0s autopkgtest [17:55:36]: starting date and time: 2024-03-23 17:55:36+0000 1s autopkgtest [17:55:37]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 1s autopkgtest [17:55:37]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.wlyi3n1v/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:sphinx --apt-upgrade pdb2pqr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/7.2.6-6 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos03-arm64-17.secgroup --name adt-noble-arm64-pdb2pqr-20240323-174135-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 67s autopkgtest [17:56:43]: testbed dpkg architecture: arm64 67s autopkgtest [17:56:43]: testbed apt version: 2.7.12 67s autopkgtest [17:56:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 68s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 68s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 68s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 68s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 68s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4030 kB] 68s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [667 kB] 68s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 68s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 68s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 68s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4346 kB] 69s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 69s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [69.8 kB] 69s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 70s Fetched 9833 kB in 2s (5607 kB/s) 71s Reading package lists... 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 75s Calculating upgrade... 75s The following packages will be upgraded: 75s cloud-init fonts-ubuntu-console libbsd0 libc-bin libc6 locales 75s python3-markupsafe 75s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 75s Need to get 8268 kB of archives. 75s After this operation, 63.5 kB disk space will be freed. 75s Get:1 http://ftpmaster.internal/ubuntu noble/main arm64 libc6 arm64 2.39-0ubuntu6 [2776 kB] 76s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libc-bin arm64 2.39-0ubuntu6 [591 kB] 76s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libbsd0 arm64 0.12.1-1 [41.0 kB] 76s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 locales all 2.39-0ubuntu6 [4232 kB] 76s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-ubuntu-console all 0.869+git20240321-0ubuntu1 [18.7 kB] 76s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 python3-markupsafe arm64 2.1.5-1build1 [12.5 kB] 76s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 cloud-init all 24.1.2-0ubuntu1 [597 kB] 76s Preconfiguring packages ... 76s Fetched 8268 kB in 1s (10.7 MB/s) 77s (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 ... 74820 files and directories currently installed.) 77s Preparing to unpack .../libc6_2.39-0ubuntu6_arm64.deb ... 77s Unpacking libc6:arm64 (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 77s Setting up libc6:arm64 (2.39-0ubuntu6) ... 78s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74820 files and directories currently installed.) 78s Preparing to unpack .../libc-bin_2.39-0ubuntu6_arm64.deb ... 78s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 78s Setting up libc-bin (2.39-0ubuntu6) ... 78s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74820 files and directories currently installed.) 78s Preparing to unpack .../libbsd0_0.12.1-1_arm64.deb ... 78s Unpacking libbsd0:arm64 (0.12.1-1) over (0.11.8-1) ... 78s Preparing to unpack .../locales_2.39-0ubuntu6_all.deb ... 78s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 78s Preparing to unpack .../fonts-ubuntu-console_0.869+git20240321-0ubuntu1_all.deb ... 78s Unpacking fonts-ubuntu-console (0.869+git20240321-0ubuntu1) over (0.869-0ubuntu1) ... 78s Preparing to unpack .../python3-markupsafe_2.1.5-1build1_arm64.deb ... 79s Unpacking python3-markupsafe (2.1.5-1build1) over (2.1.5-1) ... 79s Preparing to unpack .../cloud-init_24.1.2-0ubuntu1_all.deb ... 79s Unpacking cloud-init (24.1.2-0ubuntu1) over (24.1.1-0ubuntu1) ... 79s Setting up fonts-ubuntu-console (0.869+git20240321-0ubuntu1) ... 79s Setting up cloud-init (24.1.2-0ubuntu1) ... 81s Setting up locales (2.39-0ubuntu6) ... 81s Generating locales (this might take a while)... 83s en_US.UTF-8... done 83s Generation complete. 83s Setting up python3-markupsafe (2.1.5-1build1) ... 83s Setting up libbsd0:arm64 (0.12.1-1) ... 83s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 84s Processing triggers for man-db (2.12.0-3) ... 84s Processing triggers for libc-bin (2.39-0ubuntu6) ... 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s sh: Attempting to set up Debian/Ubuntu apt sources automatically 86s sh: Distribution appears to be Ubuntu 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 88s eatmydata is already the newest version (131-1). 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s Reading package lists... 88s Building dependency tree... 88s Reading state information... 89s dbus is already the newest version (1.14.10-4ubuntu1). 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s Reading package lists... 89s Building dependency tree... 89s Reading state information... 90s rng-tools-debian is already the newest version (2.4). 90s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 91s The following packages will be REMOVED: 91s cloud-init* python3-configobj* python3-debconf* 91s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 91s After this operation, 3256 kB disk space will be freed. 91s (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 ... 74819 files and directories currently installed.) 91s Removing cloud-init (24.1.2-0ubuntu1) ... 92s Removing python3-configobj (5.0.8-3) ... 92s Removing python3-debconf (1.5.86) ... 92s Processing triggers for man-db (2.12.0-3) ... 92s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 74430 files and directories currently installed.) 92s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 93s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 93s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 93s invoke-rc.d: policy-rc.d denied execution of try-restart. 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 94s linux-generic is already the newest version (6.8.0-11.11+1). 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 94s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 94s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 94s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 96s Reading package lists... 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 97s Calculating upgrade... 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 98s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s autopkgtest [17:57:14]: rebooting testbed after setup commands that affected boot 130s autopkgtest [17:57:46]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 133s autopkgtest [17:57:49]: @@@@@@@@@@@@@@@@@@@@ apt-source pdb2pqr 137s Get:1 http://ftpmaster.internal/ubuntu noble/universe pdb2pqr 3.6.1+dfsg-1 (dsc) [1860 B] 137s Get:2 http://ftpmaster.internal/ubuntu noble/universe pdb2pqr 3.6.1+dfsg-1 (tar) [7570 kB] 137s Get:3 http://ftpmaster.internal/ubuntu noble/universe pdb2pqr 3.6.1+dfsg-1 (diff) [9876 B] 138s gpgv: Signature made Mon Jun 12 17:36:50 2023 UTC 138s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 138s gpgv: Can't check signature: No public key 138s dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found 139s autopkgtest [17:57:55]: testing package pdb2pqr version 3.6.1+dfsg-1 139s autopkgtest [17:57:55]: build not needed 141s autopkgtest [17:57:57]: test installation-test: preparing testbed 146s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Starting pkgProblemResolver with broken count: 0 147s Starting 2 pkgProblemResolver with broken count: 0 147s Done 148s The following additional packages will be installed: 148s docutils-common libblas3 libgfortran5 liblapack3 libpython3.11-minimal 148s libpython3.11-stdlib pdb2pqr python3-docutils python3-numpy python3-pdb2pqr 148s python3-pdbx python3-propka python3-roman python3.11 python3.11-minimal 148s sgml-base xml-core 148s Suggested packages: 148s apbs docutils-doc fonts-linuxlibertine | ttf-linux-libertine 148s texlive-lang-french texlive-latex-base texlive-latex-recommended gcc 148s gfortran python3-dev python3-pytest python-pdbx-doc python-propka-doc 148s python3.11-venv python3.11-doc binfmt-support sgml-base-doc debhelper 148s Recommended packages: 148s libpaper-utils python3-pil 148s The following NEW packages will be installed: 148s autopkgtest-satdep docutils-common libblas3 libgfortran5 liblapack3 148s libpython3.11-minimal libpython3.11-stdlib pdb2pqr python3-docutils 148s python3-numpy python3-pdb2pqr python3-pdbx python3-propka python3-roman 148s python3.11 python3.11-minimal sgml-base xml-core 148s 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. 148s Need to get 13.7 MB/13.7 MB of archives. 148s After this operation, 62.6 MB of additional disk space will be used. 148s Get:1 /tmp/autopkgtest.LK7mh5/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B] 148s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-minimal arm64 3.11.8-1 [837 kB] 148s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11-minimal arm64 3.11.8-1 [2150 kB] 149s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 sgml-base all 1.31 [11.4 kB] 149s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libpython3.11-stdlib arm64 3.11.8-1 [1913 kB] 149s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 python3.11 arm64 3.11.8-1 [589 kB] 149s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 xml-core all 0.19 [20.3 kB] 149s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 docutils-common all 0.20.1+dfsg-3 [132 kB] 149s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 149s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 149s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 149s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 149s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 python3-roman all 3.3-3 [9632 B] 149s Get:14 http://ftpmaster.internal/ubuntu noble/main arm64 python3-docutils all 0.20.1+dfsg-3 [393 kB] 149s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pdbx all 2.0.1-2 [16.5 kB] 149s Get:16 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-propka all 3.5.1-1 [85.5 kB] 149s Get:17 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pdb2pqr all 3.6.1+dfsg-1 [145 kB] 149s Get:18 http://ftpmaster.internal/ubuntu noble/universe arm64 pdb2pqr all 3.6.1+dfsg-1 [10.4 kB] 149s Fetched 13.7 MB in 1s (14.7 MB/s) 149s Selecting previously unselected package libpython3.11-minimal:arm64. 150s (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 ... 74375 files and directories currently installed.) 150s Preparing to unpack .../00-libpython3.11-minimal_3.11.8-1_arm64.deb ... 150s Unpacking libpython3.11-minimal:arm64 (3.11.8-1) ... 150s Selecting previously unselected package python3.11-minimal. 150s Preparing to unpack .../01-python3.11-minimal_3.11.8-1_arm64.deb ... 150s Unpacking python3.11-minimal (3.11.8-1) ... 150s Selecting previously unselected package sgml-base. 150s Preparing to unpack .../02-sgml-base_1.31_all.deb ... 150s Unpacking sgml-base (1.31) ... 150s Selecting previously unselected package libpython3.11-stdlib:arm64. 150s Preparing to unpack .../03-libpython3.11-stdlib_3.11.8-1_arm64.deb ... 150s Unpacking libpython3.11-stdlib:arm64 (3.11.8-1) ... 150s Selecting previously unselected package python3.11. 150s Preparing to unpack .../04-python3.11_3.11.8-1_arm64.deb ... 150s Unpacking python3.11 (3.11.8-1) ... 150s Selecting previously unselected package xml-core. 150s Preparing to unpack .../05-xml-core_0.19_all.deb ... 150s Unpacking xml-core (0.19) ... 150s Selecting previously unselected package docutils-common. 150s Preparing to unpack .../06-docutils-common_0.20.1+dfsg-3_all.deb ... 150s Unpacking docutils-common (0.20.1+dfsg-3) ... 150s Selecting previously unselected package libblas3:arm64. 150s Preparing to unpack .../07-libblas3_3.12.0-3_arm64.deb ... 150s Unpacking libblas3:arm64 (3.12.0-3) ... 150s Selecting previously unselected package libgfortran5:arm64. 150s Preparing to unpack .../08-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 150s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 150s Selecting previously unselected package liblapack3:arm64. 150s Preparing to unpack .../09-liblapack3_3.12.0-3_arm64.deb ... 150s Unpacking liblapack3:arm64 (3.12.0-3) ... 150s Selecting previously unselected package python3-numpy. 150s Preparing to unpack .../10-python3-numpy_1%3a1.24.2-2_arm64.deb ... 150s Unpacking python3-numpy (1:1.24.2-2) ... 150s Selecting previously unselected package python3-roman. 150s Preparing to unpack .../11-python3-roman_3.3-3_all.deb ... 150s Unpacking python3-roman (3.3-3) ... 150s Selecting previously unselected package python3-docutils. 150s Preparing to unpack .../12-python3-docutils_0.20.1+dfsg-3_all.deb ... 150s Unpacking python3-docutils (0.20.1+dfsg-3) ... 150s Selecting previously unselected package python3-pdbx. 150s Preparing to unpack .../13-python3-pdbx_2.0.1-2_all.deb ... 150s Unpacking python3-pdbx (2.0.1-2) ... 150s Selecting previously unselected package python3-propka. 151s Preparing to unpack .../14-python3-propka_3.5.1-1_all.deb ... 151s Unpacking python3-propka (3.5.1-1) ... 151s Selecting previously unselected package python3-pdb2pqr. 151s Preparing to unpack .../15-python3-pdb2pqr_3.6.1+dfsg-1_all.deb ... 151s Unpacking python3-pdb2pqr (3.6.1+dfsg-1) ... 151s Selecting previously unselected package pdb2pqr. 151s Preparing to unpack .../16-pdb2pqr_3.6.1+dfsg-1_all.deb ... 151s Unpacking pdb2pqr (3.6.1+dfsg-1) ... 151s Selecting previously unselected package autopkgtest-satdep. 151s Preparing to unpack .../17-1-autopkgtest-satdep.deb ... 151s Unpacking autopkgtest-satdep (0) ... 151s Setting up python3-propka (3.5.1-1) ... 151s Setting up python3-pdbx (2.0.1-2) ... 151s Setting up python3-roman (3.3-3) ... 151s Setting up libblas3:arm64 (3.12.0-3) ... 151s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 151s Setting up libgfortran5:arm64 (14-20240303-1ubuntu1) ... 151s Setting up sgml-base (1.31) ... 151s Setting up libpython3.11-minimal:arm64 (3.11.8-1) ... 151s Setting up python3.11-minimal (3.11.8-1) ... 152s Setting up liblapack3:arm64 (3.12.0-3) ... 152s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 152s Setting up libpython3.11-stdlib:arm64 (3.11.8-1) ... 152s Setting up xml-core (0.19) ... 152s Setting up python3.11 (3.11.8-1) ... 153s Setting up python3-numpy (1:1.24.2-2) ... 155s Processing triggers for libc-bin (2.39-0ubuntu6) ... 155s Processing triggers for systemd (255.2-3ubuntu2) ... 155s Processing triggers for man-db (2.12.0-3) ... 156s Processing triggers for sgml-base (1.31) ... 156s Setting up docutils-common (0.20.1+dfsg-3) ... 156s Processing triggers for sgml-base (1.31) ... 156s Setting up python3-docutils (0.20.1+dfsg-3) ... 157s Setting up python3-pdb2pqr (3.6.1+dfsg-1) ... 157s Setting up pdb2pqr (3.6.1+dfsg-1) ... 157s Setting up autopkgtest-satdep (0) ... 161s (Reading database ... 76585 files and directories currently installed.) 161s Removing autopkgtest-satdep (0) ... 162s autopkgtest [17:58:18]: test installation-test: [----------------------- 162s Run pdb2pqr... 163s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 163s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 163s 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). 163s INFO:Checking and transforming input arguments. 163s INFO:Loading topology files. 163s INFO:Loading molecule: examples/1a1p/1a1p.pdb 163s INFO:Setting up molecule. 163s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 163s INFO:Created biomolecule object with 14 residues and 208 atoms. 163s INFO:Setting termini states for biomolecule chains. 163s INFO:Loading forcefield. 163s INFO:Loading hydrogen topology definitions. 163s INFO:This biomolecule is clean. No repair needed. 163s INFO:Updating disulfide bridges. 163s INFO:Debumping biomolecule. 163s INFO:Adding hydrogens to biomolecule. 163s INFO:Debumping biomolecule (again). 163s INFO:Optimizing hydrogen bonds 163s INFO:Applying force field to biomolecule states. 163s INFO:Regenerating headers. 163s INFO:Regenerating PDB lines. 163s WARNING:Ignoring 852 header lines in output. 163s WARNING:Ignoring 3 missing lines in output. 164s autopkgtest [17:58:20]: test installation-test: -----------------------] 164s autopkgtest [17:58:20]: test installation-test: - - - - - - - - - - results - - - - - - - - - - 164s installation-test PASS 165s autopkgtest [17:58:21]: test pdb2pka-test: preparing testbed 174s Reading package lists... 174s Building dependency tree... 174s Reading state information... 175s Starting pkgProblemResolver with broken count: 0 175s Starting 2 pkgProblemResolver with broken count: 0 175s Done 175s The following additional packages will be installed: 175s fonts-font-awesome fonts-lato libjs-jquery libjs-sphinxdoc libjs-underscore 175s pdb2pqr-doc sphinx-rtd-theme-common 175s Recommended packages: 175s javascript-common 175s The following NEW packages will be installed: 175s autopkgtest-satdep fonts-font-awesome fonts-lato libjs-jquery 175s libjs-sphinxdoc libjs-underscore pdb2pqr-doc sphinx-rtd-theme-common 175s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 175s Need to get 5162 kB/5162 kB of archives. 175s After this operation, 20.1 MB of additional disk space will be used. 175s Get:1 /tmp/autopkgtest.LK7mh5/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 175s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-lato all 2.015-1 [2781 kB] 176s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 176s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 176s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 176s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-sphinxdoc all 7.2.6-4 [149 kB] 176s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1012 kB] 176s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 pdb2pqr-doc all 3.6.1+dfsg-1 [258 kB] 177s Fetched 5162 kB in 1s (6059 kB/s) 177s Selecting previously unselected package fonts-lato. 177s (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 ... 76585 files and directories currently installed.) 177s Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... 177s Unpacking fonts-lato (2.015-1) ... 177s Selecting previously unselected package fonts-font-awesome. 177s Preparing to unpack .../1-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 177s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 177s Selecting previously unselected package libjs-jquery. 178s Preparing to unpack .../2-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 178s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 178s Selecting previously unselected package libjs-underscore. 178s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 178s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 178s Selecting previously unselected package libjs-sphinxdoc. 178s Preparing to unpack .../4-libjs-sphinxdoc_7.2.6-4_all.deb ... 178s Unpacking libjs-sphinxdoc (7.2.6-4) ... 178s Selecting previously unselected package sphinx-rtd-theme-common. 178s Preparing to unpack .../5-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... 178s Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 179s Selecting previously unselected package pdb2pqr-doc. 179s Preparing to unpack .../6-pdb2pqr-doc_3.6.1+dfsg-1_all.deb ... 179s Unpacking pdb2pqr-doc (3.6.1+dfsg-1) ... 179s Selecting previously unselected package autopkgtest-satdep. 179s Preparing to unpack .../7-2-autopkgtest-satdep.deb ... 179s Unpacking autopkgtest-satdep (0) ... 179s Setting up fonts-lato (2.015-1) ... 179s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 179s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 179s Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... 179s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 179s Setting up libjs-sphinxdoc (7.2.6-4) ... 179s Setting up pdb2pqr-doc (3.6.1+dfsg-1) ... 179s Setting up autopkgtest-satdep (0) ... 183s (Reading database ... 76919 files and directories currently installed.) 183s Removing autopkgtest-satdep (0) ... 184s autopkgtest [17:58:40]: test pdb2pka-test: [----------------------- 184s Run pdb2pqr... 184s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 184s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 184s 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). 184s INFO:Checking and transforming input arguments. 184s INFO:Loading topology files. 184s INFO:Loading molecule: 1a1p/1a1p.pdb 184s INFO:Setting up molecule. 184s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 184s INFO:Created biomolecule object with 14 residues and 208 atoms. 184s INFO:Setting termini states for biomolecule chains. 184s INFO:Loading forcefield. 184s INFO:Loading hydrogen topology definitions. 184s INFO:This biomolecule is clean. No repair needed. 184s INFO:Updating disulfide bridges. 184s INFO:Debumping biomolecule. 184s INFO:Adding hydrogens to biomolecule. 184s INFO:Debumping biomolecule (again). 184s INFO:Optimizing hydrogen bonds 184s INFO:Applying force field to biomolecule states. 184s INFO:Regenerating headers. 184s INFO:Regenerating PDB lines. 184s WARNING:Ignoring 852 header lines in output. 184s WARNING:Ignoring 3 missing lines in output. 185s autopkgtest [17:58:41]: test pdb2pka-test: -----------------------] 185s autopkgtest [17:58:41]: test pdb2pka-test: - - - - - - - - - - results - - - - - - - - - - 185s pdb2pka-test PASS 186s autopkgtest [17:58:42]: test command1: preparing testbed 195s Reading package lists... 195s Building dependency tree... 195s Reading state information... 195s Starting pkgProblemResolver with broken count: 0 195s Starting 2 pkgProblemResolver with broken count: 0 195s Done 196s The following additional packages will be installed: 196s python3-dateutil python3-iniconfig python3-packaging python3-pandas 196s python3-pandas-lib python3-pluggy python3-pytest python3-testfixtures 196s Suggested packages: 196s python-pandas-doc python3-statsmodels python-testfixtures-doc 196s Recommended packages: 196s python3-scipy python3-matplotlib python3-bottleneck python3-numexpr 196s python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml 196s python3-tables 196s The following NEW packages will be installed: 196s autopkgtest-satdep python3-dateutil python3-iniconfig python3-packaging 196s python3-pandas python3-pandas-lib python3-pluggy python3-pytest 196s python3-testfixtures 196s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 196s Need to get 11.2 MB/11.2 MB of archives. 196s After this operation, 63.5 MB of additional disk space will be used. 196s Get:1 /tmp/autopkgtest.LK7mh5/3-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [740 B] 196s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 196s Get:3 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 196s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 196s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 197s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 197s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pluggy all 1.4.0-1 [20.4 kB] 197s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pytest all 7.4.4-1 [305 kB] 197s Get:9 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-testfixtures all 8.1.0-1 [73.5 kB] 198s Fetched 11.2 MB in 1s (8988 kB/s) 198s Selecting previously unselected package python3-dateutil. 198s (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 ... 76919 files and directories currently installed.) 198s Preparing to unpack .../0-python3-dateutil_2.8.2-3_all.deb ... 198s Unpacking python3-dateutil (2.8.2-3) ... 198s Selecting previously unselected package python3-iniconfig. 198s Preparing to unpack .../1-python3-iniconfig_1.1.1-2_all.deb ... 198s Unpacking python3-iniconfig (1.1.1-2) ... 198s Selecting previously unselected package python3-packaging. 198s Preparing to unpack .../2-python3-packaging_23.2-1_all.deb ... 198s Unpacking python3-packaging (23.2-1) ... 198s Selecting previously unselected package python3-pandas-lib:arm64. 198s Preparing to unpack .../3-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ... 198s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 198s Selecting previously unselected package python3-pandas. 198s Preparing to unpack .../4-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 198s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 199s Selecting previously unselected package python3-pluggy. 199s Preparing to unpack .../5-python3-pluggy_1.4.0-1_all.deb ... 199s Unpacking python3-pluggy (1.4.0-1) ... 199s Selecting previously unselected package python3-pytest. 199s Preparing to unpack .../6-python3-pytest_7.4.4-1_all.deb ... 199s Unpacking python3-pytest (7.4.4-1) ... 199s Selecting previously unselected package python3-testfixtures. 199s Preparing to unpack .../7-python3-testfixtures_8.1.0-1_all.deb ... 199s Unpacking python3-testfixtures (8.1.0-1) ... 199s Selecting previously unselected package autopkgtest-satdep. 199s Preparing to unpack .../8-3-autopkgtest-satdep.deb ... 199s Unpacking autopkgtest-satdep (0) ... 199s Setting up python3-iniconfig (1.1.1-2) ... 199s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 199s Setting up python3-testfixtures (8.1.0-1) ... 199s Setting up python3-packaging (23.2-1) ... 199s Setting up python3-pluggy (1.4.0-1) ... 199s Setting up python3-dateutil (2.8.2-3) ... 200s Setting up python3-pytest (7.4.4-1) ... 200s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 204s Setting up autopkgtest-satdep (0) ... 204s Processing triggers for man-db (2.12.0-3) ... 208s (Reading database ... 78932 files and directories currently installed.) 208s Removing autopkgtest-satdep (0) ... 209s autopkgtest [17:59:05]: test command1: pytest-3 209s autopkgtest [17:59:05]: test command1: [----------------------- 211s ============================= test session starts ============================== 211s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 211s rootdir: /tmp/autopkgtest.LK7mh5/build.Ala/src 211s configfile: pytest.ini 211s 211s ----------------------------- live log collection ------------------------------ 211s WARNING py.warnings:warnings.py:110 /tmp/autopkgtest.LK7mh5/build.Ala/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 211s @pytest.mark.long_test 211s 211s ERROR regression_test:regression_test.py:173 Need to reinstate the --apbs-input test with a temporary directory as path 211s collected 316 items 211s 211s tests/core_test.py::test_short_pdb[1AQO] SKIPPED (not running tests ...) [ 0%] 211s tests/core_test.py::test_short_pdb[4E8M] SKIPPED (not running tests ...) [ 0%] 211s tests/core_test.py::test_short_pdb[1NAJ] SKIPPED (not running tests ...) [ 0%] 211s tests/core_test.py::test_short_pdb[1FAS] SKIPPED (not running tests ...) [ 1%] 211s tests/core_test.py::test_short_pdb[7BNA] SKIPPED (not running tests ...) [ 1%] 211s tests/core_test.py::test_short_pdb[4UN3] SKIPPED (not running tests ...) [ 1%] 211s tests/core_test.py::test_short_pdb[5D8V] SKIPPED (not running tests ...) [ 2%] 211s tests/core_test.py::test_short_pdb[1K1I] SKIPPED (not running tests ...) 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[ 58%] 211s tests/core_test.py::test_long_pdb[1PDO] SKIPPED (not running tests r...) [ 58%] 211s tests/core_test.py::test_long_pdb[1Z0P] SKIPPED (not running tests r...) [ 58%] 211s tests/core_test.py::test_long_pdb[4ZQA] SKIPPED (not running tests r...) [ 59%] 211s tests/core_test.py::test_long_pdb[1USE] SKIPPED (not running tests r...) [ 59%] 211s tests/core_test.py::test_long_pdb[2OP6] SKIPPED (not running tests r...) [ 59%] 211s tests/core_test.py::test_long_pdb[2G7O] SKIPPED (not running tests r...) [ 60%] 211s tests/core_test.py::test_long_pdb[5V0O] SKIPPED (not running tests r...) [ 60%] 211s tests/core_test.py::test_long_pdb[1LN4] SKIPPED (not running tests r...) [ 60%] 211s tests/core_test.py::test_long_pdb[2NSN] SKIPPED (not running tests r...) [ 61%] 211s tests/core_test.py::test_long_pdb[2FI9] SKIPPED (not running tests r...) [ 61%] 211s tests/core_test.py::test_long_pdb[4L9E] SKIPPED (not running tests r...) [ 61%] 211s tests/core_test.py::test_long_pdb[3S0A] SKIPPED (not running tests r...) [ 62%] 211s tests/core_test.py::test_long_pdb[1TQG] SKIPPED (not running tests r...) [ 62%] 211s tests/core_test.py::test_long_pdb[1KFN] SKIPPED (not running tests r...) [ 62%] 211s tests/core_test.py::test_long_pdb[2D8E] SKIPPED (not running tests r...) [ 62%] 211s tests/core_test.py::test_long_pdb[2H2C] SKIPPED (not running tests r...) [ 63%] 211s tests/core_test.py::test_long_pdb[1UG4] SKIPPED (not running tests r...) [ 63%] 211s tests/core_test.py::test_long_pdb[3HRO] SKIPPED (not running tests r...) [ 63%] 211s tests/core_test.py::test_long_pdb[2FWG] SKIPPED (not running tests r...) [ 64%] 211s tests/core_test.py::test_long_pdb[2JCP] SKIPPED (not running tests r...) [ 64%] 211s tests/core_test.py::test_long_pdb[1X91] SKIPPED (not running tests r...) [ 64%] 211s tests/core_test.py::test_long_pdb[2J6B] SKIPPED (not running tests r...) [ 65%] 211s tests/core_test.py::test_long_pdb[4EO0] SKIPPED (not running tests r...) [ 65%] 211s tests/core_test.py::test_long_pdb[5EE2] SKIPPED (not running tests r...) [ 65%] 211s tests/core_test.py::test_long_pdb[1NOA] SKIPPED (not running tests r...) [ 66%] 211s tests/core_test.py::test_broken_backbone[3U7T] 211s -------------------------------- live log call --------------------------------- 211s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_3U7T_0/3U7T.log 211s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 211s 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). 211s 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). 211s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 211s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 211s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T 212s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 212s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 212s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 652 atoms. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in PRO A 22. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in PRO A 22. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in PRO A 22. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in PRO A 22. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 22. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in PRO A 22. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in PRO A 22. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 22. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 22. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in PRO A 22. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 22. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in PRO A 22. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 22. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 22. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 22. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 22. 212s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 22. At least one of the instances is being ignored. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in LEU A 25. 212s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in LEU A 25. At least one of the instances is being ignored. 212s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 212s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 213s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 213s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 213s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 213s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 213s 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 213s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 213s XFAIL [ 66%] 213s tests/core_test.py::test_broken_backbone[4MGP] 213s -------------------------------- live log call --------------------------------- 213s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_4MGP_0/4MGP.log 213s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 213s 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). 213s 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). 213s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 213s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 213s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP 214s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 214s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 214s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 23 residues and 163 atoms. 214s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in MET A 21. 214s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in MET A 21. 214s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in MET A 21. 214s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: SD in MET A 21. 214s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE in MET A 21. 214s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in MET A 21. At least one of the instances is being ignored. 214s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 214s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 214s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 214s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 12 missing atoms in biomolecule. 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 214s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 11 at coordinates 1.430, -1.683, -11.529 214s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 11 at coordinates 1.940, -0.315, -11.800 214s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CG to residue LYS A 14 at coordinates -1.600, -8.819, -6.913 214s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CD to residue LYS A 14 at coordinates -2.056, -8.844, -8.361 214s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 14 at coordinates -3.548, -9.031, -8.498 214s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 14 at coordinates -3.947, -9.048, -9.928 214s 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 214s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 214s XFAIL [ 66%] 214s tests/core_test.py::test_broken_backbone[2V75] 214s -------------------------------- live log call --------------------------------- 214s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_2V75_0/2V75.log 214s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 214s 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). 214s 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). 214s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 214s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 214s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 214s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 214s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 214s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 90 residues and 687 atoms. 214s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 214s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 214s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 214s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 8 missing atoms in biomolecule. 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 214s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 214s 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 214s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 214s XFAIL [ 67%] 214s tests/core_test.py::test_broken_backbone[1EJG] 214s -------------------------------- live log call --------------------------------- 214s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_1EJG_0/1EJG.log 214s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 214s 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). 214s 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). 214s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 214s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 215s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG 215s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 215s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 215s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 650 atoms. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in THR A 1. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 1. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 1. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 1. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 1. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H1 in THR A 1. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H2 in THR A 1. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H3 in THR A 1. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 1. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 1. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 1. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 1. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 1. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 1. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 1. At least one of the instances is being ignored. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 2. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 2. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 2. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 2. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 2. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 2. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 2. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 2. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 2. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 2. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 2. At least one of the instances is being ignored. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 7. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 7. At least one of the instances is being ignored. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in VAL A 8. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in VAL A 8. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in VAL A 8. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in VAL A 8. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in VAL A 8. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in VAL A 8. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in VAL A 8. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in VAL A 8. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG11 in VAL A 8. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in VAL A 8. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in VAL A 8. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in VAL A 8. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in VAL A 8. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in VAL A 8. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in VAL A 8. At least one of the instances is being ignored. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NE in ARG A 10. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in ARG A 10. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH1 in ARG A 10. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH2 in ARG A 10. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE in ARG A 10. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH11 in ARG A 10. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH12 in ARG A 10. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH21 in ARG A 10. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH22 in ARG A 10. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ARG A 10. At least one of the instances is being ignored. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ASN A 12. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASN A 12. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 12. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 12. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 12. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ASN A 12. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASN A 12. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASN A 12. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 12. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 12. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 12. At least one of the instances is being ignored. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PHE A 13. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in PHE A 13. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in PHE A 13. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in PHE A 13. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in PHE A 13. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in PHE A 13. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in PHE A 13. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PHE A 13. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in PHE A 13. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in PHE A 13. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HZ in PHE A 13. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PHE A 13. At least one of the instances is being ignored. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 19. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 19. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 19. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 19. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 19. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 19. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 19. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 19. At least one of the instances is being ignored. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in SER A 22. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in SER A 22. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in SER A 22. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in SER A 22. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in SER A 22. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in SER A 22. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in SER A 22. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in SER A 22. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in SER A 22. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in SER A 22. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in SER A 22. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in SER A 22. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in SER A 22. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in SER A 22. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in SER A 22. At least one of the instances is being ignored. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in GLU A 23. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in GLU A 23. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE1 in GLU A 23. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE2 in GLU A 23. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in GLU A 23. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in GLU A 23. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in GLU A 23. At least one of the instances is being ignored. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 25. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 25. At least one of the instances is being ignored. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in TYR A 29. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in TYR A 29. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in TYR A 29. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in TYR A 29. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in TYR A 29. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in TYR A 29. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OH in TYR A 29. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in TYR A 29. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in TYR A 29. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in TYR A 29. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in TYR A 29. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH in TYR A 29. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in TYR A 29. At least one of the instances is being ignored. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 34. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 34. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 34. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 34. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 34. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 34. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 34. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 34. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 34. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 34. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 34. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 34. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 34. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 34. At least one of the instances is being ignored. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 36. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 36. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 36. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 36. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 36. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 36. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 36. At least one of the instances is being ignored. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 39. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 39. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 39. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 39. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 39. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 39. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 39. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 39. At least one of the instances is being ignored. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASP A 43. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASP A 43. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASP A 43. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD2 in ASP A 43. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASP A 43. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASP A 43. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASP A 43. At least one of the instances is being ignored. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 46. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 46. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 46. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 46. 215s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 46. 215s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 46. At least one of the instances is being ignored. 215s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 215s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 215s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 215s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 215s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 215s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 215s 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 215s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 215s XFAIL [ 67%] 215s tests/core_test.py::test_protonated_terminals[C-terminal HID] 215s -------------------------------- live log call --------------------------------- 215s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log 215s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 215s 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). 215s 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). 215s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 215s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 215s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/cterm_hid.pdb 215s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 215s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms. 215s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 215s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 215s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 215s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 215s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 215s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule. 215s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 215s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402 215s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 215s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 215s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 215s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 215s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 215s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 215s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 215s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 215s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 215s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 216s INFO common:common.py:198 0 atoms have position differences > 0 216s INFO common:common.py:198 0 atoms have position differences > 0.01 216s INFO common:common.py:198 0 atoms have charge differences > 0 216s INFO common:common.py:198 0 atoms have charge differences > 0.01 216s INFO common:common.py:198 0 atoms have radius differences > 0 216s INFO common:common.py:198 0 atoms have radius differences > 0.01 216s PASSED [ 67%] 216s tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 216s -------------------------------- live log call --------------------------------- 216s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log 216s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 216s 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). 216s 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). 216s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 216s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 216s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/5vav_cyclic_peptide.pdb 216s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 216s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms. 216s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 216s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 216s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 216s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 216s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 216s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 216s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 216s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 216s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 216s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 216s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 216s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 216s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 216s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 216s INFO common:common.py:198 0 atoms have position differences > 0 216s INFO common:common.py:198 0 atoms have position differences > 0.01 216s INFO common:common.py:198 0 atoms have charge differences > 0 216s INFO common:common.py:198 0 atoms have charge differences > 0.01 216s INFO common:common.py:198 0 atoms have radius differences > 0 216s INFO common:common.py:198 0 atoms have radius differences > 0.01 216s PASSED [ 68%] 216s tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 68%] 216s tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 68%] 216s tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 68%] 216s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 69%] 216s tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 69%] 216s tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 69%] 216s tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 70%] 216s tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 70%] 216s tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 70%] 216s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 71%] 216s tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 71%] 216s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 71%] 216s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 72%] 216s tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 72%] 216s 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 [ 72%] 216s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 73%] 216s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 73%] 216s tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 73%] 216s tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 74%] 216s tests/io_test.py::test_read_qcd PASSED [ 74%] 216s tests/io_test.py::test_dx2cube 216s -------------------------------- live log call --------------------------------- 216s INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... 216s INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... 217s INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 218s INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 218s INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... 219s INFO io_test:io_test.py:68 No differences found in output 219s PASSED [ 74%] 219s tests/ligand_test.py::test_peoe_charges 219s -------------------------------- live log call --------------------------------- 219s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 219s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 219s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 219s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 219s PASSED [ 75%] 220s tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 220s -------------------------------- live log call --------------------------------- 220s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 220s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 220s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 220s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 220s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 220s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 220s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 220s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 220s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 220s PASSED [ 75%] 220s tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 220s -------------------------------- live log call --------------------------------- 220s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 220s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 220s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 220s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 220s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 220s PASSED [ 75%] 220s tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 220s -------------------------------- live log call --------------------------------- 220s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 220s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 220s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 220s PASSED [ 75%] 220s tests/ligand_test.py::test_assign_parameters[acetate.mol2] 220s -------------------------------- live log call --------------------------------- 220s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 221s PASSED [ 76%] 221s tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 221s -------------------------------- live log call --------------------------------- 221s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 221s PASSED [ 76%] 221s tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 221s -------------------------------- live log call --------------------------------- 221s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 221s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 221s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 221s PASSED [ 76%] 221s tests/ligand_test.py::test_assign_parameters[adp.mol2] 221s -------------------------------- live log call --------------------------------- 221s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 221s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 221s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 221s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 221s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 221s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 221s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 221s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 221s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 221s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 221s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 221s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 221s INFO ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00 221s PASSED [ 77%] 221s tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 221s -------------------------------- live log call --------------------------------- 221s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 221s PASSED [ 77%] 221s tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 221s -------------------------------- live log call --------------------------------- 221s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 221s PASSED [ 77%] 221s tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 221s -------------------------------- live log call --------------------------------- 221s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 221s PASSED [ 78%] 221s tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 221s -------------------------------- live log call --------------------------------- 221s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 221s PASSED [ 78%] 221s tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 221s -------------------------------- live log call --------------------------------- 221s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 221s PASSED [ 78%] 221s tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 221s -------------------------------- live log call --------------------------------- 221s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 221s PASSED [ 79%] 221s tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 221s -------------------------------- live log call --------------------------------- 221s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 221s PASSED [ 79%] 221s tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 221s -------------------------------- live log call --------------------------------- 221s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 221s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 221s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 221s PASSED [ 79%] 221s tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 221s -------------------------------- live log call --------------------------------- 221s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 221s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 221s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 221s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 221s PASSED [ 80%] 222s tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 222s -------------------------------- live log call --------------------------------- 222s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 222s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 222s PASSED [ 80%] 222s tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 222s -------------------------------- live log call --------------------------------- 222s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 222s PASSED [ 80%] 222s tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED [ 81%] 222s tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED [ 81%] 222s tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 222s -------------------------------- live log call --------------------------------- 222s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 222s PASSED [ 81%] 222s tests/ligand_test.py::test_formal_charge[adp.mol2] 222s -------------------------------- live log call --------------------------------- 222s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 222s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 222s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 222s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 222s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 222s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 222s PASSED [ 81%] 222s tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED [ 82%] 222s tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED [ 82%] 222s tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED [ 82%] 222s tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED [ 83%] 222s tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED [ 83%] 222s tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED [ 83%] 222s tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED [ 84%] 222s tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 222s -------------------------------- live log call --------------------------------- 222s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 222s PASSED [ 84%] 222s tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED [ 84%] 222s tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED [ 85%] 222s tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED [ 85%] 222s tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED [ 85%] 222s tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED [ 86%] 222s tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED [ 86%] 222s tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED [ 86%] 223s tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED [ 87%] 223s tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED [ 87%] 223s tests/ligand_test.py::test_rings[acetate.mol2] PASSED [ 87%] 223s tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED [ 87%] 223s tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED [ 88%] 223s tests/ligand_test.py::test_rings[adp.mol2] PASSED [ 88%] 223s tests/ligand_test.py::test_rings[anthracene.mol2] PASSED [ 88%] 223s tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED [ 89%] 223s tests/ligand_test.py::test_rings[ethanol.mol2] PASSED [ 89%] 223s tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED [ 89%] 223s tests/ligand_test.py::test_rings[glycerol.mol2] PASSED [ 90%] 223s tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED [ 90%] 223s tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED [ 90%] 223s tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED [ 91%] 223s tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%] 223s tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%] 223s tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%] 223s tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%] 223s tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%] 223s tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%] 223s tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%] 223s tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%] 223s tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%] 223s tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%] 223s tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%] 223s tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] 223s tests/regression_test.py::test_basic[1AFS basic local] 223s -------------------------------- live log call --------------------------------- 223s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_basic_1AFS_basic_local_0/output.log 223s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 223s 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). 223s 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). 223s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 223s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 223s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 223s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 223s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 223s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 223s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 223s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 223s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 223s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 223s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 223s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 223s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 223s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 223s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 223s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 223s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 223s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 223s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 223s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 223s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 223s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 223s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 223s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 224s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 225s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 226s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 228s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 228s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 228s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 228s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 228s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 228s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 228s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 228s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 228s WARNING pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages 228s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 228s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 228s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 228s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 228s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 228s WARNING common:common.py:186 6 atoms have position differences > 0 228s INFO common:common.py:198 0 atoms have position differences > 0.01 228s INFO common:common.py:198 0 atoms have charge differences > 0 228s INFO common:common.py:198 0 atoms have charge differences > 0.01 228s INFO common:common.py:198 0 atoms have radius differences > 0 228s INFO common:common.py:198 0 atoms have radius differences > 0.01 228s PASSED [ 95%] 228s tests/regression_test.py::test_forcefields[1AFS whitespace AMBER] 228s -------------------------------- live log call --------------------------------- 228s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa0/output.log 228s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 228s 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). 228s 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). 228s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 228s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 228s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 228s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 228s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 228s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 228s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 228s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 228s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 228s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 228s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 228s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 228s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 228s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 228s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 228s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 228s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 228s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 228s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 228s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 228s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 228s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 228s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 228s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 228s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 229s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 232s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 232s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 232s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 232s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 232s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 232s WARNING common:common.py:186 6 atoms have position differences > 0 232s INFO common:common.py:198 0 atoms have position differences > 0.01 232s INFO common:common.py:198 0 atoms have charge differences > 0 232s INFO common:common.py:198 0 atoms have charge differences > 0.01 232s INFO common:common.py:198 0 atoms have radius differences > 0 232s INFO common:common.py:198 0 atoms have radius differences > 0.01 232s PASSED [ 95%] 232s tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] 232s -------------------------------- live log call --------------------------------- 232s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa1/output.log 232s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 232s 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). 232s 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). 232s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 232s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 232s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 232s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 233s WARNING pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages 233s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 233s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 233s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 233s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 233s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 233s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 233s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 233s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 233s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 233s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 233s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 233s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 233s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 233s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 233s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 233s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 233s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 234s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 237s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 237s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 237s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 237s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 237s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 237s WARNING common:common.py:186 5 atoms have position differences > 0 237s INFO common:common.py:198 0 atoms have position differences > 0.01 237s INFO common:common.py:198 0 atoms have charge differences > 0 237s INFO common:common.py:198 0 atoms have charge differences > 0.01 237s INFO common:common.py:198 0 atoms have radius differences > 0 237s INFO common:common.py:198 0 atoms have radius differences > 0.01 237s PASSED [ 95%] 237s tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] 237s -------------------------------- live log call --------------------------------- 237s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa2/output.log 237s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 237s 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). 237s 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). 237s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 237s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 237s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 237s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 237s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 237s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 237s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 237s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 237s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 237s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 237s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 237s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 237s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 237s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 237s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 237s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 237s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 237s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 237s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 237s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 238s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 239s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 242s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 242s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 242s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 242s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 242s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 242s WARNING common:common.py:186 6 atoms have position differences > 0 242s INFO common:common.py:198 0 atoms have position differences > 0.01 242s INFO common:common.py:198 0 atoms have charge differences > 0 242s INFO common:common.py:198 0 atoms have charge differences > 0.01 242s INFO common:common.py:198 0 atoms have radius differences > 0 242s INFO common:common.py:198 0 atoms have radius differences > 0.01 242s PASSED [ 96%] 242s tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] 242s -------------------------------- live log call --------------------------------- 242s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa3/output.log 242s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 242s 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). 242s 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). 242s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 242s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 242s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 242s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 242s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 242s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 242s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 242s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 242s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 242s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 242s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 242s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 242s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 242s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 242s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 242s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 242s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 242s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 242s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 242s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 243s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 243s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 246s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 246s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 246s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 246s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 246s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 246s WARNING common:common.py:186 6 atoms have position differences > 0 246s INFO common:common.py:198 0 atoms have position differences > 0.01 246s INFO common:common.py:198 0 atoms have charge differences > 0 246s INFO common:common.py:198 0 atoms have charge differences > 0.01 246s INFO common:common.py:198 0 atoms have radius differences > 0 246s INFO common:common.py:198 0 atoms have radius differences > 0.01 246s PASSED [ 96%] 246s tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] 246s -------------------------------- live log call --------------------------------- 246s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa4/output.log 246s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 246s 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). 246s 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). 246s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 246s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 247s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 247s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 247s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 247s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 247s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 247s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 247s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 247s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 247s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 247s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 247s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 247s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 247s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 247s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 247s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 247s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 247s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 247s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 247s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 248s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 255s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 255s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 255s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 255s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output. 255s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 255s WARNING common:common.py:186 6 atoms have position differences > 0 255s INFO common:common.py:198 0 atoms have position differences > 0.01 255s INFO common:common.py:198 0 atoms have charge differences > 0 255s INFO common:common.py:198 0 atoms have charge differences > 0.01 255s INFO common:common.py:198 0 atoms have radius differences > 0 255s INFO common:common.py:198 0 atoms have radius differences > 0.01 255s PASSED [ 96%] 255s tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] 255s -------------------------------- live log call --------------------------------- 255s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa5/output.log 255s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 255s 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). 255s 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). 255s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 255s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 255s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 255s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 255s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 255s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 255s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 255s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 255s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 255s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 255s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 255s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 255s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 255s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 255s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 255s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 255s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 255s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 255s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 255s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 255s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 255s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 255s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 255s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 255s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 255s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 255s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 255s WARNING common:common.py:186 6 atoms have position differences > 0 255s INFO common:common.py:198 0 atoms have position differences > 0.01 255s INFO common:common.py:198 0 atoms have charge differences > 0 255s INFO common:common.py:198 0 atoms have charge differences > 0.01 255s INFO common:common.py:198 0 atoms have radius differences > 0 255s INFO common:common.py:198 0 atoms have radius differences > 0.01 255s PASSED [ 97%] 255s tests/regression_test.py::test_other_options[1AFS whitespace clean] 255s -------------------------------- live log call --------------------------------- 255s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_whites0/output.log 255s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 255s 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). 255s 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). 255s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 255s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 256s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 256s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 256s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 256s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 256s INFO PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps. 256s INFO common:common.py:198 0 atoms have position differences > 0 256s INFO common:common.py:198 0 atoms have position differences > 0.01 256s INFO common:common.py:198 0 atoms have charge differences > 0 256s INFO common:common.py:198 0 atoms have charge differences > 0.01 256s INFO common:common.py:198 0 atoms have radius differences > 0 256s INFO common:common.py:198 0 atoms have radius differences > 0.01 256s PASSED [ 97%] 256s tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] 256s -------------------------------- live log call --------------------------------- 256s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_assign0/output.log 256s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 256s 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). 256s 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). 256s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 256s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 256s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 256s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 256s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 256s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 256s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 256s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 256s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 256s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 256s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 256s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 256s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 256s INFO common:common.py:198 0 atoms have position differences > 0 256s INFO common:common.py:198 0 atoms have position differences > 0.01 256s INFO common:common.py:198 0 atoms have charge differences > 0 256s INFO common:common.py:198 0 atoms have charge differences > 0.01 256s INFO common:common.py:198 0 atoms have radius differences > 0 256s INFO common:common.py:198 0 atoms have radius differences > 0.01 256s PASSED [ 97%] 256s tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] 256s -------------------------------- live log call --------------------------------- 256s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_nodebu0/output.log 256s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 256s 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). 256s 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). 256s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 256s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 256s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 256s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 256s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 256s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 256s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 256s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 256s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 256s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 256s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 256s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 256s INFO pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization... 256s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 256s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 256s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 256s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 256s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 256s INFO common:common.py:198 0 atoms have position differences > 0 256s INFO common:common.py:198 0 atoms have position differences > 0.01 256s INFO common:common.py:198 0 atoms have charge differences > 0 256s INFO common:common.py:198 0 atoms have charge differences > 0.01 256s INFO common:common.py:198 0 atoms have radius differences > 0 256s INFO common:common.py:198 0 atoms have radius differences > 0.01 256s PASSED [ 98%] 256s tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] 256s -------------------------------- live log call --------------------------------- 256s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_chain_0/output.log 256s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 256s 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). 256s 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). 256s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 256s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 256s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 256s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 256s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 256s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 256s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 256s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 256s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 256s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 256s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 256s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 256s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 256s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 256s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 256s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 256s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 256s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 256s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 256s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 258s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 258s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 260s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 260s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 260s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 260s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 260s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 261s WARNING common:common.py:186 6 atoms have position differences > 0 261s INFO common:common.py:198 0 atoms have position differences > 0.01 261s INFO common:common.py:198 0 atoms have charge differences > 0 261s INFO common:common.py:198 0 atoms have charge differences > 0.01 261s INFO common:common.py:198 0 atoms have radius differences > 0 261s INFO common:common.py:198 0 atoms have radius differences > 0.01 261s PASSED [ 98%] 261s tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] 261s -------------------------------- live log call --------------------------------- 261s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_neutra0/output.log 261s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 261s 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). 261s 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). 261s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 261s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 261s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 261s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 263s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 263s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 263s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 263s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 263s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 263s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 263s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 263s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 263s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 263s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 263s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 263s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 266s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 266s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 266s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 266s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 266s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 266s WARNING common:common.py:186 6 atoms have position differences > 0 266s INFO common:common.py:198 0 atoms have position differences > 0.01 266s INFO common:common.py:198 0 atoms have charge differences > 0 266s INFO common:common.py:198 0 atoms have charge differences > 0.01 266s INFO common:common.py:198 0 atoms have radius differences > 0 266s INFO common:common.py:198 0 atoms have radius differences > 0.01 266s PASSED [ 98%] 266s tests/regression_test.py::test_other_options[1AFS drop-water AMBER] 266s -------------------------------- live log call --------------------------------- 266s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_drop_w0/output.log 266s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 266s 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). 266s 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). 266s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 266s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 266s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 266s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 266s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 266s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms. 266s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 266s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 266s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 266s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 266s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 266s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 266s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 266s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 266s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 266s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 266s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 266s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 266s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 266s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 266s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 266s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 267s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 269s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 269s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 269s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 269s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 269s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 269s WARNING common:common.py:186 6 atoms have position differences > 0 269s INFO common:common.py:198 0 atoms have position differences > 0.01 269s INFO common:common.py:198 0 atoms have charge differences > 0 269s INFO common:common.py:198 0 atoms have charge differences > 0.01 269s INFO common:common.py:198 0 atoms have radius differences > 0 269s INFO common:common.py:198 0 atoms have radius differences > 0.01 269s PASSED [ 99%] 269s tests/regression_test.py::test_other_options[1AFS userff usernames whitespace] 269s -------------------------------- live log call --------------------------------- 269s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_userff0/output.log 269s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 269s 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). 269s 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). 269s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 269s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 269s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 269s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 269s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 269s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 269s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 269s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 269s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 269s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 269s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 269s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 269s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 269s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 269s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 269s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 269s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 269s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 269s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 270s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 270s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 271s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 275s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 275s autopkgtest [18:00:11]: test command1: -----------------------] 275s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 275s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 275s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 275s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 275s WARNING common:common.py:186 6 atoms have position differences > 0 275s INFO common:common.py:198 0 atoms have position differences > 0.01 275s INFO common:common.py:198 0 atoms have charge differences > 0 275s INFO common:common.py:198 0 atoms have charge differences > 0.01 275s INFO common:common.py:198 0 atoms have radius differences > 0 275s INFO common:common.py:198 0 atoms have radius differences > 0.01 275s PASSED [ 99%] 275s tests/test_version.py::test_version_exists PASSED [ 99%] 275s tests/test_version.py::test_version PASSED [100%] 275s 275s =============================== warnings summary =============================== 275s ../../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37 275s /usr/lib/python3/dist-packages/dateutil/tz/tz.py:37: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC). 275s EPOCH = datetime.datetime.utcfromtimestamp(0) 275s 275s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 275s ======= 92 passed, 220 skipped, 4 xfailed, 1 warning in 63.97s (0:01:03) ======= 276s command1 PASS 276s autopkgtest [18:00:12]: test command1: - - - - - - - - - - results - - - - - - - - - - 276s autopkgtest [18:00:12]: @@@@@@@@@@@@@@@@@@@@ summary 276s installation-test PASS 276s pdb2pka-test PASS 276s command1 PASS 280s Creating nova instance adt-noble-arm64-pdb2pqr-20240323-174135-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240321.img (UUID 28ecccfc-4cb0-4cc6-a280-209e2d140e10)...