0s autopkgtest [16:33:18]: starting date and time: 2025-10-20 16:33:18+0000 0s autopkgtest [16:33:18]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [16:33:18]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.nohj6miw/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:python-pluggy --apt-upgrade pdb2pqr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.4.2-1 python-pluggy/1.6.0-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-1.secgroup --name adt-resolute-s390x-pdb2pqr-20251020-163318-juju-7f2275-prod-proposed-migration-environment-2-0db92e64-a5c9-46c9-bcdf-be9f737ec753 --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-s390x-pdb2pqr-20251020-163318-juju-7f2275-prod-proposed-migration-environment-2-0db92e64-a5c9-46c9-bcdf-be9f737ec753 from image adt/ubuntu-resolute-s390x-server-20251020.img (UUID af6042e7-5f94-4102-8fd4-5557e2338897)... 52s autopkgtest [16:34:10]: testbed dpkg architecture: s390x 52s autopkgtest [16:34:10]: testbed apt version: 3.1.8ubuntu1 53s autopkgtest [16:34:11]: @@@@@@@@@@@@@@@@@@@@ test bed setup 53s autopkgtest [16:34:11]: testbed release detected to be: None 54s autopkgtest [16:34:12]: updating testbed package index (apt update) 55s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 55s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 55s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 55s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 55s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [646 kB] 56s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [14.3 kB] 56s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 56s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [56.9 kB] 56s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [107 kB] 56s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 56s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [400 kB] 56s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [3812 B] 56s Fetched 1318 kB in 1s (1076 kB/s) 56s Reading package lists... 57s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 58s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 58s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 58s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 58s Reading package lists... 58s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s Calculating upgrade... 59s The following packages will be upgraded: 59s libjson-c5 python3-inflect python3-oauthlib python3-zipp 59s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 59s Need to get 175 kB of archives. 59s After this operation, 31.7 kB of additional disk space will be used. 59s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libjson-c5 s390x 0.18+ds-1.1 [36.8 kB] 59s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3-inflect all 7.5.0-1 [33.9 kB] 59s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x python3-oauthlib all 3.3.1-1 [93.5 kB] 59s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x python3-zipp all 3.23.0-1 [10.4 kB] 59s dpkg-preconfigure: unable to re-open stdin: No such file or directory 59s Fetched 175 kB in 0s (373 kB/s) 59s (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 ... 56857 files and directories currently installed.) 59s Preparing to unpack .../libjson-c5_0.18+ds-1.1_s390x.deb ... 59s Unpacking libjson-c5:s390x (0.18+ds-1.1) over (0.18+ds-1) ... 59s Preparing to unpack .../python3-inflect_7.5.0-1_all.deb ... 59s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 59s Preparing to unpack .../python3-oauthlib_3.3.1-1_all.deb ... 59s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 60s Preparing to unpack .../python3-zipp_3.23.0-1_all.deb ... 60s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 60s Setting up python3-zipp (3.23.0-1) ... 60s Setting up python3-inflect (7.5.0-1) ... 60s Setting up python3-oauthlib (3.3.1-1) ... 60s Setting up libjson-c5:s390x (0.18+ds-1.1) ... 60s Processing triggers for libc-bin (2.42-0ubuntu3) ... 60s autopkgtest [16:34:18]: upgrading testbed (apt dist-upgrade and autopurge) 60s Reading package lists... 60s Building dependency tree... 60s Reading state information... 60s Calculating upgrade... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s Solving dependencies... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s autopkgtest [16:34:23]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP Mon Sep 22 08:56:47 UTC 2025 65s autopkgtest [16:34:23]: @@@@@@@@@@@@@@@@@@@@ apt-source pdb2pqr 71s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (dsc) [1860 B] 71s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (tar) [7570 kB] 71s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (diff) [9876 B] 71s gpgv: Signature made Mon Jun 12 17:36:50 2023 UTC 71s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 71s gpgv: Can't check signature: No public key 71s dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found 71s autopkgtest [16:34:29]: testing package pdb2pqr version 3.6.1+dfsg-1 72s autopkgtest [16:34:30]: build not needed 74s autopkgtest [16:34:32]: test installation-test: preparing testbed 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s Solving dependencies... 75s The following NEW packages will be installed: 75s docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr python3-docutils 75s python3-numpy python3-numpy-dev python3-pdb2pqr python3-pdbx python3-propka 75s python3-roman sgml-base xml-core 75s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 75s Need to get 9154 kB of archives. 75s After this operation, 38.7 MB of additional disk space will be used. 75s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.2.4+ds-1ubuntu1 [147 kB] 75s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-6build1 [245 kB] 76s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-5ubuntu1 [629 kB] 76s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-6build1 [2910 kB] 77s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.2.4+ds-1ubuntu1 [4399 kB] 77s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x sgml-base all 1.31+nmu1 [11.0 kB] 77s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x xml-core all 0.19 [20.3 kB] 77s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x docutils-common all 0.21.2+dfsg-2 [131 kB] 77s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x python3-roman all 5.1-1 [10.6 kB] 77s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x python3-docutils all 0.21.2+dfsg-2 [409 kB] 77s Get:11 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pdbx all 2.0.1-2 [16.5 kB] 77s Get:12 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-propka all 3.5.1-2 [70.1 kB] 77s Get:13 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pdb2pqr all 3.6.1+dfsg-1 [145 kB] 77s Get:14 http://ftpmaster.internal/ubuntu resolute/universe s390x pdb2pqr all 3.6.1+dfsg-1 [10.4 kB] 77s Fetched 9154 kB in 2s (4014 kB/s) 78s Selecting previously unselected package python3-numpy-dev:s390x. 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 ... 56867 files and directories currently installed.) 78s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 78s Unpacking python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 78s Selecting previously unselected package libblas3:s390x. 78s Preparing to unpack .../01-libblas3_3.12.1-6build1_s390x.deb ... 78s Unpacking libblas3:s390x (3.12.1-6build1) ... 78s Selecting previously unselected package libgfortran5:s390x. 78s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_s390x.deb ... 78s Unpacking libgfortran5:s390x (15.2.0-5ubuntu1) ... 78s Selecting previously unselected package liblapack3:s390x. 78s Preparing to unpack .../03-liblapack3_3.12.1-6build1_s390x.deb ... 78s Unpacking liblapack3:s390x (3.12.1-6build1) ... 78s Selecting previously unselected package python3-numpy. 78s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 78s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 78s Selecting previously unselected package sgml-base. 78s Preparing to unpack .../05-sgml-base_1.31+nmu1_all.deb ... 78s Unpacking sgml-base (1.31+nmu1) ... 78s Selecting previously unselected package xml-core. 78s Preparing to unpack .../06-xml-core_0.19_all.deb ... 78s Unpacking xml-core (0.19) ... 78s Selecting previously unselected package docutils-common. 78s Preparing to unpack .../07-docutils-common_0.21.2+dfsg-2_all.deb ... 78s Unpacking docutils-common (0.21.2+dfsg-2) ... 78s Selecting previously unselected package python3-roman. 78s Preparing to unpack .../08-python3-roman_5.1-1_all.deb ... 78s Unpacking python3-roman (5.1-1) ... 78s Selecting previously unselected package python3-docutils. 78s Preparing to unpack .../09-python3-docutils_0.21.2+dfsg-2_all.deb ... 78s Unpacking python3-docutils (0.21.2+dfsg-2) ... 78s Selecting previously unselected package python3-pdbx. 78s Preparing to unpack .../10-python3-pdbx_2.0.1-2_all.deb ... 78s Unpacking python3-pdbx (2.0.1-2) ... 78s Selecting previously unselected package python3-propka. 78s Preparing to unpack .../11-python3-propka_3.5.1-2_all.deb ... 78s Unpacking python3-propka (3.5.1-2) ... 78s Selecting previously unselected package python3-pdb2pqr. 78s Preparing to unpack .../12-python3-pdb2pqr_3.6.1+dfsg-1_all.deb ... 78s Unpacking python3-pdb2pqr (3.6.1+dfsg-1) ... 78s Selecting previously unselected package pdb2pqr. 78s Preparing to unpack .../13-pdb2pqr_3.6.1+dfsg-1_all.deb ... 78s Unpacking pdb2pqr (3.6.1+dfsg-1) ... 78s Setting up python3-propka (3.5.1-2) ... 78s Setting up python3-pdbx (2.0.1-2) ... 78s Setting up python3-roman (5.1-1) ... 78s Setting up libblas3:s390x (3.12.1-6build1) ... 78s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 78s Setting up python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 78s Setting up libgfortran5:s390x (15.2.0-5ubuntu1) ... 78s Setting up sgml-base (1.31+nmu1) ... 78s Setting up liblapack3:s390x (3.12.1-6build1) ... 78s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 78s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 80s Setting up xml-core (0.19) ... 80s Processing triggers for libc-bin (2.42-0ubuntu3) ... 80s Processing triggers for man-db (2.13.1-1) ... 80s Processing triggers for sgml-base (1.31+nmu1) ... 80s Setting up docutils-common (0.21.2+dfsg-2) ... 80s Processing triggers for sgml-base (1.31+nmu1) ... 80s Setting up python3-docutils (0.21.2+dfsg-2) ... 81s Setting up python3-pdb2pqr (3.6.1+dfsg-1) ... 81s Setting up pdb2pqr (3.6.1+dfsg-1) ... 82s autopkgtest [16:34:40]: test installation-test: [----------------------- 82s Run pdb2pqr... 82s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 82s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 82s 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). 82s INFO:Checking and transforming input arguments. 82s INFO:Loading topology files. 82s INFO:Loading molecule: examples/1a1p/1a1p.pdb 82s INFO:Setting up molecule. 82s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 82s INFO:Created biomolecule object with 14 residues and 208 atoms. 82s INFO:Setting termini states for biomolecule chains. 82s INFO:Loading forcefield. 82s INFO:Loading hydrogen topology definitions. 82s INFO:This biomolecule is clean. No repair needed. 82s INFO:Updating disulfide bridges. 82s INFO:Debumping biomolecule. 82s INFO:Adding hydrogens to biomolecule. 82s INFO:Debumping biomolecule (again). 82s INFO:Optimizing hydrogen bonds 82s INFO:Applying force field to biomolecule states. 82s INFO:Regenerating headers. 82s INFO:Regenerating PDB lines. 82s WARNING:Ignoring 852 header lines in output. 82s WARNING:Ignoring 3 missing lines in output. 83s autopkgtest [16:34:41]: test installation-test: -----------------------] 83s installation-test PASS 83s autopkgtest [16:34:41]: test installation-test: - - - - - - - - - - results - - - - - - - - - - 84s autopkgtest [16:34:42]: test pdb2pka-test: preparing testbed 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Solving dependencies... 84s The following NEW packages will be installed: 84s fonts-font-awesome fonts-lato libjs-jquery libjs-sphinxdoc libjs-underscore 84s pdb2pqr-doc sphinx-rtd-theme-common 84s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 84s Need to get 5041 kB of archives. 84s After this operation, 20.0 MB of additional disk space will be used. 84s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-lato all 2.015-1 [2781 kB] 85s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 85s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 85s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 86s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 86s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 86s Get:7 http://ftpmaster.internal/ubuntu resolute/universe s390x pdb2pqr-doc all 3.6.1+dfsg-1 [258 kB] 86s Fetched 5041 kB in 1s (3546 kB/s) 86s Selecting previously unselected package fonts-lato. 86s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58368 files and directories currently installed.) 86s Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... 86s Unpacking fonts-lato (2.015-1) ... 86s Selecting previously unselected package fonts-font-awesome. 86s Preparing to unpack .../1-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 86s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 86s Selecting previously unselected package libjs-jquery. 86s Preparing to unpack .../2-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 86s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 86s Selecting previously unselected package libjs-underscore. 86s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 86s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 86s Selecting previously unselected package libjs-sphinxdoc. 86s Preparing to unpack .../4-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 86s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 86s Selecting previously unselected package sphinx-rtd-theme-common. 86s Preparing to unpack .../5-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 86s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 86s Selecting previously unselected package pdb2pqr-doc. 86s Preparing to unpack .../6-pdb2pqr-doc_3.6.1+dfsg-1_all.deb ... 86s Unpacking pdb2pqr-doc (3.6.1+dfsg-1) ... 86s Setting up fonts-lato (2.015-1) ... 86s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 86s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 86s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 86s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 86s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 86s Setting up pdb2pqr-doc (3.6.1+dfsg-1) ... 88s autopkgtest [16:34:46]: test pdb2pka-test: [----------------------- 88s Run pdb2pqr... 88s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 88s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 88s 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). 88s INFO:Checking and transforming input arguments. 88s INFO:Loading topology files. 89s INFO:Loading molecule: 1a1p/1a1p.pdb 89s INFO:Setting up molecule. 89s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 89s INFO:Created biomolecule object with 14 residues and 208 atoms. 89s INFO:Setting termini states for biomolecule chains. 89s INFO:Loading forcefield. 89s INFO:Loading hydrogen topology definitions. 89s INFO:This biomolecule is clean. No repair needed. 89s INFO:Updating disulfide bridges. 89s INFO:Debumping biomolecule. 89s INFO:Adding hydrogens to biomolecule. 89s INFO:Debumping biomolecule (again). 89s INFO:Optimizing hydrogen bonds 89s INFO:Applying force field to biomolecule states. 89s INFO:Regenerating headers. 89s INFO:Regenerating PDB lines. 89s WARNING:Ignoring 852 header lines in output. 89s WARNING:Ignoring 3 missing lines in output. 89s autopkgtest [16:34:47]: test pdb2pka-test: -----------------------] 89s pdb2pka-test PASS 89s autopkgtest [16:34:47]: test pdb2pka-test: - - - - - - - - - - results - - - - - - - - - - 90s autopkgtest [16:34:48]: test command1: preparing testbed 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s Solving dependencies... 90s The following NEW packages will be installed: 90s python3-dateutil python3-iniconfig python3-packaging python3-pandas 90s python3-pandas-lib python3-pluggy python3-pytest python3-pytz 90s python3-testfixtures 91s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 91s Need to get 8770 kB of archives. 91s After this operation, 48.8 MB of additional disk space will be used. 91s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-dateutil all 2.9.0-4 [80.3 kB] 91s Get:2 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 91s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x python3-packaging all 25.0-1 [52.8 kB] 91s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x python3-pytz all 2025.2-3 [163 kB] 91s Get:5 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas-lib s390x 2.2.3+dfsg-9 [4991 kB] 92s Get:6 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas all 2.2.3+dfsg-9 [3112 kB] 93s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x python3-pluggy all 1.6.0-1 [21.0 kB] 93s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x python3-pytest all 8.4.2-1 [268 kB] 93s Get:9 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-testfixtures all 8.3.0-2 [75.6 kB] 93s Fetched 8770 kB in 2s (3844 kB/s) 93s Selecting previously unselected package python3-dateutil. 93s (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 ... 58703 files and directories currently installed.) 93s Preparing to unpack .../0-python3-dateutil_2.9.0-4_all.deb ... 93s Unpacking python3-dateutil (2.9.0-4) ... 93s Selecting previously unselected package python3-iniconfig. 93s Preparing to unpack .../1-python3-iniconfig_1.1.1-2_all.deb ... 93s Unpacking python3-iniconfig (1.1.1-2) ... 93s Selecting previously unselected package python3-packaging. 93s Preparing to unpack .../2-python3-packaging_25.0-1_all.deb ... 93s Unpacking python3-packaging (25.0-1) ... 93s Selecting previously unselected package python3-pytz. 93s Preparing to unpack .../3-python3-pytz_2025.2-3_all.deb ... 93s Unpacking python3-pytz (2025.2-3) ... 93s Selecting previously unselected package python3-pandas-lib:s390x. 93s Preparing to unpack .../4-python3-pandas-lib_2.2.3+dfsg-9_s390x.deb ... 93s Unpacking python3-pandas-lib:s390x (2.2.3+dfsg-9) ... 93s Selecting previously unselected package python3-pandas. 93s Preparing to unpack .../5-python3-pandas_2.2.3+dfsg-9_all.deb ... 93s Unpacking python3-pandas (2.2.3+dfsg-9) ... 93s Selecting previously unselected package python3-pluggy. 93s Preparing to unpack .../6-python3-pluggy_1.6.0-1_all.deb ... 93s Unpacking python3-pluggy (1.6.0-1) ... 93s Selecting previously unselected package python3-pytest. 93s Preparing to unpack .../7-python3-pytest_8.4.2-1_all.deb ... 93s Unpacking python3-pytest (8.4.2-1) ... 93s Selecting previously unselected package python3-testfixtures. 93s Preparing to unpack .../8-python3-testfixtures_8.3.0-2_all.deb ... 93s Unpacking python3-testfixtures (8.3.0-2) ... 93s Setting up python3-iniconfig (1.1.1-2) ... 94s Setting up python3-pandas-lib:s390x (2.2.3+dfsg-9) ... 94s Setting up python3-testfixtures (8.3.0-2) ... 94s Setting up python3-pytz (2025.2-3) ... 94s Setting up python3-packaging (25.0-1) ... 94s Setting up python3-pluggy (1.6.0-1) ... 94s Setting up python3-dateutil (2.9.0-4) ... 94s Setting up python3-pytest (8.4.2-1) ... 94s Setting up python3-pandas (2.2.3+dfsg-9) ... 99s Processing triggers for man-db (2.13.1-1) ... 100s autopkgtest [16:34:58]: test command1: pytest-3 100s autopkgtest [16:34:58]: test command1: [----------------------- 101s ============================= test session starts ============================== 101s platform linux -- Python 3.13.7, pytest-8.4.2, pluggy-1.6.0 101s rootdir: /tmp/autopkgtest.CVqoZi/build.0uM/src 101s configfile: pytest.ini 101s plugins: typeguard-4.4.2 101s 101s ----------------------------- live log collection ------------------------------ 101s WARNING py.warnings:warnings.py:110 /tmp/autopkgtest.CVqoZi/build.0uM/src/tests/core_test.py:81: PytestUnknownMarkWarning: Unknown pytest.mark.long_test - is this a typo? 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[ 54%] 101s tests/core_test.py::test_long_pdb[3JTE] SKIPPED (not running tests r...) [ 55%] 101s tests/core_test.py::test_long_pdb[4IL7] SKIPPED (not running tests r...) [ 55%] 101s tests/core_test.py::test_long_pdb[2PTV] SKIPPED (not running tests r...) [ 55%] 101s tests/core_test.py::test_long_pdb[2IGD] SKIPPED (not running tests r...) [ 56%] 101s tests/core_test.py::test_long_pdb[2OP6] SKIPPED (not running tests r...) [ 56%] 101s tests/core_test.py::test_long_pdb[1TG0] SKIPPED (not running tests r...) [ 56%] 101s tests/core_test.py::test_long_pdb[4OSN] SKIPPED (not running tests r...) [ 56%] 101s tests/core_test.py::test_long_pdb[2EBB] SKIPPED (not running tests r...) [ 57%] 101s tests/core_test.py::test_long_pdb[2XXC] SKIPPED (not running tests r...) [ 57%] 101s tests/core_test.py::test_long_pdb[3CSR] SKIPPED (not running tests r...) [ 57%] 101s tests/core_test.py::test_long_pdb[4NPN] SKIPPED (not running tests r...) [ 58%] 101s tests/core_test.py::test_long_pdb[4CRH] SKIPPED (not running tests r...) [ 58%] 101s tests/core_test.py::test_long_pdb[2YXF] SKIPPED (not running tests r...) [ 58%] 101s tests/core_test.py::test_long_pdb[1TQG] SKIPPED (not running tests r...) [ 59%] 101s tests/core_test.py::test_long_pdb[3T8R] SKIPPED (not running tests r...) [ 59%] 101s tests/core_test.py::test_long_pdb[3S0A] SKIPPED (not running tests r...) [ 59%] 101s tests/core_test.py::test_long_pdb[1Z0P] SKIPPED (not running tests r...) [ 60%] 101s tests/core_test.py::test_long_pdb[2CKX] SKIPPED (not running tests r...) [ 60%] 101s tests/core_test.py::test_long_pdb[1PGX] SKIPPED (not running tests r...) [ 60%] 101s tests/core_test.py::test_long_pdb[3H0X] SKIPPED (not running tests r...) [ 61%] 101s tests/core_test.py::test_long_pdb[1I2T] SKIPPED (not running tests r...) [ 61%] 101s tests/core_test.py::test_long_pdb[3LLB] SKIPPED (not running tests r...) [ 61%] 101s tests/core_test.py::test_long_pdb[1P1L] SKIPPED (not running tests r...) [ 62%] 101s tests/core_test.py::test_long_pdb[1KFN] SKIPPED (not running tests r...) [ 62%] 101s tests/core_test.py::test_long_pdb[2ZQE] SKIPPED (not running tests r...) [ 62%] 101s tests/core_test.py::test_long_pdb[2QVO] SKIPPED (not running tests r...) [ 62%] 101s tests/core_test.py::test_long_pdb[2FD4] SKIPPED (not running tests r...) [ 63%] 101s tests/core_test.py::test_long_pdb[1NXO] SKIPPED (not running tests r...) [ 63%] 101s tests/core_test.py::test_long_pdb[1DF4] SKIPPED (not running tests r...) [ 63%] 101s tests/core_test.py::test_long_pdb[2GUS] SKIPPED (not running tests r...) [ 64%] 101s tests/core_test.py::test_long_pdb[1BM8] SKIPPED (not running tests r...) [ 64%] 101s tests/core_test.py::test_long_pdb[2PII] SKIPPED (not running tests r...) [ 64%] 101s tests/core_test.py::test_long_pdb[2FRG] SKIPPED (not running tests r...) [ 65%] 101s tests/core_test.py::test_long_pdb[2QR3] SKIPPED (not running tests r...) [ 65%] 101s tests/core_test.py::test_long_pdb[1J27] SKIPPED (not running tests r...) [ 65%] 101s tests/core_test.py::test_long_pdb[5EE2] SKIPPED (not running tests r...) [ 66%] 101s tests/core_test.py::test_broken_backbone[4MGP] 101s -------------------------------- live log call --------------------------------- 101s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_4MGP_0/4MGP.log 101s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 101s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 101s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 101s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 101s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 101s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP 102s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 102s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 102s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 23 residues and 163 atoms. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in MET A 21. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in MET A 21. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in MET A 21. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: SD in MET A 21. 102s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE in MET A 21. 102s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in MET A 21. At least one of the instances is being ignored. 102s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 102s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 102s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 102s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 12 missing atoms in biomolecule. 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 102s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 102s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 11 at coordinates 1.430, -1.683, -11.529 102s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 11 at coordinates 1.940, -0.315, -11.800 102s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CG to residue LYS A 14 at coordinates -1.600, -8.819, -6.913 102s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CD to residue LYS A 14 at coordinates -2.056, -8.844, -8.361 102s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 14 at coordinates -3.548, -9.031, -8.498 102s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 14 at coordinates -3.947, -9.048, -9.928 102s 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 102s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 102s XFAIL [ 66%] 102s tests/core_test.py::test_broken_backbone[2V75] 102s -------------------------------- live log call --------------------------------- 102s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_2V75_0/2V75.log 102s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 102s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 102s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 102s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 102s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 102s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 103s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 103s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 103s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 90 residues and 687 atoms. 103s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 103s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 103s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 103s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 104s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 8 missing atoms in biomolecule. 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 104s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 104s 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 104s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 104s XFAIL [ 66%] 104s tests/core_test.py::test_broken_backbone[3U7T] 104s -------------------------------- live log call --------------------------------- 104s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_3U7T_0/3U7T.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: 3U7T 105s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 105s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 105s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 652 atoms. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in PRO A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in PRO A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in PRO A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in PRO A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in PRO A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in PRO A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in PRO A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in PRO A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 22. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 22. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 22. At least one of the instances is being ignored. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in LEU A 25. 105s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in LEU A 25. At least one of the instances is being ignored. 105s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 105s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 105s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 105s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 105s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 105s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 105s CRITICAL PDB2PQR3.6.1:main.py:800 Unable to debump biomolecule. Biomolecular structure is incomplete: Found gap in biomolecule structure for atom ATOM 313 OG PRO 22 -13.108 -5.696 -15.739 0.0000 0.0000 105s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 105s XFAIL [ 67%] 105s tests/core_test.py::test_broken_backbone[1EJG] 105s -------------------------------- live log call --------------------------------- 105s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_1EJG_0/1EJG.log 105s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 105s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 105s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 105s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 105s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 105s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG 106s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 106s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 106s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 650 atoms. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in THR A 1. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 1. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 1. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 1. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 1. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H1 in THR A 1. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H2 in THR A 1. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H3 in THR A 1. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 1. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 1. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 1. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 1. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 1. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 1. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 1. At least one of the instances is being ignored. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 2. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 2. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 2. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 2. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 2. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 2. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 2. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 2. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 2. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 2. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 2. At least one of the instances is being ignored. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 7. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 7. At least one of the instances is being ignored. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in VAL A 8. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in VAL A 8. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in VAL A 8. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in VAL A 8. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in VAL A 8. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in VAL A 8. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in VAL A 8. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in VAL A 8. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG11 in VAL A 8. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in VAL A 8. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in VAL A 8. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in VAL A 8. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in VAL A 8. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in VAL A 8. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in VAL A 8. At least one of the instances is being ignored. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NE in ARG A 10. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in ARG A 10. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH1 in ARG A 10. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH2 in ARG A 10. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE in ARG A 10. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH11 in ARG A 10. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH12 in ARG A 10. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH21 in ARG A 10. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH22 in ARG A 10. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ARG A 10. At least one of the instances is being ignored. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ASN A 12. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASN A 12. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 12. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 12. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 12. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ASN A 12. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASN A 12. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASN A 12. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 12. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 12. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 12. At least one of the instances is being ignored. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PHE A 13. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in PHE A 13. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in PHE A 13. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in PHE A 13. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in PHE A 13. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in PHE A 13. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in PHE A 13. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PHE A 13. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in PHE A 13. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in PHE A 13. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HZ in PHE A 13. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PHE A 13. At least one of the instances is being ignored. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 19. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 19. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 19. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 19. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 19. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 19. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 19. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 19. At least one of the instances is being ignored. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in SER A 22. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in SER A 22. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in SER A 22. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in SER A 22. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in SER A 22. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in SER A 22. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in SER A 22. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in SER A 22. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in SER A 22. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in SER A 22. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in SER A 22. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in SER A 22. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in SER A 22. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in SER A 22. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in SER A 22. At least one of the instances is being ignored. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in GLU A 23. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in GLU A 23. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE1 in GLU A 23. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE2 in GLU A 23. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in GLU A 23. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in GLU A 23. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in GLU A 23. At least one of the instances is being ignored. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 25. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 25. At least one of the instances is being ignored. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in TYR A 29. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in TYR A 29. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in TYR A 29. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in TYR A 29. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in TYR A 29. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in TYR A 29. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OH in TYR A 29. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in TYR A 29. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in TYR A 29. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in TYR A 29. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in TYR A 29. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH in TYR A 29. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in TYR A 29. At least one of the instances is being ignored. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 34. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 34. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 34. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 34. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 34. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 34. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 34. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 34. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 34. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 34. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 34. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 34. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 34. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 34. At least one of the instances is being ignored. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 36. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 36. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 36. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 36. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 36. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 36. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 36. At least one of the instances is being ignored. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 39. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 39. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 39. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 39. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 39. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 39. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 39. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 39. At least one of the instances is being ignored. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASP A 43. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASP A 43. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASP A 43. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD2 in ASP A 43. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASP A 43. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASP A 43. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASP A 43. At least one of the instances is being ignored. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 46. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 46. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 46. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 46. 106s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 46. 106s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 46. At least one of the instances is being ignored. 106s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 106s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 106s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 106s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 106s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 106s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 106s 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 106s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 106s XFAIL [ 67%] 106s tests/core_test.py::test_protonated_terminals[C-terminal HID] 106s -------------------------------- live log call --------------------------------- 106s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log 106s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 106s 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). 106s 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). 106s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 106s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 106s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/cterm_hid.pdb 106s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 106s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms. 106s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 106s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 106s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 106s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 106s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 106s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule. 106s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 106s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402 106s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 106s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 106s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 106s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 106s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 106s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 106s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 106s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 106s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 106s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 106s INFO common:common.py:198 0 atoms have position differences > 0 106s INFO common:common.py:198 0 atoms have position differences > 0.01 106s INFO common:common.py:198 0 atoms have charge differences > 0 106s INFO common:common.py:198 0 atoms have charge differences > 0.01 106s INFO common:common.py:198 0 atoms have radius differences > 0 106s INFO common:common.py:198 0 atoms have radius differences > 0.01 106s PASSED [ 67%] 106s tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 106s -------------------------------- live log call --------------------------------- 106s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log 106s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 106s 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). 106s 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). 106s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 106s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 106s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/5vav_cyclic_peptide.pdb 106s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 106s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms. 106s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 106s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 106s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 106s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 106s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 106s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 106s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 106s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 106s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 106s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 106s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 106s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 106s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 106s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 106s INFO common:common.py:198 0 atoms have position differences > 0 106s INFO common:common.py:198 0 atoms have position differences > 0.01 106s INFO common:common.py:198 0 atoms have charge differences > 0 106s INFO common:common.py:198 0 atoms have charge differences > 0.01 106s INFO common:common.py:198 0 atoms have radius differences > 0 106s INFO common:common.py:198 0 atoms have radius differences > 0.01 106s PASSED [ 68%] 106s tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 68%] 106s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 68%] 106s tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 68%] 106s tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 69%] 106s tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 69%] 106s tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 69%] 106s tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 70%] 106s tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 70%] 106s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 70%] 106s tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 71%] 106s tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 71%] 106s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 71%] 106s tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 72%] 106s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 72%] 106s tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 72%] 106s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 73%] 106s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 73%] 106s tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 73%] 106s 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 [ 74%] 106s tests/io_test.py::test_read_qcd PASSED [ 74%] 106s tests/io_test.py::test_dx2cube 106s -------------------------------- live log call --------------------------------- 106s INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... 106s INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... 107s INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 107s INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 107s INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... 108s INFO io_test:io_test.py:68 No differences found in output 108s PASSED [ 74%] 108s tests/ligand_test.py::test_peoe_charges 108s -------------------------------- live log call --------------------------------- 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s PASSED [ 75%] 108s tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 108s -------------------------------- live log call --------------------------------- 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 108s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 108s PASSED [ 75%] 109s tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 109s -------------------------------- live log call --------------------------------- 109s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 109s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 109s PASSED [ 75%] 109s tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 109s -------------------------------- live log call --------------------------------- 109s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 109s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 109s PASSED [ 75%] 109s tests/ligand_test.py::test_assign_parameters[acetate.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 109s PASSED [ 76%] 109s tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 109s PASSED [ 76%] 109s tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 109s -------------------------------- live log call --------------------------------- 109s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 109s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 109s PASSED [ 76%] 109s tests/ligand_test.py::test_assign_parameters[adp.mol2] 109s -------------------------------- live log call --------------------------------- 109s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 109s INFO ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00 109s PASSED [ 77%] 109s tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 109s PASSED [ 77%] 109s tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 109s PASSED [ 77%] 109s tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 109s PASSED [ 78%] 109s tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 109s PASSED [ 78%] 109s tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 109s PASSED [ 78%] 109s tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 109s PASSED [ 79%] 109s tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 109s -------------------------------- live log call --------------------------------- 109s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 109s PASSED [ 79%] 109s tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 109s -------------------------------- live log call --------------------------------- 109s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 109s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 109s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 109s PASSED [ 79%] 110s tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 110s -------------------------------- live log call --------------------------------- 110s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 110s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 110s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 110s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 110s PASSED [ 80%] 110s tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 110s -------------------------------- live log call --------------------------------- 110s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 110s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 110s PASSED [ 80%] 110s tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 110s -------------------------------- live log call --------------------------------- 110s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 110s PASSED [ 80%] 110s tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED [ 81%] 110s tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED [ 81%] 110s tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 110s -------------------------------- live log call --------------------------------- 110s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 110s PASSED [ 81%] 110s tests/ligand_test.py::test_formal_charge[adp.mol2] 110s -------------------------------- live log call --------------------------------- 110s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 110s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 110s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 110s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 110s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 110s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 110s PASSED [ 81%] 110s tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED [ 82%] 110s tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED [ 82%] 110s tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED [ 82%] 110s tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED [ 83%] 110s tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED [ 83%] 110s tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED [ 83%] 110s tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED [ 84%] 110s tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 110s -------------------------------- live log call --------------------------------- 110s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 110s PASSED [ 84%] 110s tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED [ 84%] 110s tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED [ 85%] 110s tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED [ 85%] 110s tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED [ 85%] 110s tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED [ 86%] 110s tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED [ 86%] 111s tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED [ 86%] 112s tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED [ 87%] 112s tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED [ 87%] 112s tests/ligand_test.py::test_rings[acetate.mol2] PASSED [ 87%] 112s tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED [ 87%] 112s tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED [ 88%] 112s tests/ligand_test.py::test_rings[adp.mol2] PASSED [ 88%] 112s tests/ligand_test.py::test_rings[anthracene.mol2] PASSED [ 88%] 112s tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED [ 89%] 112s tests/ligand_test.py::test_rings[ethanol.mol2] PASSED [ 89%] 112s tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED [ 89%] 112s tests/ligand_test.py::test_rings[glycerol.mol2] PASSED [ 90%] 112s tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED [ 90%] 112s tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED [ 90%] 112s tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED [ 91%] 112s tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%] 112s tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%] 112s tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%] 112s tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%] 112s tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%] 112s tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%] 112s tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%] 112s tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%] 112s tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%] 112s tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%] 112s tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%] 112s tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] 112s tests/regression_test.py::test_basic[1AFS basic local] 112s -------------------------------- live log call --------------------------------- 112s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_basic_1AFS_basic_local_0/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.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 112s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 112s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 112s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 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. 112s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 113s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 114s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 114s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 114s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 114s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 114s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 114s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 114s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 114s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 114s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 114s WARNING pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages 115s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 115s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 115s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 116s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 116s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 116s WARNING common:common.py:186 6 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 AMBER] 116s -------------------------------- live log call --------------------------------- 116s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa0/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 WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 116s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 116s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 116s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 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. 116s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 117s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 119s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 119s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 119s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 119s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 119s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 119s WARNING common:common.py:186 6 atoms have position differences > 0 119s INFO common:common.py:198 0 atoms have position differences > 0.01 119s INFO common:common.py:198 0 atoms have charge differences > 0 119s INFO common:common.py:198 0 atoms have charge differences > 0.01 119s INFO common:common.py:198 0 atoms have radius differences > 0 119s INFO common:common.py:198 0 atoms have radius differences > 0.01 119s PASSED [ 95%] 119s tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] 119s -------------------------------- live log call --------------------------------- 119s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa1/output.log 119s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 119s 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). 119s 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). 119s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 119s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 119s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 119s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 119s WARNING pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages 119s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 119s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 119s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 119s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 119s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 119s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 119s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 119s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 119s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 119s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 119s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 119s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 119s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 119s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 119s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 119s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 120s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 120s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 122s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 122s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 122s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 122s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 122s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 123s WARNING common:common.py:186 5 atoms have position differences > 0 123s INFO common:common.py:198 0 atoms have position differences > 0.01 123s INFO common:common.py:198 0 atoms have charge differences > 0 123s INFO common:common.py:198 0 atoms have charge differences > 0.01 123s INFO common:common.py:198 0 atoms have radius differences > 0 123s INFO common:common.py:198 0 atoms have radius differences > 0.01 123s PASSED [ 95%] 123s tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] 123s -------------------------------- live log call --------------------------------- 123s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa2/output.log 123s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 123s 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). 123s 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). 123s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 123s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 123s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 123s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 123s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 123s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 123s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 123s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 123s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 123s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 123s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 123s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 123s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 123s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 123s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 123s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 123s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 123s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 123s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 123s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 124s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 124s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 126s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 126s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 126s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 127s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 127s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 127s WARNING common:common.py:186 6 atoms have position differences > 0 127s INFO common:common.py:198 0 atoms have position differences > 0.01 127s INFO common:common.py:198 0 atoms have charge differences > 0 127s INFO common:common.py:198 0 atoms have charge differences > 0.01 127s INFO common:common.py:198 0 atoms have radius differences > 0 127s INFO common:common.py:198 0 atoms have radius differences > 0.01 127s PASSED [ 96%] 127s tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] 127s -------------------------------- live log call --------------------------------- 127s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa3/output.log 127s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 127s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 127s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 127s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 127s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 127s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 127s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 127s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 127s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 127s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 127s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 127s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 127s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 127s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 127s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 127s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 127s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 127s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 128s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 128s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 130s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 130s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 130s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 131s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 131s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 131s WARNING common:common.py:186 6 atoms have position differences > 0 131s INFO common:common.py:198 0 atoms have position differences > 0.01 131s INFO common:common.py:198 0 atoms have charge differences > 0 131s INFO common:common.py:198 0 atoms have charge differences > 0.01 131s INFO common:common.py:198 0 atoms have radius differences > 0 131s INFO common:common.py:198 0 atoms have radius differences > 0.01 131s PASSED [ 96%] 131s tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] 131s -------------------------------- live log call --------------------------------- 131s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa4/output.log 131s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 131s 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). 131s 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). 131s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 131s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 131s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 131s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 131s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 131s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 131s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 131s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 131s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 131s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 131s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 131s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 131s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 131s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 131s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 131s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 131s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 131s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 131s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 131s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 131s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 132s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 134s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 134s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 134s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 134s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output. 134s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 135s WARNING common:common.py:186 6 atoms have position differences > 0 135s INFO common:common.py:198 0 atoms have position differences > 0.01 135s INFO common:common.py:198 0 atoms have charge differences > 0 135s INFO common:common.py:198 0 atoms have charge differences > 0.01 135s INFO common:common.py:198 0 atoms have radius differences > 0 135s INFO common:common.py:198 0 atoms have radius differences > 0.01 135s PASSED [ 96%] 135s tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] 135s -------------------------------- live log call --------------------------------- 135s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa5/output.log 135s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 135s 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). 135s 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). 135s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 135s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 135s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 135s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 135s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 135s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 135s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 135s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 135s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 135s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 135s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 135s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 135s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 135s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 135s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 135s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 135s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 135s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 135s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 135s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 135s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 136s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 138s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 138s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 138s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 138s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 138s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 138s WARNING common:common.py:186 6 atoms have position differences > 0 138s INFO common:common.py:198 0 atoms have position differences > 0.01 138s INFO common:common.py:198 0 atoms have charge differences > 0 138s INFO common:common.py:198 0 atoms have charge differences > 0.01 138s INFO common:common.py:198 0 atoms have radius differences > 0 138s INFO common:common.py:198 0 atoms have radius differences > 0.01 138s PASSED [ 97%] 138s tests/regression_test.py::test_other_options[1AFS whitespace clean] 138s -------------------------------- live log call --------------------------------- 138s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_whites0/output.log 138s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 138s 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). 138s 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). 138s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 138s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 138s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 138s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 138s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 138s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 138s INFO PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps. 138s INFO common:common.py:198 0 atoms have position differences > 0 138s INFO common:common.py:198 0 atoms have position differences > 0.01 138s INFO common:common.py:198 0 atoms have charge differences > 0 138s INFO common:common.py:198 0 atoms have charge differences > 0.01 138s INFO common:common.py:198 0 atoms have radius differences > 0 138s INFO common:common.py:198 0 atoms have radius differences > 0.01 138s PASSED [ 97%] 138s tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] 138s -------------------------------- live log call --------------------------------- 138s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_assign0/output.log 138s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 138s 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). 138s 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). 138s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 138s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 138s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 138s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 138s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 138s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 138s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 138s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 138s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 138s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 138s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 138s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 138s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 138s INFO common:common.py:198 0 atoms have position differences > 0 138s INFO common:common.py:198 0 atoms have position differences > 0.01 138s INFO common:common.py:198 0 atoms have charge differences > 0 138s INFO common:common.py:198 0 atoms have charge differences > 0.01 138s INFO common:common.py:198 0 atoms have radius differences > 0 138s INFO common:common.py:198 0 atoms have radius differences > 0.01 138s PASSED [ 97%] 138s tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] 138s -------------------------------- live log call --------------------------------- 138s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_nodebu0/output.log 138s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 138s 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). 138s 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). 138s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 138s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 138s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 138s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 138s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 138s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 138s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 138s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 138s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 138s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 138s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 138s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 138s INFO pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization... 138s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 138s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 138s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 138s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 138s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 138s INFO common:common.py:198 0 atoms have position differences > 0 138s INFO common:common.py:198 0 atoms have position differences > 0.01 138s INFO common:common.py:198 0 atoms have charge differences > 0 138s INFO common:common.py:198 0 atoms have charge differences > 0.01 138s INFO common:common.py:198 0 atoms have radius differences > 0 138s INFO common:common.py:198 0 atoms have radius differences > 0.01 138s PASSED [ 98%] 138s tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] 138s -------------------------------- live log call --------------------------------- 138s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_chain_0/output.log 138s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 138s 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). 138s 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). 138s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 138s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 138s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 138s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 138s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 138s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 138s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 138s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 138s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 138s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 138s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 138s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 138s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 138s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 138s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 138s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 138s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 138s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 138s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 139s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 139s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 140s 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. 142s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 142s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 142s WARNING common:common.py:186 6 atoms have position differences > 0 142s INFO common:common.py:198 0 atoms have position differences > 0.01 142s INFO common:common.py:198 0 atoms have charge differences > 0 142s INFO common:common.py:198 0 atoms have charge differences > 0.01 142s INFO common:common.py:198 0 atoms have radius differences > 0 142s INFO common:common.py:198 0 atoms have radius differences > 0.01 142s PASSED [ 98%] 142s tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] 142s -------------------------------- live log call --------------------------------- 142s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_neutra0/output.log 142s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 142s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 142s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 142s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 142s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 142s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 142s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 142s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 142s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 142s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 142s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 142s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 142s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 142s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 142s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 142s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 142s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 142s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 142s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 142s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 142s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 142s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 142s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 142s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 143s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 145s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 145s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 145s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 145s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 145s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 145s WARNING common:common.py:186 6 atoms have position differences > 0 145s INFO common:common.py:198 0 atoms have position differences > 0.01 145s INFO common:common.py:198 0 atoms have charge differences > 0 145s INFO common:common.py:198 0 atoms have charge differences > 0.01 145s INFO common:common.py:198 0 atoms have radius differences > 0 145s INFO common:common.py:198 0 atoms have radius differences > 0.01 145s PASSED [ 98%] 145s tests/regression_test.py::test_other_options[1AFS drop-water AMBER] 145s -------------------------------- live log call --------------------------------- 145s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_drop_w0/output.log 145s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 145s 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). 145s 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). 145s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 145s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 145s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 145s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 145s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 145s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms. 145s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 145s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 145s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 145s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 145s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 145s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 145s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 145s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 145s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 145s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 145s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 145s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 145s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 145s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 145s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 146s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 146s 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/regression_test.py::test_other_options[1AFS userff usernames whitespace] 148s -------------------------------- live log call --------------------------------- 148s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_userff0/output.log 148s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 148s 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). 148s 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). 148s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 148s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 148s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 148s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 148s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 148s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 148s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 148s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 148s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 148s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 148s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 148s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 148s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 148s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 148s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 148s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 148s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 148s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 148s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 148s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 149s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 149s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 151s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 151s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 151s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 151s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 151s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 151s WARNING common:common.py:186 6 atoms have position differences > 0 151s INFO common:common.py:198 0 atoms have position differences > 0.01 151s INFO common:common.py:198 0 atoms have charge differences > 0 151s INFO common:common.py:198 0 atoms have charge differences > 0.01 151s INFO common:common.py:198 0 atoms have radius differences > 0 151s INFO common:common.py:198 0 atoms have radius differences > 0.01 151s PASSED [ 99%] 151s tests/test_version.py::test_version_exists PASSED [ 99%] 151s tests/test_version.py::test_version PASSED [100%] 151s 151s ================= 92 passed, 220 skipped, 4 xfailed in 50.54s ================== 152s autopkgtest [16:35:50]: test command1: -----------------------] 152s autopkgtest [16:35:50]: test command1: - - - - - - - - - - results - - - - - - - - - - 152s command1 PASS 153s autopkgtest [16:35:51]: @@@@@@@@@@@@@@@@@@@@ summary 153s installation-test PASS 153s pdb2pka-test PASS 153s command1 PASS