0s autopkgtest [02:40:45]: starting date and time: 2025-10-29 02:40:45+0000 0s autopkgtest [02:40:45]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [02:40:45]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.x0bky7gu/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:node-jquery --apt-upgrade pdb2pqr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=node-jquery/3.7.1+dfsg+~3.5.33-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-5.secgroup --name adt-resolute-s390x-pdb2pqr-20251029-024045-juju-7f2275-prod-proposed-migration-environment-15-41e9f9a9-4d30-443d-bf39-418588ab8ead --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-s390x-pdb2pqr-20251029-024045-juju-7f2275-prod-proposed-migration-environment-15-41e9f9a9-4d30-443d-bf39-418588ab8ead from image adt/ubuntu-resolute-s390x-server-20251028.img (UUID 222a8a17-8cdf-422e-baeb-91db113eb3ff)... 45s autopkgtest [02:41:30]: testbed dpkg architecture: s390x 45s autopkgtest [02:41:30]: testbed apt version: 3.1.8ubuntu1 45s autopkgtest [02:41:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup 45s autopkgtest [02:41:30]: testbed release detected to be: None 46s autopkgtest [02:41:31]: updating testbed package index (apt update) 46s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 47s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 47s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 47s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 47s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [3625 kB] 47s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5856 B] 47s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [203 kB] 47s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [70.0 kB] 47s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [247 kB] 47s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 47s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [1754 kB] 47s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [20.3 kB] 48s Fetched 6013 kB in 2s (3470 kB/s) 49s Reading package lists... 49s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 49s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 49s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 50s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 50s Reading package lists... 50s Reading package lists... 50s Building dependency tree... 50s Reading state information... 50s Calculating upgrade... 51s The following packages will be upgraded: 51s apt cloud-init cloud-init-base libapt-pkg7.0 python3-blinker 51s python3-lazr.uri 51s 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 51s Need to get 3264 kB of archives. 51s After this operation, 124 kB of additional disk space will be used. 51s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libapt-pkg7.0 s390x 3.1.11 [1150 kB] 51s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x apt s390x 3.1.11 [1462 kB] 51s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x cloud-init-base all 25.4~1gcb12e00e-0ubuntu1 [625 kB] 52s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x cloud-init all 25.4~1gcb12e00e-0ubuntu1 [2114 B] 52s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-blinker all 1.9.0-2 [10.8 kB] 52s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x python3-lazr.uri all 1.0.6-7 [13.8 kB] 52s dpkg-preconfigure: unable to re-open stdin: No such file or directory 52s Fetched 3264 kB in 1s (3447 kB/s) 52s (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 ... 56948 files and directories currently installed.) 52s Preparing to unpack .../0-libapt-pkg7.0_3.1.11_s390x.deb ... 52s Unpacking libapt-pkg7.0:s390x (3.1.11) over (3.1.8ubuntu1) ... 52s Preparing to unpack .../1-apt_3.1.11_s390x.deb ... 52s Unpacking apt (3.1.11) over (3.1.8ubuntu1) ... 52s Preparing to unpack .../2-cloud-init-base_25.4~1gcb12e00e-0ubuntu1_all.deb ... 52s Unpacking cloud-init-base (25.4~1gcb12e00e-0ubuntu1) over (25.3-0ubuntu1) ... 52s Preparing to unpack .../3-cloud-init_25.4~1gcb12e00e-0ubuntu1_all.deb ... 52s Unpacking cloud-init (25.4~1gcb12e00e-0ubuntu1) over (25.3-0ubuntu1) ... 52s Preparing to unpack .../4-python3-blinker_1.9.0-2_all.deb ... 52s Unpacking python3-blinker (1.9.0-2) over (1.9.0-1) ... 52s Preparing to unpack .../5-python3-lazr.uri_1.0.6-7_all.deb ... 53s Unpacking python3-lazr.uri (1.0.6-7) over (1.0.6-6) ... 53s Setting up python3-lazr.uri (1.0.6-7) ... 53s Setting up cloud-init-base (25.4~1gcb12e00e-0ubuntu1) ... 53s Encountered debconf setting for cloud-init-base/datasources. 54s Setting up libapt-pkg7.0:s390x (3.1.11) ... 54s Setting up python3-blinker (1.9.0-2) ... 54s Setting up apt (3.1.11) ... 54s Installing new version of config file /etc/apt/apt.conf.d/01-vendor-ubuntu ... 54s Setting up cloud-init (25.4~1gcb12e00e-0ubuntu1) ... 54s Processing triggers for rsyslog (8.2504.0-1ubuntu2) ... 54s Processing triggers for man-db (2.13.1-1) ... 56s Processing triggers for libc-bin (2.42-0ubuntu3) ... 56s autopkgtest [02:41:41]: upgrading testbed (apt dist-upgrade and autopurge) 57s Reading package lists... 57s Building dependency tree... 57s Reading state information... 57s Calculating upgrade... 57s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 57s Reading package lists... 58s Building dependency tree... 58s Reading state information... 58s Solving dependencies... 58s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 58s autopkgtest [02:41:43]: rebooting testbed after setup commands that affected boot 72s autopkgtest [02:41:57]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP Mon Sep 22 08:56:47 UTC 2025 74s autopkgtest [02:41:59]: @@@@@@@@@@@@@@@@@@@@ apt-source pdb2pqr 78s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (dsc) [1860 B] 78s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (tar) [7570 kB] 78s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (diff) [9876 B] 78s gpgv: Signature made Mon Jun 12 17:36:50 2023 UTC 78s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 78s gpgv: Can't check signature: No public key 78s dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found 79s autopkgtest [02:42:04]: testing package pdb2pqr version 3.6.1+dfsg-1 79s autopkgtest [02:42:04]: build not needed 81s autopkgtest [02:42:06]: test installation-test: preparing testbed 82s Reading package lists... 82s Building dependency tree... 82s Reading state information... 82s Solving dependencies... 82s The following NEW packages will be installed: 82s docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr python3-docutils 82s python3-numpy python3-numpy-dev python3-pdb2pqr python3-pdbx python3-propka 82s python3-roman sgml-base xml-core 82s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 82s Need to get 9154 kB of archives. 82s After this operation, 38.7 MB of additional disk space will be used. 82s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.2.4+ds-1ubuntu1 [147 kB] 82s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-6build1 [245 kB] 82s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-5ubuntu1 [629 kB] 83s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-6build1 [2910 kB] 83s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.2.4+ds-1ubuntu1 [4399 kB] 83s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x sgml-base all 1.31+nmu1 [11.0 kB] 83s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x xml-core all 0.19 [20.3 kB] 83s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x docutils-common all 0.21.2+dfsg-2 [131 kB] 83s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x python3-roman all 5.1-1 [10.6 kB] 83s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x python3-docutils all 0.21.2+dfsg-2 [409 kB] 83s Get:11 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pdbx all 2.0.1-2 [16.5 kB] 83s Get:12 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-propka all 3.5.1-2 [70.1 kB] 83s Get:13 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pdb2pqr all 3.6.1+dfsg-1 [145 kB] 83s Get:14 http://ftpmaster.internal/ubuntu resolute/universe s390x pdb2pqr all 3.6.1+dfsg-1 [10.4 kB] 83s Fetched 9154 kB in 1s (7026 kB/s) 83s Selecting previously unselected package python3-numpy-dev:s390x. 84s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 56950 files and directories currently installed.) 84s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 84s Unpacking python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 84s Selecting previously unselected package libblas3:s390x. 84s Preparing to unpack .../01-libblas3_3.12.1-6build1_s390x.deb ... 84s Unpacking libblas3:s390x (3.12.1-6build1) ... 84s Selecting previously unselected package libgfortran5:s390x. 84s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_s390x.deb ... 84s Unpacking libgfortran5:s390x (15.2.0-5ubuntu1) ... 84s Selecting previously unselected package liblapack3:s390x. 84s Preparing to unpack .../03-liblapack3_3.12.1-6build1_s390x.deb ... 84s Unpacking liblapack3:s390x (3.12.1-6build1) ... 84s Selecting previously unselected package python3-numpy. 84s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 84s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 84s Selecting previously unselected package sgml-base. 84s Preparing to unpack .../05-sgml-base_1.31+nmu1_all.deb ... 84s Unpacking sgml-base (1.31+nmu1) ... 84s Selecting previously unselected package xml-core. 84s Preparing to unpack .../06-xml-core_0.19_all.deb ... 84s Unpacking xml-core (0.19) ... 84s Selecting previously unselected package docutils-common. 84s Preparing to unpack .../07-docutils-common_0.21.2+dfsg-2_all.deb ... 84s Unpacking docutils-common (0.21.2+dfsg-2) ... 84s Selecting previously unselected package python3-roman. 84s Preparing to unpack .../08-python3-roman_5.1-1_all.deb ... 84s Unpacking python3-roman (5.1-1) ... 84s Selecting previously unselected package python3-docutils. 84s Preparing to unpack .../09-python3-docutils_0.21.2+dfsg-2_all.deb ... 84s Unpacking python3-docutils (0.21.2+dfsg-2) ... 84s Selecting previously unselected package python3-pdbx. 84s Preparing to unpack .../10-python3-pdbx_2.0.1-2_all.deb ... 84s Unpacking python3-pdbx (2.0.1-2) ... 84s Selecting previously unselected package python3-propka. 84s Preparing to unpack .../11-python3-propka_3.5.1-2_all.deb ... 84s Unpacking python3-propka (3.5.1-2) ... 84s Selecting previously unselected package python3-pdb2pqr. 84s Preparing to unpack .../12-python3-pdb2pqr_3.6.1+dfsg-1_all.deb ... 84s Unpacking python3-pdb2pqr (3.6.1+dfsg-1) ... 84s Selecting previously unselected package pdb2pqr. 84s Preparing to unpack .../13-pdb2pqr_3.6.1+dfsg-1_all.deb ... 84s Unpacking pdb2pqr (3.6.1+dfsg-1) ... 84s Setting up python3-propka (3.5.1-2) ... 84s Setting up python3-pdbx (2.0.1-2) ... 84s Setting up python3-roman (5.1-1) ... 84s Setting up libblas3:s390x (3.12.1-6build1) ... 84s 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 84s Setting up python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 84s Setting up libgfortran5:s390x (15.2.0-5ubuntu1) ... 84s Setting up sgml-base (1.31+nmu1) ... 84s Setting up liblapack3:s390x (3.12.1-6build1) ... 84s 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 84s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 86s Setting up xml-core (0.19) ... 86s Processing triggers for libc-bin (2.42-0ubuntu3) ... 86s Processing triggers for man-db (2.13.1-1) ... 87s Processing triggers for sgml-base (1.31+nmu1) ... 87s Setting up docutils-common (0.21.2+dfsg-2) ... 87s Processing triggers for sgml-base (1.31+nmu1) ... 87s Setting up python3-docutils (0.21.2+dfsg-2) ... 87s Setting up python3-pdb2pqr (3.6.1+dfsg-1) ... 87s Setting up pdb2pqr (3.6.1+dfsg-1) ... 88s autopkgtest [02:42:13]: test installation-test: [----------------------- 88s Run pdb2pqr... 89s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 89s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 89s 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). 89s INFO:Checking and transforming input arguments. 89s INFO:Loading topology files. 89s INFO:Loading molecule: examples/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 [02:42:14]: test installation-test: -----------------------] 89s autopkgtest [02:42:14]: test installation-test: - - - - - - - - - - results - - - - - - - - - - 89s installation-test PASS 90s autopkgtest [02:42:15]: test pdb2pka-test: 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 fonts-font-awesome fonts-lato libjs-jquery libjs-sphinxdoc libjs-underscore 90s pdb2pqr-doc sphinx-rtd-theme-common 90s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 90s Need to get 5035 kB of archives. 90s After this operation, 20.0 MB of additional disk space will be used. 90s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-lato all 2.015-1 [2781 kB] 91s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 91s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 91s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 91s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 91s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 91s Get:7 http://ftpmaster.internal/ubuntu resolute/universe s390x pdb2pqr-doc all 3.6.1+dfsg-1 [258 kB] 92s Fetched 5035 kB in 1s (4112 kB/s) 92s Selecting previously unselected package fonts-lato. 92s (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 ... 58451 files and directories currently installed.) 92s Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... 92s Unpacking fonts-lato (2.015-1) ... 92s Selecting previously unselected package fonts-font-awesome. 92s Preparing to unpack .../1-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 92s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 92s Selecting previously unselected package libjs-jquery. 92s Preparing to unpack .../2-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 92s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 92s Selecting previously unselected package libjs-underscore. 92s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 92s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 92s Selecting previously unselected package libjs-sphinxdoc. 92s Preparing to unpack .../4-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 92s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 92s Selecting previously unselected package sphinx-rtd-theme-common. 92s Preparing to unpack .../5-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 92s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 92s Selecting previously unselected package pdb2pqr-doc. 92s Preparing to unpack .../6-pdb2pqr-doc_3.6.1+dfsg-1_all.deb ... 92s Unpacking pdb2pqr-doc (3.6.1+dfsg-1) ... 92s Setting up fonts-lato (2.015-1) ... 92s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 92s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 92s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 92s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 92s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 92s Setting up pdb2pqr-doc (3.6.1+dfsg-1) ... 93s autopkgtest [02:42:18]: test pdb2pka-test: [----------------------- 93s Run pdb2pqr... 94s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 94s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 94s 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). 94s INFO:Checking and transforming input arguments. 94s INFO:Loading topology files. 94s INFO:Loading molecule: 1a1p/1a1p.pdb 94s INFO:Setting up molecule. 94s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 94s INFO:Created biomolecule object with 14 residues and 208 atoms. 94s INFO:Setting termini states for biomolecule chains. 94s INFO:Loading forcefield. 94s INFO:Loading hydrogen topology definitions. 94s INFO:This biomolecule is clean. No repair needed. 94s INFO:Updating disulfide bridges. 94s INFO:Debumping biomolecule. 94s INFO:Adding hydrogens to biomolecule. 94s INFO:Debumping biomolecule (again). 94s INFO:Optimizing hydrogen bonds 94s INFO:Applying force field to biomolecule states. 94s INFO:Regenerating headers. 94s INFO:Regenerating PDB lines. 94s WARNING:Ignoring 852 header lines in output. 94s WARNING:Ignoring 3 missing lines in output. 94s autopkgtest [02:42:19]: test pdb2pka-test: -----------------------] 94s autopkgtest [02:42:19]: test pdb2pka-test: - - - - - - - - - - results - - - - - - - - - - 94s pdb2pka-test PASS 95s autopkgtest [02:42:20]: test command1: preparing testbed 95s Reading package lists... 95s Building dependency tree... 95s Reading state information... 95s Solving dependencies... 95s The following NEW packages will be installed: 95s python3-dateutil python3-iniconfig python3-packaging python3-pandas 95s python3-pandas-lib python3-pluggy python3-pytest python3-pytz 95s python3-testfixtures 96s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 96s Need to get 12.1 MB of archives. 96s After this operation, 68.4 MB of additional disk space will be used. 96s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-dateutil all 2.9.0-4 [80.3 kB] 96s Get:2 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 96s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x python3-packaging all 25.0-1 [52.8 kB] 96s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x python3-pytz all 2025.2-4 [32.3 kB] 96s Get:5 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas-lib s390x 2.3.3+dfsg-1ubuntu1 [8668 kB] 98s Get:6 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 99s Get:7 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pluggy all 1.6.0-1 [21.0 kB] 99s Get:8 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytest all 8.3.5-2 [252 kB] 99s Get:9 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-testfixtures all 9.2.0-1 [79.2 kB] 99s Fetched 12.1 MB in 3s (3563 kB/s) 99s Selecting previously unselected package python3-dateutil. 99s (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 ... 58786 files and directories currently installed.) 99s Preparing to unpack .../0-python3-dateutil_2.9.0-4_all.deb ... 99s Unpacking python3-dateutil (2.9.0-4) ... 99s Selecting previously unselected package python3-iniconfig. 99s Preparing to unpack .../1-python3-iniconfig_1.1.1-2_all.deb ... 99s Unpacking python3-iniconfig (1.1.1-2) ... 99s Selecting previously unselected package python3-packaging. 99s Preparing to unpack .../2-python3-packaging_25.0-1_all.deb ... 99s Unpacking python3-packaging (25.0-1) ... 99s Selecting previously unselected package python3-pytz. 99s Preparing to unpack .../3-python3-pytz_2025.2-4_all.deb ... 99s Unpacking python3-pytz (2025.2-4) ... 99s Selecting previously unselected package python3-pandas-lib:s390x. 99s Preparing to unpack .../4-python3-pandas-lib_2.3.3+dfsg-1ubuntu1_s390x.deb ... 99s Unpacking python3-pandas-lib:s390x (2.3.3+dfsg-1ubuntu1) ... 100s Selecting previously unselected package python3-pandas. 100s Preparing to unpack .../5-python3-pandas_2.3.3+dfsg-1ubuntu1_all.deb ... 100s Unpacking python3-pandas (2.3.3+dfsg-1ubuntu1) ... 100s Selecting previously unselected package python3-pluggy. 100s Preparing to unpack .../6-python3-pluggy_1.6.0-1_all.deb ... 100s Unpacking python3-pluggy (1.6.0-1) ... 100s Selecting previously unselected package python3-pytest. 100s Preparing to unpack .../7-python3-pytest_8.3.5-2_all.deb ... 100s Unpacking python3-pytest (8.3.5-2) ... 100s Selecting previously unselected package python3-testfixtures. 100s Preparing to unpack .../8-python3-testfixtures_9.2.0-1_all.deb ... 100s Unpacking python3-testfixtures (9.2.0-1) ... 100s Setting up python3-iniconfig (1.1.1-2) ... 100s Setting up python3-pandas-lib:s390x (2.3.3+dfsg-1ubuntu1) ... 100s Setting up python3-testfixtures (9.2.0-1) ... 100s Setting up python3-pytz (2025.2-4) ... 100s Setting up python3-packaging (25.0-1) ... 100s Setting up python3-pluggy (1.6.0-1) ... 100s Setting up python3-dateutil (2.9.0-4) ... 100s Setting up python3-pytest (8.3.5-2) ... 100s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 105s Processing triggers for man-db (2.13.1-1) ... 106s autopkgtest [02:42:31]: test command1: pytest-3 106s autopkgtest [02:42:31]: test command1: [----------------------- 107s ============================= test session starts ============================== 107s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 107s rootdir: /tmp/autopkgtest.4i8sqd/build.qh2/src 107s configfile: pytest.ini 107s plugins: typeguard-4.4.2 107s 107s ----------------------------- live log collection ------------------------------ 107s WARNING py.warnings:warnings.py:110 /tmp/autopkgtest.4i8sqd/build.qh2/src/tests/core_test.py:81: PytestUnknownMarkWarning: Unknown pytest.mark.long_test - is this a typo? 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[ 54%] 107s tests/core_test.py::test_long_pdb[4GMQ] SKIPPED (not running tests r...) [ 55%] 107s tests/core_test.py::test_long_pdb[2ESK] SKIPPED (not running tests r...) [ 55%] 107s tests/core_test.py::test_long_pdb[3KZD] SKIPPED (not running tests r...) [ 55%] 107s tests/core_test.py::test_long_pdb[2PTV] SKIPPED (not running tests r...) [ 56%] 107s tests/core_test.py::test_long_pdb[3V1A] SKIPPED (not running tests r...) [ 56%] 107s tests/core_test.py::test_long_pdb[3LS0] SKIPPED (not running tests r...) [ 56%] 107s tests/core_test.py::test_long_pdb[2YGS] SKIPPED (not running tests r...) [ 56%] 107s tests/core_test.py::test_long_pdb[2X4J] SKIPPED (not running tests r...) [ 57%] 107s tests/core_test.py::test_long_pdb[2FD4] SKIPPED (not running tests r...) [ 57%] 107s tests/core_test.py::test_long_pdb[3RJS] SKIPPED (not running tests r...) [ 57%] 107s tests/core_test.py::test_long_pdb[3S0A] SKIPPED (not running tests r...) [ 58%] 107s tests/core_test.py::test_long_pdb[4NPN] SKIPPED (not running tests r...) [ 58%] 107s tests/core_test.py::test_long_pdb[3I1G] SKIPPED (not running tests r...) [ 58%] 107s tests/core_test.py::test_long_pdb[3QE1] SKIPPED (not running tests r...) [ 59%] 107s tests/core_test.py::test_long_pdb[2JIC] SKIPPED (not running tests r...) [ 59%] 107s tests/core_test.py::test_long_pdb[4EO0] SKIPPED (not running tests r...) [ 59%] 107s tests/core_test.py::test_long_pdb[1RJ1] SKIPPED (not running tests r...) [ 60%] 107s tests/core_test.py::test_long_pdb[1NOA] SKIPPED (not running tests r...) [ 60%] 107s tests/core_test.py::test_long_pdb[2JCP] SKIPPED (not running tests r...) [ 60%] 107s tests/core_test.py::test_long_pdb[2CJJ] SKIPPED (not running tests r...) [ 61%] 107s tests/core_test.py::test_long_pdb[2ZQE] SKIPPED (not running tests r...) [ 61%] 107s tests/core_test.py::test_long_pdb[3HRN] SKIPPED (not running tests r...) [ 61%] 107s tests/core_test.py::test_long_pdb[1XAK] SKIPPED (not running tests r...) [ 62%] 107s tests/core_test.py::test_long_pdb[3LLB] SKIPPED (not running tests r...) [ 62%] 107s tests/core_test.py::test_long_pdb[1IS5] SKIPPED (not running tests r...) [ 62%] 107s tests/core_test.py::test_long_pdb[1OPS] SKIPPED (not running tests r...) [ 62%] 107s tests/core_test.py::test_long_pdb[4O7Q] SKIPPED (not running tests r...) [ 63%] 107s tests/core_test.py::test_long_pdb[1J2A] SKIPPED (not running tests r...) [ 63%] 107s tests/core_test.py::test_long_pdb[1PGX] SKIPPED (not running tests r...) [ 63%] 107s tests/core_test.py::test_long_pdb[3US6] SKIPPED (not running tests r...) [ 64%] 107s tests/core_test.py::test_long_pdb[1X3O] SKIPPED (not running tests r...) [ 64%] 107s tests/core_test.py::test_long_pdb[1X91] SKIPPED (not running tests r...) [ 64%] 107s tests/core_test.py::test_long_pdb[2SGA] SKIPPED (not running tests r...) [ 65%] 107s tests/core_test.py::test_long_pdb[3FH2] SKIPPED (not running tests r...) [ 65%] 107s tests/core_test.py::test_long_pdb[3LMO] SKIPPED (not running tests r...) [ 65%] 107s tests/core_test.py::test_long_pdb[1PZC] SKIPPED (not running tests r...) [ 66%] 107s tests/core_test.py::test_broken_backbone[3U7T] 107s -------------------------------- live log call --------------------------------- 107s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_3U7T_0/3U7T.log 107s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 107s 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). 107s 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). 107s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 107s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 107s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T 108s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 108s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 108s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 652 atoms. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in PRO A 22. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in PRO A 22. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in PRO A 22. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in PRO A 22. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 22. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in PRO A 22. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in PRO A 22. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 22. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 22. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in PRO A 22. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 22. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in PRO A 22. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 22. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 22. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 22. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 22. 108s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 22. At least one of the instances is being ignored. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in LEU A 25. 108s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in LEU A 25. At least one of the instances is being ignored. 108s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 108s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 108s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 108s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 108s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 108s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 108s 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 108s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 108s XFAIL [ 66%] 108s tests/core_test.py::test_broken_backbone[4MGP] 108s -------------------------------- live log call --------------------------------- 108s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_4MGP_0/4MGP.log 108s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 108s 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). 108s 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). 108s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 108s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 108s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP 110s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 110s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 110s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 23 residues and 163 atoms. 110s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in MET A 21. 110s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in MET A 21. 110s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in MET A 21. 110s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: SD in MET A 21. 110s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE in MET A 21. 110s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in MET A 21. At least one of the instances is being ignored. 110s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 110s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 110s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 110s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 12 missing atoms in biomolecule. 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 110s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 110s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 11 at coordinates 1.430, -1.683, -11.529 110s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 11 at coordinates 1.940, -0.315, -11.800 110s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CG to residue LYS A 14 at coordinates -1.600, -8.819, -6.913 110s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CD to residue LYS A 14 at coordinates -2.056, -8.844, -8.361 110s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 14 at coordinates -3.548, -9.031, -8.498 110s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 14 at coordinates -3.947, -9.048, -9.928 110s 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 110s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 110s XFAIL [ 66%] 110s tests/core_test.py::test_broken_backbone[2V75] 110s -------------------------------- live log call --------------------------------- 110s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_2V75_0/2V75.log 110s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 110s 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). 110s 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). 110s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 110s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 110s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 111s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 111s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 111s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 90 residues and 687 atoms. 111s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 111s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 111s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 111s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 8 missing atoms in biomolecule. 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 111s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 111s 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 111s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 111s XFAIL [ 67%] 111s tests/core_test.py::test_broken_backbone[1EJG] 111s -------------------------------- live log call --------------------------------- 111s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_1EJG_0/1EJG.log 111s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 111s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 111s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 111s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 111s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 111s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG 112s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 112s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 112s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 650 atoms. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in THR A 1. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 1. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 1. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 1. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 1. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H1 in THR A 1. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H2 in THR A 1. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H3 in THR A 1. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 1. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 1. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 1. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 1. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 1. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 1. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 1. At least one of the instances is being ignored. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 2. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 2. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 2. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 2. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 2. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 2. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 2. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 2. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 2. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 2. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 2. At least one of the instances is being ignored. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 7. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 7. At least one of the instances is being ignored. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in VAL A 8. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in VAL A 8. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in VAL A 8. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in VAL A 8. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in VAL A 8. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in VAL A 8. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in VAL A 8. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in VAL A 8. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG11 in VAL A 8. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in VAL A 8. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in VAL A 8. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in VAL A 8. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in VAL A 8. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in VAL A 8. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in VAL A 8. At least one of the instances is being ignored. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NE in ARG A 10. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in ARG A 10. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH1 in ARG A 10. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH2 in ARG A 10. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE in ARG A 10. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH11 in ARG A 10. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH12 in ARG A 10. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH21 in ARG A 10. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH22 in ARG A 10. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ARG A 10. At least one of the instances is being ignored. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ASN A 12. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASN A 12. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 12. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 12. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 12. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ASN A 12. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASN A 12. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASN A 12. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 12. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 12. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 12. At least one of the instances is being ignored. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PHE A 13. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in PHE A 13. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in PHE A 13. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in PHE A 13. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in PHE A 13. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in PHE A 13. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in PHE A 13. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PHE A 13. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in PHE A 13. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in PHE A 13. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HZ in PHE A 13. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PHE A 13. At least one of the instances is being ignored. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 19. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 19. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 19. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 19. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 19. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 19. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 19. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 19. At least one of the instances is being ignored. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in SER A 22. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in SER A 22. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in SER A 22. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in SER A 22. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in SER A 22. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in SER A 22. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in SER A 22. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in SER A 22. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in SER A 22. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in SER A 22. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in SER A 22. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in SER A 22. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in SER A 22. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in SER A 22. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in SER A 22. At least one of the instances is being ignored. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in GLU A 23. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in GLU A 23. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE1 in GLU A 23. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE2 in GLU A 23. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in GLU A 23. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in GLU A 23. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in GLU A 23. At least one of the instances is being ignored. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 25. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 25. At least one of the instances is being ignored. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in TYR A 29. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in TYR A 29. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in TYR A 29. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in TYR A 29. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in TYR A 29. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in TYR A 29. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OH in TYR A 29. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in TYR A 29. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in TYR A 29. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in TYR A 29. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in TYR A 29. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH in TYR A 29. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in TYR A 29. At least one of the instances is being ignored. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 34. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 34. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 34. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 34. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 34. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 34. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 34. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 34. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 34. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 34. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 34. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 34. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 34. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 34. At least one of the instances is being ignored. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 36. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 36. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 36. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 36. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 36. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 36. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 36. At least one of the instances is being ignored. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 39. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 39. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 39. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 39. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 39. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 39. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 39. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 39. At least one of the instances is being ignored. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASP A 43. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASP A 43. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASP A 43. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD2 in ASP A 43. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASP A 43. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASP A 43. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASP A 43. At least one of the instances is being ignored. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 46. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 46. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 46. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 46. 112s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 46. 112s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 46. At least one of the instances is being ignored. 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 INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 112s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 112s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 112s 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 112s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 112s XFAIL [ 67%] 112s tests/core_test.py::test_protonated_terminals[C-terminal HID] 112s -------------------------------- live log call --------------------------------- 112s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_protonated_terminals_C_te0/cterm_hid.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/cterm_hid.pdb 112s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 112s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 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 HIS B 209 112s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 112s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule. 112s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 112s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402 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). 112s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 112s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 112s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 112s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 112s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 112s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 112s INFO common:common.py:198 0 atoms have position differences > 0 112s INFO common:common.py:198 0 atoms have position differences > 0.01 112s INFO common:common.py:198 0 atoms have charge differences > 0 112s INFO common:common.py:198 0 atoms have charge differences > 0.01 112s INFO common:common.py:198 0 atoms have radius differences > 0 112s INFO common:common.py:198 0 atoms have radius differences > 0.01 112s PASSED [ 67%] 112s tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 112s -------------------------------- live log call --------------------------------- 112s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.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/5vav_cyclic_peptide.pdb 112s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 112s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 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 INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 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). 112s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 112s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 112s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 112s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 112s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 112s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 112s INFO common:common.py:198 0 atoms have position differences > 0 112s INFO common:common.py:198 0 atoms have position differences > 0.01 112s INFO common:common.py:198 0 atoms have charge differences > 0 112s INFO common:common.py:198 0 atoms have charge differences > 0.01 112s INFO common:common.py:198 0 atoms have radius differences > 0 112s INFO common:common.py:198 0 atoms have radius differences > 0.01 112s PASSED [ 68%] 112s tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 68%] 112s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 68%] 112s tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 68%] 112s tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 69%] 112s tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 69%] 112s tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 69%] 112s tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 70%] 112s tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 70%] 112s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 70%] 112s tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 71%] 112s tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 71%] 112s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 71%] 112s tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 72%] 112s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 72%] 112s tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 72%] 112s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 73%] 112s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 73%] 112s tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 73%] 112s 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%] 112s tests/io_test.py::test_read_qcd PASSED [ 74%] 112s tests/io_test.py::test_dx2cube 112s -------------------------------- live log call --------------------------------- 112s INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... 113s INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... 113s INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 114s INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 114s INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... 114s INFO io_test:io_test.py:68 No differences found in output 115s PASSED [ 74%] 115s tests/ligand_test.py::test_peoe_charges 115s -------------------------------- live log call --------------------------------- 115s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 115s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 115s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 115s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 115s PASSED [ 75%] 116s tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 116s -------------------------------- live log call --------------------------------- 116s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 116s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 116s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 116s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 116s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 116s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 116s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 116s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 116s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 116s PASSED [ 75%] 116s tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 116s -------------------------------- live log call --------------------------------- 116s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 116s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 116s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 116s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 116s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 116s PASSED [ 75%] 116s tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 116s -------------------------------- live log call --------------------------------- 116s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 116s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 116s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 116s PASSED [ 75%] 116s tests/ligand_test.py::test_assign_parameters[acetate.mol2] 116s -------------------------------- live log call --------------------------------- 116s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 116s PASSED [ 76%] 116s tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 116s -------------------------------- live log call --------------------------------- 116s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 116s PASSED [ 76%] 116s tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 116s -------------------------------- live log call --------------------------------- 116s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 116s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 116s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 116s PASSED [ 76%] 117s tests/ligand_test.py::test_assign_parameters[adp.mol2] 117s -------------------------------- live log call --------------------------------- 117s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 117s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 117s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 117s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 117s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 117s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 117s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 117s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 117s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 117s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 117s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 117s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 117s INFO ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00 117s PASSED [ 77%] 117s tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 117s -------------------------------- live log call --------------------------------- 117s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 117s PASSED [ 77%] 117s tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 117s -------------------------------- live log call --------------------------------- 117s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 117s PASSED [ 77%] 117s tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 117s -------------------------------- live log call --------------------------------- 117s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 117s PASSED [ 78%] 117s tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 117s -------------------------------- live log call --------------------------------- 117s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 117s PASSED [ 78%] 117s tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 117s -------------------------------- live log call --------------------------------- 117s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 117s PASSED [ 78%] 117s tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 117s -------------------------------- live log call --------------------------------- 117s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 117s PASSED [ 79%] 117s tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 117s -------------------------------- live log call --------------------------------- 117s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 117s PASSED [ 79%] 117s tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 117s -------------------------------- live log call --------------------------------- 117s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 117s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 117s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 117s PASSED [ 79%] 117s tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 117s -------------------------------- live log call --------------------------------- 117s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 117s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 117s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 117s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 117s PASSED [ 80%] 118s tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 118s -------------------------------- live log call --------------------------------- 118s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 118s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 118s PASSED [ 80%] 118s tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 118s -------------------------------- live log call --------------------------------- 118s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 118s PASSED [ 80%] 118s tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED [ 81%] 118s tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED [ 81%] 118s tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 118s -------------------------------- live log call --------------------------------- 118s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 118s PASSED [ 81%] 118s tests/ligand_test.py::test_formal_charge[adp.mol2] 118s -------------------------------- live log call --------------------------------- 118s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 118s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 118s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 118s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 118s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 118s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 118s PASSED [ 81%] 118s tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED [ 82%] 118s tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED [ 82%] 118s tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED [ 82%] 118s tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED [ 83%] 118s tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED [ 83%] 118s tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED [ 83%] 118s tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED [ 84%] 118s tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 118s -------------------------------- live log call --------------------------------- 118s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 118s PASSED [ 84%] 118s tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED [ 84%] 118s tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED [ 85%] 118s tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED [ 85%] 118s tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED [ 85%] 118s tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED [ 86%] 118s tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED [ 86%] 118s tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED [ 86%] 119s tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED [ 87%] 119s tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED [ 87%] 119s tests/ligand_test.py::test_rings[acetate.mol2] PASSED [ 87%] 119s tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED [ 87%] 119s tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED [ 88%] 119s tests/ligand_test.py::test_rings[adp.mol2] PASSED [ 88%] 119s tests/ligand_test.py::test_rings[anthracene.mol2] PASSED [ 88%] 119s tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED [ 89%] 119s tests/ligand_test.py::test_rings[ethanol.mol2] PASSED [ 89%] 119s tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED [ 89%] 119s tests/ligand_test.py::test_rings[glycerol.mol2] PASSED [ 90%] 119s tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED [ 90%] 119s tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED [ 90%] 119s tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED [ 91%] 119s tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%] 119s tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%] 119s tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%] 119s tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%] 119s tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%] 119s tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%] 119s tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%] 119s tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%] 119s tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%] 119s tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%] 119s tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%] 119s tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] 119s tests/regression_test.py::test_basic[1AFS basic local] 119s -------------------------------- live log call --------------------------------- 119s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_basic_1AFS_basic_local_0/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.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 119s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 119s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 119s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 120s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 120s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 120s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 120s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 120s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 120s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 120s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 120s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 120s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 120s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 120s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 120s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 120s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 121s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 121s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 121s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 121s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 121s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 121s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 121s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 121s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 121s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 121s WARNING pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages 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. 123s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 123s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 123s WARNING common:common.py:186 6 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 AMBER] 123s -------------------------------- live log call --------------------------------- 123s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa0/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 WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 123s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 123s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 123s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 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. 123s 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. 126s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 126s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 126s WARNING common:common.py:186 6 atoms have position differences > 0 126s INFO common:common.py:198 0 atoms have position differences > 0.01 126s INFO common:common.py:198 0 atoms have charge differences > 0 126s INFO common:common.py:198 0 atoms have charge differences > 0.01 126s INFO common:common.py:198 0 atoms have radius differences > 0 126s INFO common:common.py:198 0 atoms have radius differences > 0.01 126s PASSED [ 95%] 126s tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] 126s -------------------------------- live log call --------------------------------- 126s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa1/output.log 126s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 126s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 126s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 126s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 126s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 126s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 126s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 126s WARNING pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages 126s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 126s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 126s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 126s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 126s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 126s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 126s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 126s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 126s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 126s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 126s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 126s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 126s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 126s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 126s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 127s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 127s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 128s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 131s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 131s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 131s 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 5 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 [ 95%] 131s tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] 131s -------------------------------- live log call --------------------------------- 131s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa2/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. 132s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 133s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 135s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 135s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 135s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 135s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 135s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 136s WARNING common:common.py:186 6 atoms have position differences > 0 136s INFO common:common.py:198 0 atoms have position differences > 0.01 136s INFO common:common.py:198 0 atoms have charge differences > 0 136s INFO common:common.py:198 0 atoms have charge differences > 0.01 136s INFO common:common.py:198 0 atoms have radius differences > 0 136s INFO common:common.py:198 0 atoms have radius differences > 0.01 136s PASSED [ 96%] 136s tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] 136s -------------------------------- live log call --------------------------------- 136s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa3/output.log 136s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 136s 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). 136s 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). 136s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 136s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 136s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 136s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 136s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 136s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 136s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 136s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 136s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 136s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 136s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 136s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 136s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 136s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 136s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 136s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 136s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 136s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 136s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 136s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 137s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 137s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 139s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 139s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 139s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 140s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 140s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 140s WARNING common:common.py:186 6 atoms have position differences > 0 140s INFO common:common.py:198 0 atoms have position differences > 0.01 140s INFO common:common.py:198 0 atoms have charge differences > 0 140s INFO common:common.py:198 0 atoms have charge differences > 0.01 140s INFO common:common.py:198 0 atoms have radius differences > 0 140s INFO common:common.py:198 0 atoms have radius differences > 0.01 140s PASSED [ 96%] 140s tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] 140s -------------------------------- live log call --------------------------------- 140s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa4/output.log 140s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 140s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 140s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 140s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 140s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 140s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 140s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 140s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 140s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 140s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 140s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 140s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 140s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 140s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 140s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 140s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 140s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 140s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 140s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 140s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 140s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 140s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 140s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 141s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 141s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 144s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 144s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 144s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 144s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output. 144s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 144s WARNING common:common.py:186 6 atoms have position differences > 0 144s INFO common:common.py:198 0 atoms have position differences > 0.01 144s INFO common:common.py:198 0 atoms have charge differences > 0 144s INFO common:common.py:198 0 atoms have charge differences > 0.01 144s INFO common:common.py:198 0 atoms have radius differences > 0 144s INFO common:common.py:198 0 atoms have radius differences > 0.01 144s PASSED [ 96%] 144s tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] 144s -------------------------------- live log call --------------------------------- 144s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa5/output.log 144s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 144s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 144s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 144s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 144s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 144s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 144s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 144s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 144s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 144s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 144s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 144s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 144s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 144s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 144s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 144s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 144s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 144s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 144s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 144s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 144s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 144s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 145s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 145s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 146s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 149s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 149s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 149s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 149s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 149s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 149s WARNING common:common.py:186 6 atoms have position differences > 0 149s INFO common:common.py:198 0 atoms have position differences > 0.01 149s INFO common:common.py:198 0 atoms have charge differences > 0 149s INFO common:common.py:198 0 atoms have charge differences > 0.01 149s INFO common:common.py:198 0 atoms have radius differences > 0 149s INFO common:common.py:198 0 atoms have radius differences > 0.01 149s PASSED [ 97%] 149s tests/regression_test.py::test_other_options[1AFS whitespace clean] 149s -------------------------------- live log call --------------------------------- 149s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_whites0/output.log 149s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 149s 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). 149s 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). 149s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 149s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 149s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 149s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 149s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 149s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 149s INFO PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps. 149s INFO common:common.py:198 0 atoms have position differences > 0 149s INFO common:common.py:198 0 atoms have position differences > 0.01 149s INFO common:common.py:198 0 atoms have charge differences > 0 149s INFO common:common.py:198 0 atoms have charge differences > 0.01 149s INFO common:common.py:198 0 atoms have radius differences > 0 149s INFO common:common.py:198 0 atoms have radius differences > 0.01 149s PASSED [ 97%] 149s tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] 149s -------------------------------- live log call --------------------------------- 149s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_assign0/output.log 149s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 149s 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). 149s 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). 149s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 149s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 149s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 149s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 149s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 149s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 149s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 149s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 149s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 149s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 149s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 149s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 149s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 149s INFO common:common.py:198 0 atoms have position differences > 0 149s INFO common:common.py:198 0 atoms have position differences > 0.01 149s INFO common:common.py:198 0 atoms have charge differences > 0 149s INFO common:common.py:198 0 atoms have charge differences > 0.01 149s INFO common:common.py:198 0 atoms have radius differences > 0 149s INFO common:common.py:198 0 atoms have radius differences > 0.01 149s PASSED [ 97%] 149s tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] 149s -------------------------------- live log call --------------------------------- 149s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_nodebu0/output.log 149s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 149s 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). 149s 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). 149s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 149s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 149s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 149s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 149s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 149s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 149s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 149s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 149s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 149s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 149s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 149s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 149s INFO pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization... 149s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 149s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 149s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 149s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 149s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 149s INFO common:common.py:198 0 atoms have position differences > 0 149s INFO common:common.py:198 0 atoms have position differences > 0.01 149s INFO common:common.py:198 0 atoms have charge differences > 0 149s INFO common:common.py:198 0 atoms have charge differences > 0.01 149s INFO common:common.py:198 0 atoms have radius differences > 0 149s INFO common:common.py:198 0 atoms have radius differences > 0.01 149s PASSED [ 98%] 149s tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] 149s -------------------------------- live log call --------------------------------- 149s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_chain_0/output.log 149s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 149s 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). 149s 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). 149s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 149s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 149s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 149s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 149s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 149s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 149s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 149s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 149s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 149s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 149s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 149s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 149s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 149s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 149s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 149s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 149s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 149s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 149s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 150s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 150s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 151s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 153s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 153s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 153s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 153s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 153s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 153s WARNING common:common.py:186 6 atoms have position differences > 0 153s INFO common:common.py:198 0 atoms have position differences > 0.01 153s INFO common:common.py:198 0 atoms have charge differences > 0 153s INFO common:common.py:198 0 atoms have charge differences > 0.01 153s INFO common:common.py:198 0 atoms have radius differences > 0 153s INFO common:common.py:198 0 atoms have radius differences > 0.01 153s PASSED [ 98%] 153s tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] 153s -------------------------------- live log call --------------------------------- 153s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_neutra0/output.log 153s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 153s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 153s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 153s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 153s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 153s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 153s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 153s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 153s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 153s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 153s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 153s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 153s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 153s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 153s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 153s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 153s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 153s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 154s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 154s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 154s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 154s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 154s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 154s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 155s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 157s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 157s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 157s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 157s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 157s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 158s WARNING common:common.py:186 6 atoms have position differences > 0 158s INFO common:common.py:198 0 atoms have position differences > 0.01 158s INFO common:common.py:198 0 atoms have charge differences > 0 158s INFO common:common.py:198 0 atoms have charge differences > 0.01 158s INFO common:common.py:198 0 atoms have radius differences > 0 158s INFO common:common.py:198 0 atoms have radius differences > 0.01 158s PASSED [ 98%] 158s tests/regression_test.py::test_other_options[1AFS drop-water AMBER] 158s -------------------------------- live log call --------------------------------- 158s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_drop_w0/output.log 158s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 158s 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). 158s 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). 158s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 158s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 158s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 158s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 158s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 158s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms. 158s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 158s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 158s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 158s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 158s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 158s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 158s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 158s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 158s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 158s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 158s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 158s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 158s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 158s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 158s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 158s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 159s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 160s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 160s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 160s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 161s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 161s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 161s WARNING common:common.py:186 6 atoms have position differences > 0 161s INFO common:common.py:198 0 atoms have position differences > 0.01 161s INFO common:common.py:198 0 atoms have charge differences > 0 161s INFO common:common.py:198 0 atoms have charge differences > 0.01 161s INFO common:common.py:198 0 atoms have radius differences > 0 161s INFO common:common.py:198 0 atoms have radius differences > 0.01 161s PASSED [ 99%] 161s tests/regression_test.py::test_other_options[1AFS userff usernames whitespace] 161s -------------------------------- live log call --------------------------------- 161s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_userff0/output.log 161s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 161s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 161s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 161s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 161s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 161s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 161s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 161s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 161s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 161s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 161s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 161s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 161s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 161s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 161s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 161s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 161s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 161s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 161s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 161s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 161s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 161s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 161s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 161s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 162s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 165s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 165s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 165s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 165s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 165s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 165s WARNING common:common.py:186 6 atoms have position differences > 0 165s INFO common:common.py:198 0 atoms have position differences > 0.01 165s INFO common:common.py:198 0 atoms have charge differences > 0 165s INFO common:common.py:198 0 atoms have charge differences > 0.01 165s INFO common:common.py:198 0 atoms have radius differences > 0 165s INFO common:common.py:198 0 atoms have radius differences > 0.01 165s PASSED [ 99%] 165s tests/test_version.py::test_version_exists PASSED [ 99%] 165s tests/test_version.py::test_version PASSED [100%] 165s 165s ================= 92 passed, 220 skipped, 4 xfailed in 58.06s ================== 165s autopkgtest [02:43:30]: test command1: -----------------------] 166s command1 PASS 166s autopkgtest [02:43:31]: test command1: - - - - - - - - - - results - - - - - - - - - - 166s autopkgtest [02:43:31]: @@@@@@@@@@@@@@@@@@@@ summary 166s installation-test PASS 166s pdb2pka-test PASS 166s command1 PASS