 74s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 74s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 74s 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). 74s INFO:Checking and transforming input arguments. 74s INFO:Loading topology files. 74s INFO:Loading molecule: examples/1a1p/1a1p.pdb 74s INFO:Setting up molecule. 74s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 74s INFO:Created biomolecule object with 14 residues and 208 atoms. 74s INFO:Setting termini states for biomolecule chains. 74s INFO:Loading forcefield. 74s INFO:Loading hydrogen topology definitions. 74s INFO:This biomolecule is clean. No repair needed. 74s INFO:Updating disulfide bridges. 74s INFO:Debumping biomolecule. 74s INFO:Adding hydrogens to biomolecule. 74s INFO:Debumping biomolecule (again). 74s INFO:Optimizing hydrogen bonds 74s INFO:Applying force field to biomolecule states. 74s INFO:Regenerating headers. 74s INFO:Regenerating PDB lines. 74s WARNING:Ignoring 852 header lines in output. 74s WARNING:Ignoring 3 missing lines in output. 75s autopkgtest [14:50:42]: test installation-test: -----------------------] 75s installation-test PASS 75s autopkgtest [14:50:42]: test installation-test: - - - - - - - - - - results - - - - - - - - - - 76s autopkgtest [14:50:43]: test pdb2pka-test: preparing testbed 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 76s Solving dependencies... 76s The following NEW packages will be installed: 76s fonts-font-awesome fonts-lato libjs-jquery libjs-sphinxdoc libjs-underscore 76s pdb2pqr-doc sphinx-rtd-theme-common 77s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 77s Need to get 5035 kB of archives. 77s After this operation, 20.0 MB of additional disk space will be used. 77s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-lato all 2.015-1 [2781 kB] 78s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 78s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 78s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 78s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 78s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 78s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 pdb2pqr-doc all 3.6.1+dfsg-1 [258 kB] 78s Fetched 5035 kB in 1s (3703 kB/s) 78s Selecting previously unselected package fonts-lato. 78s (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 ... 80032 files and directories currently installed.) 78s Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... 78s Unpacking fonts-lato (2.015-1) ... 78s Selecting previously unselected package fonts-font-awesome. 78s Preparing to unpack .../1-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 78s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 78s Selecting previously unselected package libjs-jquery. 78s Preparing to unpack .../2-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 78s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 78s Selecting previously unselected package libjs-underscore. 78s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 78s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 78s Selecting previously unselected package libjs-sphinxdoc. 78s Preparing to unpack .../4-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 78s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 78s Selecting previously unselected package sphinx-rtd-theme-common. 78s Preparing to unpack .../5-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 78s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 78s Selecting previously unselected package pdb2pqr-doc. 78s Preparing to unpack .../6-pdb2pqr-doc_3.6.1+dfsg-1_all.deb ... 78s Unpacking pdb2pqr-doc (3.6.1+dfsg-1) ... 78s Setting up fonts-lato (2.015-1) ... 78s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 78s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 78s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 78s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 78s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 78s Setting up pdb2pqr-doc (3.6.1+dfsg-1) ... 79s autopkgtest [14:50:46]: test pdb2pka-test: [----------------------- 80s Run pdb2pqr... 80s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 80s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 80s INFO:Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 80s INFO:Checking and transforming input arguments. 80s INFO:Loading topology files. 80s INFO:Loading molecule: 1a1p/1a1p.pdb 80s INFO:Setting up molecule. 80s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 80s INFO:Created biomolecule object with 14 residues and 208 atoms. 80s INFO:Setting termini states for biomolecule chains. 80s INFO:Loading forcefield. 80s INFO:Loading hydrogen topology definitions. 80s INFO:This biomolecule is clean. No repair needed. 80s INFO:Updating disulfide bridges. 80s INFO:Debumping biomolecule. 80s INFO:Adding hydrogens to biomolecule. 80s INFO:Debumping biomolecule (again). 80s INFO:Optimizing hydrogen bonds 80s INFO:Applying force field to biomolecule states. 80s INFO:Regenerating headers. 80s INFO:Regenerating PDB lines. 80s WARNING:Ignoring 852 header lines in output. 80s WARNING:Ignoring 3 missing lines in output. 80s autopkgtest [14:50:47]: test pdb2pka-test: -----------------------] 81s autopkgtest [14:50:48]: test pdb2pka-test: - - - - - - - - - - results - - - - - - - - - - 81s pdb2pka-test PASS 81s autopkgtest [14:50:48]: test command1: preparing testbed 81s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s Solving dependencies... 82s The following NEW packages will be installed: 82s python3-dateutil python3-iniconfig python3-packaging python3-pandas 82s python3-pandas-lib python3-pluggy python3-pytest python3-pytz 82s python3-testfixtures 82s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 82s Need to get 11.1 MB of archives. 82s After this operation, 72.2 MB of additional disk space will be used. 82s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-dateutil all 2.9.0-4 [80.3 kB] 82s Get:2 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 82s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-packaging all 25.0-1 [52.8 kB] 82s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pytz all 2025.2-4 [32.3 kB] 82s Get:5 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.3.3+dfsg-1ubuntu1 [7668 kB] 83s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 84s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-1 [21.0 kB] 84s Get:8 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pytest all 8.3.5-2 [252 kB] 84s Get:9 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-testfixtures all 9.2.0-1 [79.2 kB] 84s Fetched 11.1 MB in 2s (5415 kB/s) 84s Selecting previously unselected package python3-dateutil. 84s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80367 files and directories currently installed.) 84s Preparing to unpack .../0-python3-dateutil_2.9.0-4_all.deb ... 84s Unpacking python3-dateutil (2.9.0-4) ... 84s Selecting previously unselected package python3-iniconfig. 84s Preparing to unpack .../1-python3-iniconfig_1.1.1-2_all.deb ... 84s Unpacking python3-iniconfig (1.1.1-2) ... 84s Selecting previously unselected package python3-packaging. 84s Preparing to unpack .../2-python3-packaging_25.0-1_all.deb ... 84s Unpacking python3-packaging (25.0-1) ... 84s Selecting previously unselected package python3-pytz. 84s Preparing to unpack .../3-python3-pytz_2025.2-4_all.deb ... 84s Unpacking python3-pytz (2025.2-4) ... 84s Selecting previously unselected package python3-pandas-lib:amd64. 84s Preparing to unpack .../4-python3-pandas-lib_2.3.3+dfsg-1ubuntu1_amd64.deb ... 84s Unpacking python3-pandas-lib:amd64 (2.3.3+dfsg-1ubuntu1) ... 84s Selecting previously unselected package python3-pandas. 84s Preparing to unpack .../5-python3-pandas_2.3.3+dfsg-1ubuntu1_all.deb ... 84s Unpacking python3-pandas (2.3.3+dfsg-1ubuntu1) ... 84s Selecting previously unselected package python3-pluggy. 84s Preparing to unpack .../6-python3-pluggy_1.6.0-1_all.deb ... 84s Unpacking python3-pluggy (1.6.0-1) ... 84s Selecting previously unselected package python3-pytest. 84s Preparing to unpack .../7-python3-pytest_8.3.5-2_all.deb ... 84s Unpacking python3-pytest (8.3.5-2) ... 84s Selecting previously unselected package python3-testfixtures. 84s Preparing to unpack .../8-python3-testfixtures_9.2.0-1_all.deb ... 84s Unpacking python3-testfixtures (9.2.0-1) ... 85s Setting up python3-iniconfig (1.1.1-2) ... 85s Setting up python3-pandas-lib:amd64 (2.3.3+dfsg-1ubuntu1) ... 85s Setting up python3-testfixtures (9.2.0-1) ... 85s Setting up python3-pytz (2025.2-4) ... 85s Setting up python3-packaging (25.0-1) ... 85s Setting up python3-pluggy (1.6.0-1) ... 85s Setting up python3-dateutil (2.9.0-4) ... 85s Setting up python3-pytest (8.3.5-2) ... 85s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 89s Processing triggers for man-db (2.13.1-1) ... 91s autopkgtest [14:50:58]: test command1: pytest-3 91s autopkgtest [14:50:58]: test command1: [----------------------- 92s ============================= test session starts ============================== 92s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 92s rootdir: /tmp/autopkgtest.SwKZqB/build.fSK/src 92s configfile: pytest.ini 92s plugins: typeguard-4.4.2 92s 92s ----------------------------- live log collection ------------------------------ 92s WARNING py.warnings:warnings.py:110 /tmp/autopkgtest.SwKZqB/build.fSK/src/tests/core_test.py:81: PytestUnknownMarkWarning: Unknown pytest.mark.long_test - is this a typo? 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[ 51%] 92s tests/core_test.py::test_long_pdb[1I2T] SKIPPED (not running tests r...) [ 52%] 92s tests/core_test.py::test_long_pdb[3LLB] SKIPPED (not running tests r...) [ 52%] 92s tests/core_test.py::test_long_pdb[2D8E] SKIPPED (not running tests r...) [ 52%] 92s tests/core_test.py::test_long_pdb[1TQG] SKIPPED (not running tests r...) [ 53%] 92s tests/core_test.py::test_long_pdb[1J2A] SKIPPED (not running tests r...) [ 53%] 92s tests/core_test.py::test_long_pdb[1RJ1] SKIPPED (not running tests r...) [ 53%] 92s tests/core_test.py::test_long_pdb[4PGR] SKIPPED (not running tests r...) [ 54%] 92s tests/core_test.py::test_long_pdb[2PND] SKIPPED (not running tests r...) [ 54%] 92s tests/core_test.py::test_long_pdb[3ONJ] SKIPPED (not running tests r...) [ 54%] 92s tests/core_test.py::test_long_pdb[3CP1] SKIPPED (not running tests r...) [ 55%] 92s tests/core_test.py::test_long_pdb[1YZM] SKIPPED (not running tests r...) [ 55%] 92s tests/core_test.py::test_long_pdb[1FAS] SKIPPED (not running tests r...) [ 55%] 92s tests/core_test.py::test_long_pdb[1TEN] SKIPPED (not running tests r...) [ 56%] 92s tests/core_test.py::test_long_pdb[3ISU] SKIPPED (not running tests r...) [ 56%] 92s tests/core_test.py::test_long_pdb[1LN4] SKIPPED (not running tests r...) [ 56%] 92s tests/core_test.py::test_long_pdb[5V0O] SKIPPED (not running tests r...) [ 56%] 92s tests/core_test.py::test_long_pdb[1PHT] SKIPPED (not running tests r...) [ 57%] 92s tests/core_test.py::test_long_pdb[4L9E] SKIPPED (not running tests r...) [ 57%] 92s tests/core_test.py::test_long_pdb[1AFS] SKIPPED (not running tests r...) [ 57%] 92s tests/core_test.py::test_long_pdb[2FRG] SKIPPED (not running tests r...) [ 58%] 92s tests/core_test.py::test_long_pdb[2ZQE] SKIPPED (not running tests r...) [ 58%] 92s tests/core_test.py::test_long_pdb[2CWR] SKIPPED (not running tests r...) [ 58%] 92s tests/core_test.py::test_long_pdb[4LJ1] SKIPPED (not running tests r...) [ 59%] 92s tests/core_test.py::test_long_pdb[1WOU] SKIPPED (not running tests r...) [ 59%] 92s tests/core_test.py::test_long_pdb[2HDZ] SKIPPED (not running tests r...) [ 59%] 92s tests/core_test.py::test_long_pdb[3I1G] SKIPPED (not running tests r...) [ 60%] 92s tests/core_test.py::test_long_pdb[2PTV] SKIPPED (not running tests r...) [ 60%] 92s tests/core_test.py::test_long_pdb[4GS3] SKIPPED (not running tests r...) [ 60%] 92s tests/core_test.py::test_long_pdb[1SJV] SKIPPED (not running tests r...) [ 61%] 92s tests/core_test.py::test_long_pdb[1AIL] SKIPPED (not running tests r...) [ 61%] 92s tests/core_test.py::test_long_pdb[1PDO] SKIPPED (not running tests r...) [ 61%] 92s tests/core_test.py::test_long_pdb[3I35] SKIPPED (not running tests r...) [ 62%] 92s tests/core_test.py::test_long_pdb[3ZSL] SKIPPED (not running tests r...) [ 62%] 92s tests/core_test.py::test_long_pdb[2R6Q] SKIPPED (not running tests r...) [ 62%] 92s tests/core_test.py::test_long_pdb[3SO2] SKIPPED (not running tests r...) [ 62%] 92s tests/core_test.py::test_long_pdb[2PII] SKIPPED (not running tests r...) [ 63%] 92s tests/core_test.py::test_long_pdb[2QVO] SKIPPED (not running tests r...) [ 63%] 92s tests/core_test.py::test_long_pdb[2XXC] SKIPPED (not running tests r...) [ 63%] 92s tests/core_test.py::test_long_pdb[2YXF] SKIPPED (not running tests r...) [ 64%] 92s tests/core_test.py::test_long_pdb[3RJS] SKIPPED (not running tests r...) [ 64%] 92s tests/core_test.py::test_long_pdb[1ZX6] SKIPPED (not running tests r...) [ 64%] 92s tests/core_test.py::test_long_pdb[1ZLM] SKIPPED (not running tests r...) [ 65%] 92s tests/core_test.py::test_long_pdb[4GMQ] SKIPPED (not running tests r...) [ 65%] 92s tests/core_test.py::test_long_pdb[4TTW] SKIPPED (not running tests r...) [ 65%] 92s tests/core_test.py::test_long_pdb[4O7Q] SKIPPED (not running tests r...) [ 66%] 92s tests/core_test.py::test_broken_backbone[4MGP] 92s -------------------------------- live log call --------------------------------- 92s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_4MGP_0/4MGP.log 92s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 92s 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). 92s 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). 92s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 92s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 92s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP 93s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 93s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 93s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 23 residues and 163 atoms. 93s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in MET A 21. 93s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in MET A 21. 93s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in MET A 21. 93s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: SD in MET A 21. 93s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE in MET A 21. 93s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in MET A 21. At least one of the instances is being ignored. 93s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 93s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 93s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 93s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 12 missing atoms in biomolecule. 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 93s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 11 at coordinates 1.430, -1.683, -11.529 93s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 11 at coordinates 1.940, -0.315, -11.800 93s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CG to residue LYS A 14 at coordinates -1.600, -8.819, -6.913 93s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CD to residue LYS A 14 at coordinates -2.056, -8.844, -8.361 93s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 14 at coordinates -3.548, -9.031, -8.498 93s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 14 at coordinates -3.947, -9.048, -9.928 93s 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 93s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 93s XFAIL [ 66%] 93s tests/core_test.py::test_broken_backbone[1EJG] 93s -------------------------------- live log call --------------------------------- 93s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_1EJG_0/1EJG.log 93s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 93s 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). 93s 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). 93s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 93s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 93s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG 94s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 94s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 94s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 650 atoms. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in THR A 1. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 1. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 1. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 1. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 1. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H1 in THR A 1. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H2 in THR A 1. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H3 in THR A 1. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 1. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 1. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 1. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 1. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 1. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 1. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 1. At least one of the instances is being ignored. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 2. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 2. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 2. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 2. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 2. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 2. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 2. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 2. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 2. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 2. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 2. At least one of the instances is being ignored. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 7. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 7. At least one of the instances is being ignored. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in VAL A 8. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in VAL A 8. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in VAL A 8. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in VAL A 8. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in VAL A 8. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in VAL A 8. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in VAL A 8. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in VAL A 8. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG11 in VAL A 8. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in VAL A 8. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in VAL A 8. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in VAL A 8. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in VAL A 8. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in VAL A 8. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in VAL A 8. At least one of the instances is being ignored. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NE in ARG A 10. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in ARG A 10. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH1 in ARG A 10. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH2 in ARG A 10. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE in ARG A 10. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH11 in ARG A 10. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH12 in ARG A 10. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH21 in ARG A 10. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH22 in ARG A 10. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ARG A 10. At least one of the instances is being ignored. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ASN A 12. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASN A 12. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 12. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 12. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 12. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ASN A 12. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASN A 12. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASN A 12. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 12. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 12. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 12. At least one of the instances is being ignored. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PHE A 13. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in PHE A 13. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in PHE A 13. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in PHE A 13. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in PHE A 13. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in PHE A 13. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in PHE A 13. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PHE A 13. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in PHE A 13. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in PHE A 13. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HZ in PHE A 13. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PHE A 13. At least one of the instances is being ignored. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 19. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 19. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 19. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 19. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 19. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 19. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 19. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 19. At least one of the instances is being ignored. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in SER A 22. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in SER A 22. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in SER A 22. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in SER A 22. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in SER A 22. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in SER A 22. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in SER A 22. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in SER A 22. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in SER A 22. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in SER A 22. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in SER A 22. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in SER A 22. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in SER A 22. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in SER A 22. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in SER A 22. At least one of the instances is being ignored. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in GLU A 23. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in GLU A 23. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE1 in GLU A 23. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE2 in GLU A 23. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in GLU A 23. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in GLU A 23. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in GLU A 23. At least one of the instances is being ignored. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 25. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 25. At least one of the instances is being ignored. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in TYR A 29. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in TYR A 29. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in TYR A 29. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in TYR A 29. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in TYR A 29. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in TYR A 29. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OH in TYR A 29. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in TYR A 29. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in TYR A 29. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in TYR A 29. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in TYR A 29. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH in TYR A 29. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in TYR A 29. At least one of the instances is being ignored. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 34. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 34. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 34. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 34. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 34. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 34. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 34. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 34. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 34. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 34. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 34. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 34. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 34. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 34. At least one of the instances is being ignored. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 36. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 36. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 36. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 36. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 36. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 36. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 36. At least one of the instances is being ignored. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 39. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 39. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 39. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 39. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 39. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 39. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 39. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 39. At least one of the instances is being ignored. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASP A 43. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASP A 43. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASP A 43. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD2 in ASP A 43. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASP A 43. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASP A 43. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASP A 43. At least one of the instances is being ignored. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 46. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 46. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 46. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 46. 94s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 46. 94s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 46. At least one of the instances is being ignored. 94s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 94s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 94s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 94s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 94s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 94s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 94s 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 94s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 94s XFAIL [ 66%] 94s tests/core_test.py::test_broken_backbone[3U7T] 94s -------------------------------- live log call --------------------------------- 94s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_3U7T_0/3U7T.log 94s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 94s 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). 94s 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). 94s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 94s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 94s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T 95s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 95s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 95s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 652 atoms. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in PRO A 22. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in PRO A 22. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in PRO A 22. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in PRO A 22. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 22. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in PRO A 22. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in PRO A 22. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 22. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 22. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in PRO A 22. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 22. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in PRO A 22. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 22. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 22. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 22. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 22. 95s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 22. At least one of the instances is being ignored. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in LEU A 25. 95s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in LEU A 25. At least one of the instances is being ignored. 95s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 95s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 95s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 95s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 95s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 95s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 95s 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 95s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 95s XFAIL [ 67%] 95s tests/core_test.py::test_broken_backbone[2V75] 95s -------------------------------- live log call --------------------------------- 95s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_2V75_0/2V75.log 95s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 95s 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). 95s 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). 95s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 95s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 95s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 96s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 96s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 96s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 90 residues and 687 atoms. 96s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 96s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 96s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 96s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 8 missing atoms in biomolecule. 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 96s 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 96s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 96s XFAIL [ 67%] 96s tests/core_test.py::test_protonated_terminals[C-terminal HID] 96s -------------------------------- live log call --------------------------------- 96s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log 96s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 96s 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). 96s 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). 96s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 96s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 96s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/cterm_hid.pdb 96s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 96s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms. 96s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 96s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 96s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 96s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule. 96s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 96s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402 96s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 96s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 96s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 96s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 96s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 96s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 96s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 96s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 96s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 96s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 96s INFO common:common.py:198 0 atoms have position differences > 0 96s INFO common:common.py:198 0 atoms have position differences > 0.01 96s INFO common:common.py:198 0 atoms have charge differences > 0 96s INFO common:common.py:198 0 atoms have charge differences > 0.01 96s INFO common:common.py:198 0 atoms have radius differences > 0 96s INFO common:common.py:198 0 atoms have radius differences > 0.01 96s PASSED [ 67%] 96s tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 96s -------------------------------- live log call --------------------------------- 96s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log 96s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 96s 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). 96s 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). 96s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 96s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 96s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/5vav_cyclic_peptide.pdb 96s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 96s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms. 96s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 96s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 96s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 96s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 96s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 96s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 96s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 96s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 96s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 96s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 96s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 96s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 96s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 96s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 96s INFO common:common.py:198 0 atoms have position differences > 0 96s INFO common:common.py:198 0 atoms have position differences > 0.01 96s INFO common:common.py:198 0 atoms have charge differences > 0 96s INFO common:common.py:198 0 atoms have charge differences > 0.01 96s INFO common:common.py:198 0 atoms have radius differences > 0 96s INFO common:common.py:198 0 atoms have radius differences > 0.01 96s PASSED [ 68%] 96s tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 68%] 96s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 68%] 96s tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 68%] 96s tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 69%] 96s tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 69%] 96s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 69%] 96s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 70%] 96s tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 70%] 96s tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 70%] 96s 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 [ 71%] 96s tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 71%] 96s tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 71%] 96s tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 72%] 96s tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 72%] 96s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 72%] 97s tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 73%] 97s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 73%] 97s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 73%] 97s tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 74%] 97s tests/io_test.py::test_read_qcd PASSED [ 74%] 97s tests/io_test.py::test_dx2cube 97s -------------------------------- live log call --------------------------------- 97s INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... 97s INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... 97s INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 98s INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 98s INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... 98s INFO io_test:io_test.py:68 No differences found in output 98s PASSED [ 74%] 99s tests/ligand_test.py::test_peoe_charges 99s -------------------------------- live log call --------------------------------- 99s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 99s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 99s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 99s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 99s PASSED [ 75%] 100s tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 100s -------------------------------- live log call --------------------------------- 100s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 100s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 100s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 100s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 100s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 100s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 100s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 100s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 100s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 100s PASSED [ 75%] 100s tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 100s -------------------------------- live log call --------------------------------- 100s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 100s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 100s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 100s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 100s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 100s PASSED [ 75%] 100s tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 100s -------------------------------- live log call --------------------------------- 100s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 100s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 100s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 100s PASSED [ 75%] 100s tests/ligand_test.py::test_assign_parameters[acetate.mol2] 100s -------------------------------- live log call --------------------------------- 100s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 100s PASSED [ 76%] 100s tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 100s -------------------------------- live log call --------------------------------- 100s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 100s PASSED [ 76%] 100s tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 100s -------------------------------- live log call --------------------------------- 100s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 100s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 100s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 100s PASSED [ 76%] 101s tests/ligand_test.py::test_assign_parameters[adp.mol2] 101s -------------------------------- live log call --------------------------------- 101s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 101s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 101s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 101s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 101s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 101s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 101s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 101s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 101s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 101s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 101s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 101s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 101s INFO ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00 101s PASSED [ 77%] 101s tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 101s -------------------------------- live log call --------------------------------- 101s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 101s PASSED [ 77%] 101s tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 101s -------------------------------- live log call --------------------------------- 101s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 101s PASSED [ 77%] 101s tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 101s -------------------------------- live log call --------------------------------- 101s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 101s PASSED [ 78%] 101s tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 101s -------------------------------- live log call --------------------------------- 101s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 101s PASSED [ 78%] 101s tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 101s -------------------------------- live log call --------------------------------- 101s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 101s PASSED [ 78%] 101s tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 101s -------------------------------- live log call --------------------------------- 101s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 101s PASSED [ 79%] 101s tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 101s -------------------------------- live log call --------------------------------- 101s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 101s PASSED [ 79%] 101s tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 101s -------------------------------- live log call --------------------------------- 101s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 101s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 101s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 101s PASSED [ 79%] 101s tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 101s -------------------------------- live log call --------------------------------- 101s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 101s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 101s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 101s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 101s PASSED [ 80%] 102s tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 102s -------------------------------- live log call --------------------------------- 102s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 102s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 102s PASSED [ 80%] 102s tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 102s -------------------------------- live log call --------------------------------- 102s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 102s PASSED [ 80%] 102s tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED [ 81%] 102s tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED [ 81%] 102s tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 102s -------------------------------- live log call --------------------------------- 102s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 102s PASSED [ 81%] 102s tests/ligand_test.py::test_formal_charge[adp.mol2] 102s -------------------------------- live log call --------------------------------- 102s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 102s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 102s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 102s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 102s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 102s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 102s PASSED [ 81%] 102s tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED [ 82%] 102s tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED [ 82%] 102s tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED [ 82%] 102s tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED [ 83%] 102s tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED [ 83%] 102s tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED [ 83%] 102s tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED [ 84%] 102s tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 102s -------------------------------- live log call --------------------------------- 102s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 102s PASSED [ 84%] 102s tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED [ 84%] 102s tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED [ 85%] 102s tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED [ 85%] 102s tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED [ 85%] 102s tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED [ 86%] 102s tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED [ 86%] 103s tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED [ 86%] 104s tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED [ 87%] 104s tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED [ 87%] 104s tests/ligand_test.py::test_rings[acetate.mol2] PASSED [ 87%] 104s tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED [ 87%] 104s tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED [ 88%] 104s tests/ligand_test.py::test_rings[adp.mol2] PASSED [ 88%] 104s tests/ligand_test.py::test_rings[anthracene.mol2] PASSED [ 88%] 104s tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED [ 89%] 104s tests/ligand_test.py::test_rings[ethanol.mol2] PASSED [ 89%] 104s tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED [ 89%] 104s tests/ligand_test.py::test_rings[glycerol.mol2] PASSED [ 90%] 104s tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED [ 90%] 104s tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED [ 90%] 104s tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED [ 91%] 104s tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%] 104s tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%] 104s tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%] 104s tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%] 104s tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%] 104s tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%] 104s tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%] 104s tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%] 104s tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%] 104s tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%] 104s tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%] 104s tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] 104s tests/regression_test.py::test_basic[1AFS basic local] 104s -------------------------------- live log call --------------------------------- 104s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_basic_1AFS_basic_local_0/output.log 104s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 104s 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). 104s 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). 104s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 104s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 104s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 104s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 104s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 104s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 104s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 104s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 104s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 104s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 104s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 104s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 104s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 104s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 104s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 104s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 104s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 104s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 105s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 106s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 106s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 106s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 106s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 106s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 106s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 106s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 106s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 106s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 106s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 106s WARNING pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages 111s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 111s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 111s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 111s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 111s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 111s WARNING common:common.py:186 6 atoms have position differences > 0 111s INFO common:common.py:198 0 atoms have position differences > 0.01 111s INFO common:common.py:198 0 atoms have charge differences > 0 111s INFO common:common.py:198 0 atoms have charge differences > 0.01 111s INFO common:common.py:198 0 atoms have radius differences > 0 111s INFO common:common.py:198 0 atoms have radius differences > 0.01 111s PASSED [ 95%] 111s tests/regression_test.py::test_forcefields[1AFS whitespace AMBER] 111s -------------------------------- live log call --------------------------------- 111s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa0/output.log 111s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 111s 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). 111s 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). 111s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 111s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 111s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 111s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 111s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 111s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 111s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 111s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 111s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 111s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 111s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 111s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 111s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 111s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 111s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 111s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 111s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 111s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 111s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 111s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 112s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 112s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 112s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 112s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 112s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 112s WARNING common:common.py:186 6 atoms have position differences > 0 112s INFO common:common.py:198 0 atoms have position differences > 0.01 112s INFO common:common.py:198 0 atoms have charge differences > 0 112s INFO common:common.py:198 0 atoms have charge differences > 0.01 112s INFO common:common.py:198 0 atoms have radius differences > 0 112s INFO common:common.py:198 0 atoms have radius differences > 0.01 112s PASSED [ 95%] 112s tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] 112s -------------------------------- live log call --------------------------------- 112s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa1/output.log 112s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 112s 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). 112s 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). 112s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 112s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 112s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 112s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 112s WARNING pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages 112s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 112s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 112s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 112s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 112s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 112s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 112s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 112s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 112s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 112s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 112s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 112s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 112s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 112s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 112s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 112s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 113s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 114s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 116s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 116s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 116s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 116s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 116s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 116s WARNING common:common.py:186 5 atoms have position differences > 0 116s INFO common:common.py:198 0 atoms have position differences > 0.01 116s INFO common:common.py:198 0 atoms have charge differences > 0 116s INFO common:common.py:198 0 atoms have charge differences > 0.01 116s INFO common:common.py:198 0 atoms have radius differences > 0 116s INFO common:common.py:198 0 atoms have radius differences > 0.01 116s PASSED [ 95%] 116s tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] 116s -------------------------------- live log call --------------------------------- 116s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa2/output.log 116s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 116s 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). 116s 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). 116s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 116s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 116s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 116s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 116s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 116s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 116s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 116s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 116s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 116s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 116s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 116s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 116s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 116s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 116s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 116s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 116s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 116s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 116s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 116s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 117s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 118s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 120s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 120s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 120s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 120s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 120s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 120s WARNING common:common.py:186 6 atoms have position differences > 0 120s INFO common:common.py:198 0 atoms have position differences > 0.01 120s INFO common:common.py:198 0 atoms have charge differences > 0 120s INFO common:common.py:198 0 atoms have charge differences > 0.01 120s INFO common:common.py:198 0 atoms have radius differences > 0 120s INFO common:common.py:198 0 atoms have radius differences > 0.01 120s PASSED [ 96%] 120s tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] 120s -------------------------------- live log call --------------------------------- 120s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa3/output.log 120s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 120s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 120s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 120s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 120s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 120s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 120s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 120s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 120s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 120s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 120s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 120s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 120s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 120s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 120s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 120s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 120s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 121s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 122s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 124s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 124s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 124s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 124s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 124s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 124s WARNING common:common.py:186 6 atoms have position differences > 0 124s INFO common:common.py:198 0 atoms have position differences > 0.01 124s INFO common:common.py:198 0 atoms have charge differences > 0 124s INFO common:common.py:198 0 atoms have charge differences > 0.01 124s INFO common:common.py:198 0 atoms have radius differences > 0 124s INFO common:common.py:198 0 atoms have radius differences > 0.01 124s PASSED [ 96%] 124s tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] 124s -------------------------------- live log call --------------------------------- 124s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa4/output.log 124s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 124s 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). 124s 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). 124s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 124s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 124s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 124s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 124s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 124s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 124s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 124s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 124s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 124s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 124s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 124s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 124s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 124s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 124s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 124s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 124s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 124s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 124s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 125s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 125s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 126s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 128s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 128s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 128s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 128s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output. 128s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 128s WARNING common:common.py:186 6 atoms have position differences > 0 128s INFO common:common.py:198 0 atoms have position differences > 0.01 128s INFO common:common.py:198 0 atoms have charge differences > 0 128s INFO common:common.py:198 0 atoms have charge differences > 0.01 128s INFO common:common.py:198 0 atoms have radius differences > 0 128s INFO common:common.py:198 0 atoms have radius differences > 0.01 128s PASSED [ 96%] 128s tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] 128s -------------------------------- live log call --------------------------------- 128s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa5/output.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: tests/data/1AFS.pdb 128s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 128s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 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 WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 128s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 128s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 128s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 128s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 129s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 129s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 129s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 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). 130s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 132s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 132s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 132s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 132s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 132s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 132s WARNING common:common.py:186 6 atoms have position differences > 0 132s INFO common:common.py:198 0 atoms have position differences > 0.01 132s INFO common:common.py:198 0 atoms have charge differences > 0 132s INFO common:common.py:198 0 atoms have charge differences > 0.01 132s INFO common:common.py:198 0 atoms have radius differences > 0 132s INFO common:common.py:198 0 atoms have radius differences > 0.01 132s PASSED [ 97%] 132s tests/regression_test.py::test_other_options[1AFS whitespace clean] 132s -------------------------------- live log call --------------------------------- 132s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_whites0/output.log 132s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 132s 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). 132s 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). 132s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 132s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 132s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 132s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 132s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 132s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 132s INFO PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps. 133s INFO common:common.py:198 0 atoms have position differences > 0 133s INFO common:common.py:198 0 atoms have position differences > 0.01 133s INFO common:common.py:198 0 atoms have charge differences > 0 133s INFO common:common.py:198 0 atoms have charge differences > 0.01 133s INFO common:common.py:198 0 atoms have radius differences > 0 133s INFO common:common.py:198 0 atoms have radius differences > 0.01 133s PASSED [ 97%] 133s tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] 133s -------------------------------- live log call --------------------------------- 133s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_assign0/output.log 133s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 133s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 133s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 133s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 133s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 133s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 133s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 133s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 133s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 133s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 133s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 133s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 133s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 133s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 133s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 133s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 133s INFO common:common.py:198 0 atoms have position differences > 0 133s INFO common:common.py:198 0 atoms have position differences > 0.01 133s INFO common:common.py:198 0 atoms have charge differences > 0 133s INFO common:common.py:198 0 atoms have charge differences > 0.01 133s INFO common:common.py:198 0 atoms have radius differences > 0 133s INFO common:common.py:198 0 atoms have radius differences > 0.01 133s PASSED [ 97%] 133s tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] 133s -------------------------------- live log call --------------------------------- 133s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_nodebu0/output.log 133s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 133s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 133s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 133s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 133s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 133s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 133s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 133s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 133s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 133s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 133s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 133s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 133s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 133s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 133s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 133s INFO pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization... 133s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 133s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 133s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 133s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 133s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 133s INFO common:common.py:198 0 atoms have position differences > 0 133s INFO common:common.py:198 0 atoms have position differences > 0.01 133s INFO common:common.py:198 0 atoms have charge differences > 0 133s INFO common:common.py:198 0 atoms have charge differences > 0.01 133s INFO common:common.py:198 0 atoms have radius differences > 0 133s INFO common:common.py:198 0 atoms have radius differences > 0.01 133s PASSED [ 98%] 133s tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] 133s -------------------------------- live log call --------------------------------- 133s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_chain_0/output.log 133s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 133s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 133s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 133s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 133s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 133s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 133s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 133s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 133s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 133s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 133s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 133s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 133s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 133s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 133s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 133s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 133s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 133s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 133s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 133s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 133s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 133s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 133s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 134s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 134s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 137s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 137s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 137s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 137s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 137s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 137s WARNING common:common.py:186 6 atoms have position differences > 0 137s INFO common:common.py:198 0 atoms have position differences > 0.01 137s INFO common:common.py:198 0 atoms have charge differences > 0 137s INFO common:common.py:198 0 atoms have charge differences > 0.01 137s INFO common:common.py:198 0 atoms have radius differences > 0 137s INFO common:common.py:198 0 atoms have radius differences > 0.01 137s PASSED [ 98%] 137s tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] 137s -------------------------------- live log call --------------------------------- 137s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_neutra0/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 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 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. 141s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 141s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 141s WARNING common:common.py:186 6 atoms have position differences > 0 141s INFO common:common.py:198 0 atoms have position differences > 0.01 141s INFO common:common.py:198 0 atoms have charge differences > 0 141s INFO common:common.py:198 0 atoms have charge differences > 0.01 141s INFO common:common.py:198 0 atoms have radius differences > 0 141s INFO common:common.py:198 0 atoms have radius differences > 0.01 141s PASSED [ 98%] 141s tests/regression_test.py::test_other_options[1AFS drop-water AMBER] 141s -------------------------------- live log call --------------------------------- 141s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_drop_w0/output.log 141s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 141s 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). 141s 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). 141s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 141s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 141s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 141s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 141s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 141s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms. 141s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 141s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 141s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 141s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 141s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 141s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 141s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 141s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 141s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 141s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 141s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 141s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 141s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 141s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 141s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 142s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 142s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 144s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 144s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 144s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 144s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 144s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 144s WARNING common:common.py:186 6 atoms have position differences > 0 144s INFO common:common.py:198 0 atoms have position differences > 0.01 144s INFO common:common.py:198 0 atoms have charge differences > 0 144s INFO common:common.py:198 0 atoms have charge differences > 0.01 144s INFO common:common.py:198 0 atoms have radius differences > 0 144s INFO common:common.py:198 0 atoms have radius differences > 0.01 144s PASSED [ 99%] 144s tests/regression_test.py::test_other_options[1AFS userff usernames whitespace] 144s -------------------------------- live log call --------------------------------- 144s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_userff0/output.log 144s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 144s 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). 144s 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). 144s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 144s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 144s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 144s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 144s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 144s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 144s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 144s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 144s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 144s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 144s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 144s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 144s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 144s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 144s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 144s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 144s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 144s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 144s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 144s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 145s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 145s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 148s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 148s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 148s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 148s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 148s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 148s WARNING common:common.py:186 6 atoms have position differences > 0 148s INFO common:common.py:198 0 atoms have position differences > 0.01 148s INFO common:common.py:198 0 atoms have charge differences > 0 148s INFO common:common.py:198 0 atoms have charge differences > 0.01 148s INFO common:common.py:198 0 atoms have radius differences > 0 148s INFO common:common.py:198 0 atoms have radius differences > 0.01 148s PASSED [ 99%] 148s tests/test_version.py::test_version_exists PASSED [ 99%] 148s tests/test_version.py::test_version PASSED [100%] 148s 148s ================= 92 passed, 220 skipped, 4 xfailed in 56.77s ================== 148s autopkgtest [14:51:55]: test command1: -----------------------] 149s command1 PASS 149s autopkgtest [14:51:56]: test command1: - - - - - - - - - - results - - - - - - - - - - 149s autopkgtest [14:51:56]: @@@@@@@@@@@@@@@@@@@@ summary 149s installation-test PASS 149s pdb2pka-test PASS 149s command1 PASS