0s autopkgtest [06:02:11]: starting date and time: 2025-10-24 06:02:11+0000 0s autopkgtest [06:02:11]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [06:02:11]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9xnq7q6q/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:python-pluggy --apt-upgrade pdb2pqr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.4.2-1 python-pluggy/1.6.0-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-amd64 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-6.secgroup --name adt-resolute-amd64-pdb2pqr-20251024-060211-juju-7f2275-prod-proposed-migration-environment-15-9cf33925-0473-4088-a033-8077da406b4b --image adt/ubuntu-resolute-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-amd64 -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-amd64-pdb2pqr-20251024-060211-juju-7f2275-prod-proposed-migration-environment-15-9cf33925-0473-4088-a033-8077da406b4b from image adt/ubuntu-resolute-amd64-server-20251024.img (UUID 310022dd-8dd9-48c7-a816-c2d8419ef402)... 33s autopkgtest [06:02:44]: testbed dpkg architecture: amd64 33s autopkgtest [06:02:44]: testbed apt version: 3.1.8ubuntu1 33s autopkgtest [06:02:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 33s autopkgtest [06:02:44]: testbed release detected to be: None 34s autopkgtest [06:02:45]: updating testbed package index (apt update) 34s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 34s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 34s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 34s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 34s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [533 kB] 35s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 35s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.0 kB] 35s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [61.6 kB] 35s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main i386 Packages [97.2 kB] 35s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 Packages [147 kB] 35s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/main amd64 c-n-f Metadata [3040 B] 35s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 Packages [28.0 kB] 35s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/restricted i386 Packages [3208 B] 35s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/restricted amd64 c-n-f Metadata [336 B] 35s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 Packages [385 kB] 35s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/universe i386 Packages [145 kB] 35s Get:17 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 c-n-f Metadata [10.8 kB] 35s Get:18 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 Packages [6744 B] 35s Get:19 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse i386 Packages [3156 B] 35s Get:20 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse amd64 c-n-f Metadata [492 B] 36s Fetched 1532 kB in 1s (1509 kB/s) 36s Reading package lists... 37s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 37s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 37s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 37s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 37s Reading package lists... 37s Reading package lists... 37s Building dependency tree... 37s Reading state information... 38s Calculating upgrade... 38s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 38s autopkgtest [06:02:49]: upgrading testbed (apt dist-upgrade and autopurge) 38s Reading package lists... 38s Building dependency tree... 38s Reading state information... 38s Calculating upgrade... 38s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 38s Reading package lists... 39s Building dependency tree... 39s Reading state information... 39s Solving dependencies... 39s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 41s autopkgtest [06:02:52]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 10:00:33 UTC 2025 41s autopkgtest [06:02:52]: @@@@@@@@@@@@@@@@@@@@ apt-source pdb2pqr 43s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (dsc) [1860 B] 43s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (tar) [7570 kB] 43s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (diff) [9876 B] 43s gpgv: Signature made Mon Jun 12 17:36:50 2023 UTC 43s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 43s gpgv: Can't check signature: No public key 43s dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found 44s autopkgtest [06:02:55]: testing package pdb2pqr version 3.6.1+dfsg-1 44s autopkgtest [06:02:55]: build not needed 46s autopkgtest [06:02:57]: test installation-test: preparing testbed 46s Reading package lists... 46s Building dependency tree... 46s Reading state information... 47s Solving dependencies... 47s The following NEW packages will be installed: 47s docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr python3-docutils 47s python3-numpy python3-numpy-dev python3-pdb2pqr python3-pdbx python3-propka 47s python3-roman sgml-base xml-core 47s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 47s Need to get 10.3 MB of archives. 47s After this operation, 45.1 MB of additional disk space will be used. 47s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1ubuntu1 [147 kB] 47s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 libblas3 amd64 3.12.1-6build1 [263 kB] 47s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libgfortran5 amd64 15.2.0-5ubuntu1 [939 kB] 47s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 liblapack3 amd64 3.12.1-6build1 [2762 kB] 47s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-numpy amd64 1:2.2.4+ds-1ubuntu1 [5377 kB] 48s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 sgml-base all 1.31+nmu1 [11.0 kB] 48s Get:7 http://ftpmaster.internal/ubuntu resolute/main amd64 xml-core all 0.19 [20.3 kB] 48s Get:8 http://ftpmaster.internal/ubuntu resolute/main amd64 docutils-common all 0.21.2+dfsg-2 [131 kB] 48s Get:9 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-roman all 5.1-1 [10.6 kB] 48s Get:10 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 48s Get:11 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pdbx all 2.0.1-2 [16.5 kB] 48s Get:12 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-propka all 3.5.1-2 [70.1 kB] 48s Get:13 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pdb2pqr all 3.6.1+dfsg-1 [145 kB] 48s Get:14 http://ftpmaster.internal/ubuntu resolute/universe amd64 pdb2pqr all 3.6.1+dfsg-1 [10.4 kB] 48s Fetched 10.3 MB in 1s (7646 kB/s) 48s Selecting previously unselected package python3-numpy-dev:amd64. 48s (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 ... 78459 files and directories currently installed.) 48s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 48s Unpacking python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 48s Selecting previously unselected package libblas3:amd64. 48s Preparing to unpack .../01-libblas3_3.12.1-6build1_amd64.deb ... 48s Unpacking libblas3:amd64 (3.12.1-6build1) ... 48s Selecting previously unselected package libgfortran5:amd64. 48s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_amd64.deb ... 48s Unpacking libgfortran5:amd64 (15.2.0-5ubuntu1) ... 48s Selecting previously unselected package liblapack3:amd64. 48s Preparing to unpack .../03-liblapack3_3.12.1-6build1_amd64.deb ... 48s Unpacking liblapack3:amd64 (3.12.1-6build1) ... 48s Selecting previously unselected package python3-numpy. 48s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_amd64.deb ... 48s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 49s Selecting previously unselected package sgml-base. 49s Preparing to unpack .../05-sgml-base_1.31+nmu1_all.deb ... 49s Unpacking sgml-base (1.31+nmu1) ... 49s Selecting previously unselected package xml-core. 49s Preparing to unpack .../06-xml-core_0.19_all.deb ... 49s Unpacking xml-core (0.19) ... 49s Selecting previously unselected package docutils-common. 49s Preparing to unpack .../07-docutils-common_0.21.2+dfsg-2_all.deb ... 49s Unpacking docutils-common (0.21.2+dfsg-2) ... 49s Selecting previously unselected package python3-roman. 49s Preparing to unpack .../08-python3-roman_5.1-1_all.deb ... 49s Unpacking python3-roman (5.1-1) ... 49s Selecting previously unselected package python3-docutils. 49s Preparing to unpack .../09-python3-docutils_0.21.2+dfsg-2_all.deb ... 49s Unpacking python3-docutils (0.21.2+dfsg-2) ... 49s Selecting previously unselected package python3-pdbx. 49s Preparing to unpack .../10-python3-pdbx_2.0.1-2_all.deb ... 49s Unpacking python3-pdbx (2.0.1-2) ... 49s Selecting previously unselected package python3-propka. 49s Preparing to unpack .../11-python3-propka_3.5.1-2_all.deb ... 49s Unpacking python3-propka (3.5.1-2) ... 49s Selecting previously unselected package python3-pdb2pqr. 49s Preparing to unpack .../12-python3-pdb2pqr_3.6.1+dfsg-1_all.deb ... 49s Unpacking python3-pdb2pqr (3.6.1+dfsg-1) ... 49s Selecting previously unselected package pdb2pqr. 49s Preparing to unpack .../13-pdb2pqr_3.6.1+dfsg-1_all.deb ... 49s Unpacking pdb2pqr (3.6.1+dfsg-1) ... 49s Setting up python3-propka (3.5.1-2) ... 49s Setting up python3-pdbx (2.0.1-2) ... 49s Setting up python3-roman (5.1-1) ... 49s Setting up libblas3:amd64 (3.12.1-6build1) ... 49s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 49s Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1ubuntu1) ... 49s Setting up libgfortran5:amd64 (15.2.0-5ubuntu1) ... 49s Setting up sgml-base (1.31+nmu1) ... 49s Setting up liblapack3:amd64 (3.12.1-6build1) ... 49s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 49s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 50s Setting up xml-core (0.19) ... 50s Processing triggers for libc-bin (2.42-0ubuntu3) ... 50s Processing triggers for man-db (2.13.1-1) ... 51s Processing triggers for sgml-base (1.31+nmu1) ... 51s Setting up docutils-common (0.21.2+dfsg-2) ... 51s Processing triggers for sgml-base (1.31+nmu1) ... 51s Setting up python3-docutils (0.21.2+dfsg-2) ... 51s Setting up python3-pdb2pqr (3.6.1+dfsg-1) ... 51s Setting up pdb2pqr (3.6.1+dfsg-1) ... 52s autopkgtest [06:03:03]: test installation-test: [----------------------- 52s Run pdb2pqr... 52s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 52s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 52s 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). 52s INFO:Checking and transforming input arguments. 52s INFO:Loading topology files. 52s INFO:Loading molecule: examples/1a1p/1a1p.pdb 52s INFO:Setting up molecule. 52s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 52s INFO:Created biomolecule object with 14 residues and 208 atoms. 52s INFO:Setting termini states for biomolecule chains. 52s INFO:Loading forcefield. 52s INFO:Loading hydrogen topology definitions. 52s INFO:This biomolecule is clean. No repair needed. 52s INFO:Updating disulfide bridges. 52s INFO:Debumping biomolecule. 52s INFO:Adding hydrogens to biomolecule. 52s INFO:Debumping biomolecule (again). 52s INFO:Optimizing hydrogen bonds 52s INFO:Applying force field to biomolecule states. 52s INFO:Regenerating headers. 52s INFO:Regenerating PDB lines. 52s WARNING:Ignoring 852 header lines in output. 52s WARNING:Ignoring 3 missing lines in output. 53s autopkgtest [06:03:04]: test installation-test: -----------------------] 53s autopkgtest [06:03:04]: test installation-test: - - - - - - - - - - results - - - - - - - - - - 53s installation-test PASS 53s autopkgtest [06:03:04]: test pdb2pka-test: preparing testbed 53s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s Solving dependencies... 54s The following NEW packages will be installed: 54s fonts-font-awesome fonts-lato libjs-jquery libjs-sphinxdoc libjs-underscore 54s pdb2pqr-doc sphinx-rtd-theme-common 54s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 54s Need to get 5041 kB of archives. 54s After this operation, 20.0 MB of additional disk space will be used. 54s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-lato all 2.015-1 [2781 kB] 54s Get:2 http://ftpmaster.internal/ubuntu resolute/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 54s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 54s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 54s Get:5 http://ftpmaster.internal/ubuntu resolute/main amd64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 54s Get:6 http://ftpmaster.internal/ubuntu resolute/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 54s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 pdb2pqr-doc all 3.6.1+dfsg-1 [258 kB] 55s Fetched 5041 kB in 1s (9532 kB/s) 55s Selecting previously unselected package fonts-lato. 55s (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 ... 79960 files and directories currently installed.) 55s Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... 55s Unpacking fonts-lato (2.015-1) ... 55s Selecting previously unselected package fonts-font-awesome. 55s Preparing to unpack .../1-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 55s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 55s Selecting previously unselected package libjs-jquery. 55s Preparing to unpack .../2-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 55s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 55s Selecting previously unselected package libjs-underscore. 55s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 55s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 55s Selecting previously unselected package libjs-sphinxdoc. 55s Preparing to unpack .../4-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 55s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 55s Selecting previously unselected package sphinx-rtd-theme-common. 55s Preparing to unpack .../5-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 55s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 55s Selecting previously unselected package pdb2pqr-doc. 55s Preparing to unpack .../6-pdb2pqr-doc_3.6.1+dfsg-1_all.deb ... 55s Unpacking pdb2pqr-doc (3.6.1+dfsg-1) ... 55s Setting up fonts-lato (2.015-1) ... 55s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 55s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 55s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 55s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 55s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 55s Setting up pdb2pqr-doc (3.6.1+dfsg-1) ... 56s autopkgtest [06:03:07]: test pdb2pka-test: [----------------------- 56s Run pdb2pqr... 56s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 56s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 56s 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). 56s INFO:Checking and transforming input arguments. 56s INFO:Loading topology files. 56s INFO:Loading molecule: 1a1p/1a1p.pdb 56s INFO:Setting up molecule. 56s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 56s INFO:Created biomolecule object with 14 residues and 208 atoms. 56s INFO:Setting termini states for biomolecule chains. 56s INFO:Loading forcefield. 56s INFO:Loading hydrogen topology definitions. 56s INFO:This biomolecule is clean. No repair needed. 56s INFO:Updating disulfide bridges. 56s INFO:Debumping biomolecule. 56s INFO:Adding hydrogens to biomolecule. 56s INFO:Debumping biomolecule (again). 56s INFO:Optimizing hydrogen bonds 56s INFO:Applying force field to biomolecule states. 56s INFO:Regenerating headers. 56s INFO:Regenerating PDB lines. 56s WARNING:Ignoring 852 header lines in output. 56s WARNING:Ignoring 3 missing lines in output. 56s autopkgtest [06:03:07]: test pdb2pka-test: -----------------------] 57s pdb2pka-test PASS 57s autopkgtest [06:03:08]: test pdb2pka-test: - - - - - - - - - - results - - - - - - - - - - 57s autopkgtest [06:03:08]: test command1: preparing testbed 57s Reading package lists... 57s Building dependency tree... 57s Reading state information... 57s Solving dependencies... 58s The following NEW packages will be installed: 58s python3-dateutil python3-iniconfig python3-packaging python3-pandas 58s python3-pandas-lib python3-pluggy python3-pytest python3-pytz 58s python3-testfixtures 58s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 58s Need to get 11.2 MB of archives. 58s After this operation, 72.3 MB of additional disk space will be used. 58s Get:1 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-dateutil all 2.9.0-4 [80.3 kB] 58s Get:2 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 58s Get:3 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-packaging all 25.0-1 [52.8 kB] 58s Get:4 http://ftpmaster.internal/ubuntu resolute/main amd64 python3-pytz all 2025.2-4 [32.3 kB] 58s Get:5 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas-lib amd64 2.3.3+dfsg-1ubuntu1 [7668 kB] 58s Get:6 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 58s Get:7 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-pluggy all 1.6.0-1 [21.0 kB] 58s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe amd64 python3-pytest all 8.4.2-1 [268 kB] 58s Get:9 http://ftpmaster.internal/ubuntu resolute/universe amd64 python3-testfixtures all 9.2.0-1 [79.2 kB] 58s Fetched 11.2 MB in 0s (45.7 MB/s) 58s Selecting previously unselected package python3-dateutil. 58s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 80295 files and directories currently installed.) 58s Preparing to unpack .../0-python3-dateutil_2.9.0-4_all.deb ... 58s Unpacking python3-dateutil (2.9.0-4) ... 58s Selecting previously unselected package python3-iniconfig. 58s Preparing to unpack .../1-python3-iniconfig_1.1.1-2_all.deb ... 58s Unpacking python3-iniconfig (1.1.1-2) ... 58s Selecting previously unselected package python3-packaging. 58s Preparing to unpack .../2-python3-packaging_25.0-1_all.deb ... 58s Unpacking python3-packaging (25.0-1) ... 58s Selecting previously unselected package python3-pytz. 58s Preparing to unpack .../3-python3-pytz_2025.2-4_all.deb ... 58s Unpacking python3-pytz (2025.2-4) ... 58s Selecting previously unselected package python3-pandas-lib:amd64. 58s Preparing to unpack .../4-python3-pandas-lib_2.3.3+dfsg-1ubuntu1_amd64.deb ... 58s Unpacking python3-pandas-lib:amd64 (2.3.3+dfsg-1ubuntu1) ... 58s Selecting previously unselected package python3-pandas. 58s Preparing to unpack .../5-python3-pandas_2.3.3+dfsg-1ubuntu1_all.deb ... 58s Unpacking python3-pandas (2.3.3+dfsg-1ubuntu1) ... 58s Selecting previously unselected package python3-pluggy. 58s Preparing to unpack .../6-python3-pluggy_1.6.0-1_all.deb ... 58s Unpacking python3-pluggy (1.6.0-1) ... 58s Selecting previously unselected package python3-pytest. 58s Preparing to unpack .../7-python3-pytest_8.4.2-1_all.deb ... 58s Unpacking python3-pytest (8.4.2-1) ... 58s Selecting previously unselected package python3-testfixtures. 58s Preparing to unpack .../8-python3-testfixtures_9.2.0-1_all.deb ... 58s Unpacking python3-testfixtures (9.2.0-1) ... 58s Setting up python3-iniconfig (1.1.1-2) ... 58s Setting up python3-pandas-lib:amd64 (2.3.3+dfsg-1ubuntu1) ... 58s Setting up python3-testfixtures (9.2.0-1) ... 58s Setting up python3-pytz (2025.2-4) ... 59s Setting up python3-packaging (25.0-1) ... 59s Setting up python3-pluggy (1.6.0-1) ... 59s Setting up python3-dateutil (2.9.0-4) ... 59s Setting up python3-pytest (8.4.2-1) ... 59s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 62s Processing triggers for man-db (2.13.1-1) ... 63s autopkgtest [06:03:14]: test command1: pytest-3 63s autopkgtest [06:03:14]: test command1: [----------------------- 64s ============================= test session starts ============================== 64s platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 64s rootdir: /tmp/autopkgtest.7kBJH6/build.wcN/src 64s configfile: pytest.ini 64s plugins: typeguard-4.4.2 64s 64s ----------------------------- live log collection ------------------------------ 64s WARNING py.warnings:warnings.py:110 /tmp/autopkgtest.7kBJH6/build.wcN/src/tests/core_test.py:81: PytestUnknownMarkWarning: Unknown pytest.mark.long_test - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 64s @pytest.mark.long_test 64s 64s ERROR regression_test:regression_test.py:173 Need to reinstate the --apbs-input test with a temporary directory as path 64s collected 316 items 64s 64s tests/core_test.py::test_short_pdb[4UN3] SKIPPED (not running tests ...) [ 0%] 64s tests/core_test.py::test_short_pdb[7BNA] SKIPPED (not running tests ...) [ 0%] 64s tests/core_test.py::test_short_pdb[4E8M] SKIPPED (not running tests ...) [ 0%] 64s tests/core_test.py::test_short_pdb[1K1I] SKIPPED (not running tests ...) [ 1%] 64s tests/core_test.py::test_short_pdb[5D8V] SKIPPED (not running tests ...) [ 1%] 64s tests/core_test.py::test_short_pdb[1AQO] SKIPPED (not running tests ...) [ 1%] 64s tests/core_test.py::test_short_pdb[1NAJ] SKIPPED (not running tests ...) [ 2%] 64s tests/core_test.py::test_short_pdb[1FAS] SKIPPED (not running tests ...) 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[ 51%] 64s tests/core_test.py::test_long_pdb[4L9E] SKIPPED (not running tests r...) [ 52%] 64s tests/core_test.py::test_long_pdb[1OA4] SKIPPED (not running tests r...) [ 52%] 64s tests/core_test.py::test_long_pdb[2JCP] SKIPPED (not running tests r...) [ 52%] 64s tests/core_test.py::test_long_pdb[2IBL] SKIPPED (not running tests r...) [ 53%] 64s tests/core_test.py::test_long_pdb[1V2Z] SKIPPED (not running tests r...) [ 53%] 64s tests/core_test.py::test_long_pdb[1RJ1] SKIPPED (not running tests r...) [ 53%] 64s tests/core_test.py::test_long_pdb[3KT2] SKIPPED (not running tests r...) [ 54%] 64s tests/core_test.py::test_long_pdb[4GS3] SKIPPED (not running tests r...) [ 54%] 64s tests/core_test.py::test_long_pdb[1R7J] SKIPPED (not running tests r...) [ 54%] 64s tests/core_test.py::test_long_pdb[4IL7] SKIPPED (not running tests r...) [ 55%] 64s tests/core_test.py::test_long_pdb[1ZLM] SKIPPED (not running tests r...) [ 55%] 64s tests/core_test.py::test_long_pdb[2OP6] SKIPPED (not running tests r...) [ 55%] 64s tests/core_test.py::test_long_pdb[1DF4] SKIPPED (not running tests r...) [ 56%] 64s tests/core_test.py::test_long_pdb[5EE2] SKIPPED (not running tests r...) [ 56%] 64s tests/core_test.py::test_long_pdb[1PDO] SKIPPED (not running tests r...) [ 56%] 64s tests/core_test.py::test_long_pdb[1ZVA] SKIPPED (not running tests r...) [ 56%] 64s tests/core_test.py::test_long_pdb[1X6J] SKIPPED (not running tests r...) [ 57%] 64s tests/core_test.py::test_long_pdb[2J6B] SKIPPED (not running tests r...) [ 57%] 64s tests/core_test.py::test_long_pdb[3ISU] SKIPPED (not running tests r...) [ 57%] 64s tests/core_test.py::test_long_pdb[1HOE] SKIPPED (not running tests r...) [ 58%] 64s tests/core_test.py::test_long_pdb[4POY] SKIPPED (not running tests r...) [ 58%] 64s tests/core_test.py::test_long_pdb[1XAK] SKIPPED (not running tests r...) [ 58%] 64s tests/core_test.py::test_long_pdb[1OPC] SKIPPED (not running tests r...) [ 59%] 64s tests/core_test.py::test_long_pdb[4YPC] SKIPPED (not running tests r...) [ 59%] 64s tests/core_test.py::test_long_pdb[4LJ1] SKIPPED (not running tests r...) [ 59%] 64s tests/core_test.py::test_long_pdb[1ZX6] SKIPPED (not running tests r...) [ 60%] 64s tests/core_test.py::test_long_pdb[1JQ0] SKIPPED (not running tests r...) [ 60%] 64s tests/core_test.py::test_long_pdb[1UG4] SKIPPED (not running tests r...) [ 60%] 64s tests/core_test.py::test_long_pdb[1YQB] SKIPPED (not running tests r...) [ 61%] 64s tests/core_test.py::test_long_pdb[2HP7] SKIPPED (not running tests r...) [ 61%] 64s tests/core_test.py::test_long_pdb[1SJV] SKIPPED (not running tests r...) [ 61%] 64s tests/core_test.py::test_long_pdb[2CJJ] SKIPPED (not running tests r...) [ 62%] 64s tests/core_test.py::test_long_pdb[1E7G] SKIPPED (not running tests r...) [ 62%] 64s tests/core_test.py::test_long_pdb[1H75] SKIPPED (not running tests r...) [ 62%] 64s tests/core_test.py::test_long_pdb[3CSR] SKIPPED (not running tests r...) [ 62%] 64s tests/core_test.py::test_long_pdb[1ZZK] SKIPPED (not running tests r...) [ 63%] 64s tests/core_test.py::test_long_pdb[3ZZP] SKIPPED (not running tests r...) [ 63%] 64s tests/core_test.py::test_long_pdb[1TGN] SKIPPED (not running tests r...) [ 63%] 64s tests/core_test.py::test_long_pdb[3RFF] SKIPPED (not running tests r...) [ 64%] 64s tests/core_test.py::test_long_pdb[1TEN] SKIPPED (not running tests r...) [ 64%] 64s tests/core_test.py::test_long_pdb[1NH9] SKIPPED (not running tests r...) [ 64%] 64s tests/core_test.py::test_long_pdb[3DVI] SKIPPED (not running tests r...) [ 65%] 64s tests/core_test.py::test_long_pdb[2NWD] SKIPPED (not running tests r...) [ 65%] 64s tests/core_test.py::test_long_pdb[3H0X] SKIPPED (not running tests r...) [ 65%] 64s tests/core_test.py::test_long_pdb[3IDW] SKIPPED (not running tests r...) [ 66%] 64s tests/core_test.py::test_broken_backbone[2V75] 64s -------------------------------- live log call --------------------------------- 64s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_2V75_0/2V75.log 64s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 64s 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). 64s 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). 64s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 64s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 64s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 65s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 65s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 65s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 90 residues and 687 atoms. 65s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 65s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 65s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 65s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 8 missing atoms in biomolecule. 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 65s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 65s 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 65s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 65s XFAIL [ 66%] 65s tests/core_test.py::test_broken_backbone[1EJG] 65s -------------------------------- live log call --------------------------------- 65s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_1EJG_0/1EJG.log 65s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 65s 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). 65s 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). 65s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 65s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 65s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG 67s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 67s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 67s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 650 atoms. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in THR A 1. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 1. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 1. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 1. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 1. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H1 in THR A 1. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H2 in THR A 1. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H3 in THR A 1. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 1. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 1. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 1. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 1. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 1. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 1. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 1. At least one of the instances is being ignored. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 2. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 2. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 2. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 2. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 2. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 2. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 2. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 2. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 2. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 2. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 2. At least one of the instances is being ignored. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 7. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 7. At least one of the instances is being ignored. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in VAL A 8. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in VAL A 8. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in VAL A 8. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in VAL A 8. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in VAL A 8. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in VAL A 8. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in VAL A 8. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in VAL A 8. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG11 in VAL A 8. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in VAL A 8. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in VAL A 8. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in VAL A 8. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in VAL A 8. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in VAL A 8. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in VAL A 8. At least one of the instances is being ignored. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NE in ARG A 10. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in ARG A 10. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH1 in ARG A 10. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH2 in ARG A 10. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE in ARG A 10. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH11 in ARG A 10. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH12 in ARG A 10. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH21 in ARG A 10. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH22 in ARG A 10. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ARG A 10. At least one of the instances is being ignored. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ASN A 12. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASN A 12. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 12. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 12. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 12. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ASN A 12. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASN A 12. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASN A 12. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 12. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 12. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 12. At least one of the instances is being ignored. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PHE A 13. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in PHE A 13. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in PHE A 13. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in PHE A 13. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in PHE A 13. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in PHE A 13. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in PHE A 13. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PHE A 13. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in PHE A 13. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in PHE A 13. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HZ in PHE A 13. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PHE A 13. At least one of the instances is being ignored. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 19. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 19. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 19. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 19. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 19. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 19. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 19. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 19. At least one of the instances is being ignored. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in SER A 22. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in SER A 22. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in SER A 22. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in SER A 22. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in SER A 22. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in SER A 22. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in SER A 22. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in SER A 22. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in SER A 22. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in SER A 22. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in SER A 22. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in SER A 22. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in SER A 22. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in SER A 22. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in SER A 22. At least one of the instances is being ignored. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in GLU A 23. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in GLU A 23. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE1 in GLU A 23. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE2 in GLU A 23. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in GLU A 23. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in GLU A 23. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in GLU A 23. At least one of the instances is being ignored. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 25. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 25. At least one of the instances is being ignored. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in TYR A 29. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in TYR A 29. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in TYR A 29. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in TYR A 29. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in TYR A 29. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in TYR A 29. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OH in TYR A 29. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in TYR A 29. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in TYR A 29. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in TYR A 29. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in TYR A 29. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH in TYR A 29. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in TYR A 29. At least one of the instances is being ignored. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 34. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 34. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 34. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 34. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 34. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 34. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 34. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 34. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 34. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 34. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 34. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 34. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 34. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 34. At least one of the instances is being ignored. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 36. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 36. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 36. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 36. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 36. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 36. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 36. At least one of the instances is being ignored. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 39. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 39. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 39. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 39. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 39. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 39. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 39. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 39. At least one of the instances is being ignored. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASP A 43. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASP A 43. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASP A 43. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD2 in ASP A 43. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASP A 43. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASP A 43. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASP A 43. At least one of the instances is being ignored. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 46. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 46. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 46. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 46. 67s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 46. 67s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 46. At least one of the instances is being ignored. 67s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 67s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 67s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 67s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 67s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 67s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 67s 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 67s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 67s XFAIL [ 66%] 67s tests/core_test.py::test_broken_backbone[3U7T] 67s -------------------------------- live log call --------------------------------- 67s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_3U7T_0/3U7T.log 67s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 67s 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). 67s 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). 67s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 67s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 67s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T 68s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 68s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 68s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 652 atoms. 68s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in PRO A 22. 68s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in PRO A 22. 68s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in PRO A 22. 68s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in PRO A 22. 68s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 22. 68s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in PRO A 22. 68s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in PRO A 22. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 22. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 22. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in PRO A 22. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 22. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in PRO A 22. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 22. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 22. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 22. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 22. 69s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 22. At least one of the instances is being ignored. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in LEU A 25. 69s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in LEU A 25. At least one of the instances is being ignored. 69s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 69s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 69s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 69s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 69s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 69s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 69s 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 69s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 69s XFAIL [ 67%] 69s tests/core_test.py::test_broken_backbone[4MGP] 69s -------------------------------- live log call --------------------------------- 69s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_4MGP_0/4MGP.log 69s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 69s 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). 69s 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). 69s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 69s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 69s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP 70s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 70s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 70s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 23 residues and 163 atoms. 70s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in MET A 21. 70s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in MET A 21. 70s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in MET A 21. 70s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: SD in MET A 21. 70s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE in MET A 21. 70s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in MET A 21. At least one of the instances is being ignored. 70s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 70s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 70s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 70s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 12 missing atoms in biomolecule. 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 70s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 11 at coordinates 1.430, -1.683, -11.529 70s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 11 at coordinates 1.940, -0.315, -11.800 70s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CG to residue LYS A 14 at coordinates -1.600, -8.819, -6.913 70s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CD to residue LYS A 14 at coordinates -2.056, -8.844, -8.361 70s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 14 at coordinates -3.548, -9.031, -8.498 70s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 14 at coordinates -3.947, -9.048, -9.928 70s 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 70s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 70s XFAIL [ 67%] 70s tests/core_test.py::test_protonated_terminals[C-terminal HID] 70s -------------------------------- live log call --------------------------------- 70s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log 70s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 70s 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). 70s 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). 70s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 70s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 70s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/cterm_hid.pdb 70s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 70s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms. 70s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 70s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 70s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 70s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule. 70s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 70s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402 70s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 70s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 70s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 70s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 70s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 70s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 70s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 70s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 70s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 70s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 70s INFO common:common.py:198 0 atoms have position differences > 0 70s INFO common:common.py:198 0 atoms have position differences > 0.01 70s INFO common:common.py:198 0 atoms have charge differences > 0 70s INFO common:common.py:198 0 atoms have charge differences > 0.01 70s INFO common:common.py:198 0 atoms have radius differences > 0 70s INFO common:common.py:198 0 atoms have radius differences > 0.01 70s PASSED [ 67%] 70s tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 70s -------------------------------- live log call --------------------------------- 70s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log 70s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 70s 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). 70s 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). 70s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 70s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 70s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/5vav_cyclic_peptide.pdb 70s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 70s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms. 70s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 70s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 70s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 70s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 70s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 70s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 70s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 70s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 70s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 70s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 70s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 70s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 70s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 70s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 70s INFO common:common.py:198 0 atoms have position differences > 0 70s INFO common:common.py:198 0 atoms have position differences > 0.01 70s INFO common:common.py:198 0 atoms have charge differences > 0 70s INFO common:common.py:198 0 atoms have charge differences > 0.01 70s INFO common:common.py:198 0 atoms have radius differences > 0 70s INFO common:common.py:198 0 atoms have radius differences > 0.01 70s PASSED [ 68%] 70s tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 68%] 70s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 68%] 70s tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 68%] 70s tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 69%] 70s tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 69%] 70s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 69%] 70s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 70%] 70s tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 70%] 70s tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 70%] 70s tests/io_test.py::test_read_pqr[tests/data/1HPX_with-ph=7.00_titration_state_method=propka_ligand=LIG_1HPX_ff=AMBER.pqr] PASSED [ 71%] 70s tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 71%] 70s tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 71%] 70s tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 72%] 70s tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 72%] 70s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 72%] 70s tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 73%] 70s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 73%] 70s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 73%] 70s tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 74%] 70s tests/io_test.py::test_read_qcd PASSED [ 74%] 70s tests/io_test.py::test_dx2cube 70s -------------------------------- live log call --------------------------------- 70s INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... 70s INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... 71s INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 71s INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 71s INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... 71s INFO io_test:io_test.py:68 No differences found in output 71s PASSED [ 74%] 72s tests/ligand_test.py::test_peoe_charges 72s -------------------------------- live log call --------------------------------- 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s PASSED [ 75%] 72s tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 72s -------------------------------- live log call --------------------------------- 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 72s PASSED [ 75%] 72s tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 72s -------------------------------- live log call --------------------------------- 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 72s PASSED [ 75%] 72s tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 72s -------------------------------- live log call --------------------------------- 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 72s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 72s PASSED [ 75%] 72s tests/ligand_test.py::test_assign_parameters[acetate.mol2] 72s -------------------------------- live log call --------------------------------- 72s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 72s PASSED [ 76%] 72s tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 72s -------------------------------- live log call --------------------------------- 72s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 72s PASSED [ 76%] 72s tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 72s -------------------------------- live log call --------------------------------- 72s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 72s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 72s PASSED [ 76%] 72s tests/ligand_test.py::test_assign_parameters[adp.mol2] 72s -------------------------------- live log call --------------------------------- 72s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 72s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 72s INFO ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00 72s PASSED [ 77%] 73s tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 73s -------------------------------- live log call --------------------------------- 73s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 73s PASSED [ 77%] 73s tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 73s -------------------------------- live log call --------------------------------- 73s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 73s PASSED [ 77%] 73s tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 73s -------------------------------- live log call --------------------------------- 73s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 73s PASSED [ 78%] 73s tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 73s -------------------------------- live log call --------------------------------- 73s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 73s PASSED [ 78%] 73s tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 73s -------------------------------- live log call --------------------------------- 73s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 73s PASSED [ 78%] 73s tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 73s -------------------------------- live log call --------------------------------- 73s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 73s PASSED [ 79%] 73s tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 73s -------------------------------- live log call --------------------------------- 73s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 73s PASSED [ 79%] 73s tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 73s -------------------------------- live log call --------------------------------- 73s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 73s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 73s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 73s PASSED [ 79%] 73s tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 73s -------------------------------- live log call --------------------------------- 73s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 73s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 73s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 73s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 73s PASSED [ 80%] 73s tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 73s -------------------------------- live log call --------------------------------- 73s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 73s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 73s PASSED [ 80%] 73s tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 73s -------------------------------- live log call --------------------------------- 73s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 73s PASSED [ 80%] 73s tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED [ 81%] 73s tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED [ 81%] 73s tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 73s -------------------------------- live log call --------------------------------- 73s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 73s PASSED [ 81%] 73s tests/ligand_test.py::test_formal_charge[adp.mol2] 73s -------------------------------- live log call --------------------------------- 73s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 73s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 73s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 73s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 73s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 73s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 73s PASSED [ 81%] 73s tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED [ 82%] 73s tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED [ 82%] 73s tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED [ 82%] 73s tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED [ 83%] 73s tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED [ 83%] 73s tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED [ 83%] 73s tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED [ 84%] 73s tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 73s -------------------------------- live log call --------------------------------- 73s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 73s PASSED [ 84%] 73s tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED [ 84%] 73s tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED [ 85%] 73s tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED [ 85%] 73s tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED [ 85%] 73s tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED [ 86%] 73s tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED [ 86%] 74s tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED [ 86%] 74s tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED [ 87%] 74s tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED [ 87%] 74s tests/ligand_test.py::test_rings[acetate.mol2] PASSED [ 87%] 74s tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED [ 87%] 74s tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED [ 88%] 74s tests/ligand_test.py::test_rings[adp.mol2] PASSED [ 88%] 74s tests/ligand_test.py::test_rings[anthracene.mol2] PASSED [ 88%] 74s tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED [ 89%] 74s tests/ligand_test.py::test_rings[ethanol.mol2] PASSED [ 89%] 74s tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED [ 89%] 74s tests/ligand_test.py::test_rings[glycerol.mol2] PASSED [ 90%] 74s tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED [ 90%] 74s tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED [ 90%] 74s tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED [ 91%] 74s tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%] 74s tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%] 74s tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%] 74s tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%] 74s tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%] 74s tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%] 74s tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%] 74s tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%] 74s tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%] 74s tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%] 74s tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%] 74s tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] 74s tests/regression_test.py::test_basic[1AFS basic local] 74s -------------------------------- live log call --------------------------------- 74s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_basic_1AFS_basic_local_0/output.log 74s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 74s 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). 74s 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). 74s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 74s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 74s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 74s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 74s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 74s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 74s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 74s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 74s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 74s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 74s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 74s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 74s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 74s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 74s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 74s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 74s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 74s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 74s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 74s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 74s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 74s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 74s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 74s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 75s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 75s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 75s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 75s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 75s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 75s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 75s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 75s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 75s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 75s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 75s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 75s WARNING pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages 77s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 77s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 77s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 77s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 77s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 77s WARNING common:common.py:186 6 atoms have position differences > 0 77s INFO common:common.py:198 0 atoms have position differences > 0.01 77s INFO common:common.py:198 0 atoms have charge differences > 0 77s INFO common:common.py:198 0 atoms have charge differences > 0.01 77s INFO common:common.py:198 0 atoms have radius differences > 0 77s INFO common:common.py:198 0 atoms have radius differences > 0.01 77s PASSED [ 95%] 77s tests/regression_test.py::test_forcefields[1AFS whitespace AMBER] 77s -------------------------------- live log call --------------------------------- 77s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa0/output.log 77s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 77s 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). 77s 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). 77s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 77s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 77s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 77s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 77s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 77s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 77s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 77s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 77s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 77s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 77s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 77s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 77s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 77s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 77s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 77s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 77s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 77s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 77s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 77s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 77s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 77s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 77s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 77s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 77s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 77s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 79s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 79s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 79s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 79s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 79s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 79s WARNING common:common.py:186 6 atoms have position differences > 0 79s INFO common:common.py:198 0 atoms have position differences > 0.01 79s INFO common:common.py:198 0 atoms have charge differences > 0 79s INFO common:common.py:198 0 atoms have charge differences > 0.01 79s INFO common:common.py:198 0 atoms have radius differences > 0 79s INFO common:common.py:198 0 atoms have radius differences > 0.01 79s PASSED [ 95%] 79s tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] 79s -------------------------------- live log call --------------------------------- 79s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa1/output.log 79s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 79s 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). 79s 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). 79s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 79s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 79s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 79s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 79s WARNING pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages 79s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 79s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 79s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 79s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 79s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 79s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 79s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 79s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 79s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 79s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 79s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 79s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 79s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 79s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 79s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 79s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 80s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 80s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 82s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 82s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 82s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 82s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 82s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 82s WARNING common:common.py:186 5 atoms have position differences > 0 82s INFO common:common.py:198 0 atoms have position differences > 0.01 82s INFO common:common.py:198 0 atoms have charge differences > 0 82s INFO common:common.py:198 0 atoms have charge differences > 0.01 82s INFO common:common.py:198 0 atoms have radius differences > 0 82s INFO common:common.py:198 0 atoms have radius differences > 0.01 82s PASSED [ 95%] 82s tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] 82s -------------------------------- live log call --------------------------------- 82s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa2/output.log 82s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 82s 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). 82s 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). 82s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 82s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 82s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 82s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 82s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 82s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 82s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 82s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 82s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 82s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 82s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 82s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 82s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 82s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 82s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 82s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 82s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 82s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 82s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 82s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 82s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 83s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 84s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 84s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 84s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 84s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 84s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 84s WARNING common:common.py:186 6 atoms have position differences > 0 84s INFO common:common.py:198 0 atoms have position differences > 0.01 84s INFO common:common.py:198 0 atoms have charge differences > 0 84s INFO common:common.py:198 0 atoms have charge differences > 0.01 84s INFO common:common.py:198 0 atoms have radius differences > 0 84s INFO common:common.py:198 0 atoms have radius differences > 0.01 84s PASSED [ 96%] 84s tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] 84s -------------------------------- live log call --------------------------------- 84s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa3/output.log 84s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 84s 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). 84s 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). 84s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 84s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 84s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 84s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 84s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 84s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 84s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 84s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 84s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 84s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 84s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 84s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 84s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 84s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 84s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 84s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 84s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 84s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 84s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 85s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 85s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 85s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 87s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 87s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 87s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 87s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 87s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 87s WARNING common:common.py:186 6 atoms have position differences > 0 87s INFO common:common.py:198 0 atoms have position differences > 0.01 87s INFO common:common.py:198 0 atoms have charge differences > 0 87s INFO common:common.py:198 0 atoms have charge differences > 0.01 87s INFO common:common.py:198 0 atoms have radius differences > 0 87s INFO common:common.py:198 0 atoms have radius differences > 0.01 87s PASSED [ 96%] 87s tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] 87s -------------------------------- live log call --------------------------------- 87s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa4/output.log 87s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 87s 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). 87s 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). 87s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 87s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 87s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 87s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 87s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 87s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 87s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 87s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 87s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 87s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 87s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 87s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 87s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 87s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 87s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 87s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 87s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 87s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 87s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 87s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 88s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 88s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 89s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 89s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 89s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 89s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output. 89s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 90s WARNING common:common.py:186 6 atoms have position differences > 0 90s INFO common:common.py:198 0 atoms have position differences > 0.01 90s INFO common:common.py:198 0 atoms have charge differences > 0 90s INFO common:common.py:198 0 atoms have charge differences > 0.01 90s INFO common:common.py:198 0 atoms have radius differences > 0 90s INFO common:common.py:198 0 atoms have radius differences > 0.01 90s PASSED [ 96%] 90s tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] 90s -------------------------------- live log call --------------------------------- 90s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa5/output.log 90s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 90s 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). 90s 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). 90s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 90s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 90s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 90s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 90s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 90s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 90s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 90s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 90s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 90s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 90s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 90s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 90s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 90s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 90s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 90s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 90s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 90s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 90s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 90s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 90s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 90s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 92s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 92s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 92s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 92s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 92s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 92s WARNING common:common.py:186 6 atoms have position differences > 0 92s INFO common:common.py:198 0 atoms have position differences > 0.01 92s INFO common:common.py:198 0 atoms have charge differences > 0 92s INFO common:common.py:198 0 atoms have charge differences > 0.01 92s INFO common:common.py:198 0 atoms have radius differences > 0 92s INFO common:common.py:198 0 atoms have radius differences > 0.01 92s PASSED [ 97%] 92s tests/regression_test.py::test_other_options[1AFS whitespace clean] 92s -------------------------------- live log call --------------------------------- 92s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_whites0/output.log 92s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 92s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 92s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 92s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 92s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 92s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 92s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 92s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 92s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 92s INFO PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps. 92s INFO common:common.py:198 0 atoms have position differences > 0 92s INFO common:common.py:198 0 atoms have position differences > 0.01 92s INFO common:common.py:198 0 atoms have charge differences > 0 92s INFO common:common.py:198 0 atoms have charge differences > 0.01 92s INFO common:common.py:198 0 atoms have radius differences > 0 92s INFO common:common.py:198 0 atoms have radius differences > 0.01 92s PASSED [ 97%] 92s tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] 92s -------------------------------- live log call --------------------------------- 92s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_assign0/output.log 92s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 92s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 92s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 92s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 92s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 92s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 92s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 92s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 92s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 92s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 92s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 92s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 92s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 92s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 92s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 92s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 92s INFO common:common.py:198 0 atoms have position differences > 0 92s INFO common:common.py:198 0 atoms have position differences > 0.01 92s INFO common:common.py:198 0 atoms have charge differences > 0 92s INFO common:common.py:198 0 atoms have charge differences > 0.01 92s INFO common:common.py:198 0 atoms have radius differences > 0 92s INFO common:common.py:198 0 atoms have radius differences > 0.01 92s PASSED [ 97%] 92s tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] 92s -------------------------------- live log call --------------------------------- 92s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_nodebu0/output.log 92s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 92s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 92s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 92s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 92s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 92s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 92s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 92s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 92s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 92s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 92s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 92s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 92s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 92s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 92s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 92s INFO pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization... 92s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 92s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 92s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 92s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 92s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 92s INFO common:common.py:198 0 atoms have position differences > 0 92s INFO common:common.py:198 0 atoms have position differences > 0.01 92s INFO common:common.py:198 0 atoms have charge differences > 0 92s INFO common:common.py:198 0 atoms have charge differences > 0.01 92s INFO common:common.py:198 0 atoms have radius differences > 0 92s INFO common:common.py:198 0 atoms have radius differences > 0.01 92s PASSED [ 98%] 92s tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] 92s -------------------------------- live log call --------------------------------- 92s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_chain_0/output.log 92s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 92s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 92s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 92s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 92s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 92s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 93s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 93s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 93s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 93s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 93s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 93s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 93s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 93s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 93s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 93s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 93s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 93s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 93s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 94s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 95s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 95s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 95s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 95s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 95s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 95s WARNING common:common.py:186 6 atoms have position differences > 0 95s INFO common:common.py:198 0 atoms have position differences > 0.01 95s INFO common:common.py:198 0 atoms have charge differences > 0 95s INFO common:common.py:198 0 atoms have charge differences > 0.01 95s INFO common:common.py:198 0 atoms have radius differences > 0 95s INFO common:common.py:198 0 atoms have radius differences > 0.01 95s PASSED [ 98%] 95s tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] 95s -------------------------------- live log call --------------------------------- 95s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_neutra0/output.log 95s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 95s INFO PDB2PQR3.6.1:main.py:242 Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 95s INFO PDB2PQR3.6.1:main.py:242 Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007). 95s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 95s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 95s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 95s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 95s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 95s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 95s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 95s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 95s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 95s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 95s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 95s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 95s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 95s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 95s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 95s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 95s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 95s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 95s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 95s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 96s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 96s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 98s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 98s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 98s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 98s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 98s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 98s WARNING common:common.py:186 6 atoms have position differences > 0 98s INFO common:common.py:198 0 atoms have position differences > 0.01 98s INFO common:common.py:198 0 atoms have charge differences > 0 98s INFO common:common.py:198 0 atoms have charge differences > 0.01 98s INFO common:common.py:198 0 atoms have radius differences > 0 98s INFO common:common.py:198 0 atoms have radius differences > 0.01 98s PASSED [ 98%] 98s tests/regression_test.py::test_other_options[1AFS drop-water AMBER] 98s -------------------------------- live log call --------------------------------- 98s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_drop_w0/output.log 98s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 98s 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). 98s 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). 98s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 98s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 98s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 98s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 98s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 98s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms. 98s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 98s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 98s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 98s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 98s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 98s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 98s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 98s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 98s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 98s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 98s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 98s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 98s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 98s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 98s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 98s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 99s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 99s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 99s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 99s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 99s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 99s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 100s WARNING common:common.py:186 6 atoms have position differences > 0 100s INFO common:common.py:198 0 atoms have position differences > 0.01 100s INFO common:common.py:198 0 atoms have charge differences > 0 100s INFO common:common.py:198 0 atoms have charge differences > 0.01 100s INFO common:common.py:198 0 atoms have radius differences > 0 100s INFO common:common.py:198 0 atoms have radius differences > 0.01 100s PASSED [ 99%] 100s tests/regression_test.py::test_other_options[1AFS userff usernames whitespace] 100s -------------------------------- live log call --------------------------------- 100s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_userff0/output.log 100s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 100s 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). 100s 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). 100s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 100s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 100s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 100s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 100s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 100s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 100s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 100s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 100s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 100s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 100s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 100s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 100s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 100s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 100s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 100s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 100s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 100s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 100s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 100s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 100s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 101s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 102s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 102s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 102s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 102s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 102s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 102s WARNING common:common.py:186 6 atoms have position differences > 0 102s INFO common:common.py:198 0 atoms have position differences > 0.01 102s INFO common:common.py:198 0 atoms have charge differences > 0 102s INFO common:common.py:198 0 atoms have charge differences > 0.01 102s INFO common:common.py:198 0 atoms have radius differences > 0 102s INFO common:common.py:198 0 atoms have radius differences > 0.01 102s PASSED [ 99%] 102s tests/test_version.py::test_version_exists PASSED [ 99%] 102s tests/test_version.py::test_version PASSED [100%] 102s 102s ================= 92 passed, 220 skipped, 4 xfailed in 39.09s ================== 103s autopkgtest [06:03:54]: test command1: -----------------------] 103s autopkgtest [06:03:54]: test command1: - - - - - - - - - - results - - - - - - - - - - 103s command1 PASS 104s autopkgtest [06:03:55]: @@@@@@@@@@@@@@@@@@@@ summary 104s installation-test PASS 104s pdb2pka-test PASS 104s command1 PASS