0s autopkgtest [07:12:29]: starting date and time: 2025-10-29 07:12:29+0000 0s autopkgtest [07:12:29]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [07:12:29]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.0p55_mew/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:node-jquery --apt-upgrade pdb2pqr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=node-jquery/3.7.1+dfsg+~3.5.33-1build1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-4.secgroup --name adt-resolute-arm64-pdb2pqr-20251029-071229-juju-7f2275-prod-proposed-migration-environment-2-dd83fa6c-2e8a-4a09-81b0-4da30b1a9512 --image adt/ubuntu-resolute-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-arm64-pdb2pqr-20251029-071229-juju-7f2275-prod-proposed-migration-environment-2-dd83fa6c-2e8a-4a09-81b0-4da30b1a9512 from image adt/ubuntu-resolute-arm64-server-20251027.img (UUID 0c8717a7-1983-4858-8ad5-6d56cfcb3438)... 68s autopkgtest [07:13:37]: testbed dpkg architecture: arm64 68s autopkgtest [07:13:37]: testbed apt version: 3.1.8ubuntu1 69s autopkgtest [07:13:38]: @@@@@@@@@@@@@@@@@@@@ test bed setup 69s autopkgtest [07:13:38]: testbed release detected to be: None 70s autopkgtest [07:13:39]: updating testbed package index (apt update) 70s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 70s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 70s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 70s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 70s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [3645 kB] 72s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5856 B] 72s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [70.5 kB] 72s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [203 kB] 72s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 Packages [270 kB] 73s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 c-n-f Metadata [5404 B] 73s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 Packages [44.3 kB] 73s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/restricted arm64 c-n-f Metadata [324 B] 73s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 Packages [2440 kB] 73s Get:14 http://ftpmaster.internal/ubuntu resolute-proposed/universe arm64 c-n-f Metadata [58.0 kB] 73s Get:15 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 Packages [41.4 kB] 73s Get:16 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse arm64 c-n-f Metadata [536 B] 74s Fetched 6873 kB in 4s (1928 kB/s) 75s Reading package lists... 76s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 76s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 76s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 76s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 77s Reading package lists... 77s Reading package lists... 77s Building dependency tree... 77s Reading state information... 78s Calculating upgrade... 78s The following NEW packages will be installed: 78s util-linux-extra 78s The following packages will be upgraded: 78s apt bsdextrautils bsdutils cloud-init cloud-init-base fdisk libapt-pkg7.0 78s libblkid1 libefiboot1t64 libefivar1t64 libfdisk1 liblastlog2-2 libmount1 78s libsmartcols1 libuuid1 login mount python3-blinker python3-cffi-backend 78s python3-lazr.uri util-linux uuid-runtime 78s 22 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 78s Need to get 6061 kB of archives. 78s After this operation, 1866 kB of additional disk space will be used. 78s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 fdisk arm64 2.41.2-4ubuntu1 [149 kB] 79s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblkid1 arm64 2.41.2-4ubuntu1 [139 kB] 79s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libmount1 arm64 2.41.2-4ubuntu1 [173 kB] 79s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libsmartcols1 arm64 2.41.2-4ubuntu1 [96.2 kB] 79s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 mount arm64 2.41.2-4ubuntu1 [145 kB] 79s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 uuid-runtime arm64 2.41.2-4ubuntu1 [56.9 kB] 79s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 libuuid1 arm64 2.41.2-4ubuntu1 [45.3 kB] 79s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 libfdisk1 arm64 2.41.2-4ubuntu1 [173 kB] 79s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 bsdutils arm64 1:2.41.2-4ubuntu1 [93.0 kB] 79s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 util-linux arm64 2.41.2-4ubuntu1 [1082 kB] 79s Get:11 http://ftpmaster.internal/ubuntu resolute/main arm64 bsdextrautils arm64 2.41.2-4ubuntu1 [94.1 kB] 79s Get:12 http://ftpmaster.internal/ubuntu resolute/main arm64 login arm64 1:4.16.0-2+really2.41.2-4ubuntu1 [94.9 kB] 79s Get:13 http://ftpmaster.internal/ubuntu resolute/main arm64 liblastlog2-2 arm64 2.41.2-4ubuntu1 [35.7 kB] 79s Get:14 http://ftpmaster.internal/ubuntu resolute/main arm64 libapt-pkg7.0 arm64 3.1.11 [1063 kB] 80s Get:15 http://ftpmaster.internal/ubuntu resolute/main arm64 apt arm64 3.1.11 [1402 kB] 80s Get:16 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-cffi-backend arm64 2.0.0-2 [110 kB] 80s Get:17 http://ftpmaster.internal/ubuntu resolute/main arm64 cloud-init-base all 25.4~1gcb12e00e-0ubuntu1 [625 kB] 80s Get:18 http://ftpmaster.internal/ubuntu resolute/main arm64 cloud-init all 25.4~1gcb12e00e-0ubuntu1 [2114 B] 80s Get:19 http://ftpmaster.internal/ubuntu resolute/main arm64 libefivar1t64 arm64 39-2 [57.3 kB] 80s Get:20 http://ftpmaster.internal/ubuntu resolute/main arm64 libefiboot1t64 arm64 39-2 [40.1 kB] 80s Get:21 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-blinker all 1.9.0-2 [10.8 kB] 80s Get:22 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-lazr.uri all 1.0.6-7 [13.8 kB] 80s Get:23 http://ftpmaster.internal/ubuntu resolute/universe arm64 util-linux-extra arm64 2.41.2-4ubuntu1 [361 kB] 80s dpkg-preconfigure: unable to re-open stdin: No such file or directory 80s Fetched 6061 kB in 2s (3207 kB/s) 81s (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 ... 83387 files and directories currently installed.) 81s Preparing to unpack .../fdisk_2.41.2-4ubuntu1_arm64.deb ... 81s Unpacking fdisk (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 81s Preparing to unpack .../libblkid1_2.41.2-4ubuntu1_arm64.deb ... 81s Unpacking libblkid1:arm64 (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 81s Setting up libblkid1:arm64 (2.41.2-4ubuntu1) ... 81s (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 ... 83387 files and directories currently installed.) 81s Preparing to unpack .../libmount1_2.41.2-4ubuntu1_arm64.deb ... 81s Unpacking libmount1:arm64 (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 81s Setting up libmount1:arm64 (2.41.2-4ubuntu1) ... 81s (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 ... 83387 files and directories currently installed.) 81s Preparing to unpack .../libsmartcols1_2.41.2-4ubuntu1_arm64.deb ... 81s Unpacking libsmartcols1:arm64 (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 81s Setting up libsmartcols1:arm64 (2.41.2-4ubuntu1) ... 81s (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 ... 83387 files and directories currently installed.) 81s Preparing to unpack .../mount_2.41.2-4ubuntu1_arm64.deb ... 81s Unpacking mount (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 81s Preparing to unpack .../uuid-runtime_2.41.2-4ubuntu1_arm64.deb ... 81s Unpacking uuid-runtime (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 82s Preparing to unpack .../libuuid1_2.41.2-4ubuntu1_arm64.deb ... 82s Unpacking libuuid1:arm64 (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 82s Setting up libuuid1:arm64 (2.41.2-4ubuntu1) ... 82s (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 ... 83387 files and directories currently installed.) 82s Preparing to unpack .../libfdisk1_2.41.2-4ubuntu1_arm64.deb ... 82s Unpacking libfdisk1:arm64 (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 82s Preparing to unpack .../bsdutils_1%3a2.41.2-4ubuntu1_arm64.deb ... 82s Unpacking bsdutils (1:2.41.2-4ubuntu1) over (1:2.41-4ubuntu4) ... 82s Setting up bsdutils (1:2.41.2-4ubuntu1) ... 82s (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 ... 83384 files and directories currently installed.) 82s Preparing to unpack .../util-linux_2.41.2-4ubuntu1_arm64.deb ... 82s Unpacking util-linux (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 82s Setting up util-linux (2.41.2-4ubuntu1) ... 83s fstrim.service is a disabled or a static unit not running, not starting it. 83s (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 ... 83355 files and directories currently installed.) 83s Preparing to unpack .../bsdextrautils_2.41.2-4ubuntu1_arm64.deb ... 83s Unpacking bsdextrautils (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 83s Preparing to unpack .../login_1%3a4.16.0-2+really2.41.2-4ubuntu1_arm64.deb ... 83s Unpacking login (1:4.16.0-2+really2.41.2-4ubuntu1) over (1:4.16.0-2+really2.41-4ubuntu4) ... 83s Preparing to unpack .../liblastlog2-2_2.41.2-4ubuntu1_arm64.deb ... 83s Unpacking liblastlog2-2:arm64 (2.41.2-4ubuntu1) over (2.41-4ubuntu4) ... 83s Setting up liblastlog2-2:arm64 (2.41.2-4ubuntu1) ... 83s (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 ... 83350 files and directories currently installed.) 83s Preparing to unpack .../0-libapt-pkg7.0_3.1.11_arm64.deb ... 83s Unpacking libapt-pkg7.0:arm64 (3.1.11) over (3.1.8ubuntu1) ... 84s Preparing to unpack .../1-apt_3.1.11_arm64.deb ... 84s Unpacking apt (3.1.11) over (3.1.8ubuntu1) ... 84s Preparing to unpack .../2-python3-cffi-backend_2.0.0-2_arm64.deb ... 84s Unpacking python3-cffi-backend:arm64 (2.0.0-2) over (1.17.1-3build1) ... 84s Preparing to unpack .../3-cloud-init-base_25.4~1gcb12e00e-0ubuntu1_all.deb ... 84s Unpacking cloud-init-base (25.4~1gcb12e00e-0ubuntu1) over (25.3-0ubuntu1) ... 84s Preparing to unpack .../4-cloud-init_25.4~1gcb12e00e-0ubuntu1_all.deb ... 84s Unpacking cloud-init (25.4~1gcb12e00e-0ubuntu1) over (25.3-0ubuntu1) ... 85s Preparing to unpack .../5-libefivar1t64_39-2_arm64.deb ... 85s Unpacking libefivar1t64:arm64 (39-2) over (38-3.1build1) ... 85s Preparing to unpack .../6-libefiboot1t64_39-2_arm64.deb ... 85s Unpacking libefiboot1t64:arm64 (39-2) over (38-3.1build1) ... 85s Preparing to unpack .../7-python3-blinker_1.9.0-2_all.deb ... 85s Unpacking python3-blinker (1.9.0-2) over (1.9.0-1) ... 85s Preparing to unpack .../8-python3-lazr.uri_1.0.6-7_all.deb ... 85s Unpacking python3-lazr.uri (1.0.6-7) over (1.0.6-6) ... 85s Selecting previously unselected package util-linux-extra. 85s Preparing to unpack .../9-util-linux-extra_2.41.2-4ubuntu1_arm64.deb ... 85s Unpacking util-linux-extra (2.41.2-4ubuntu1) ... 85s Setting up bsdextrautils (2.41.2-4ubuntu1) ... 85s Setting up libefivar1t64:arm64 (39-2) ... 85s Setting up python3-lazr.uri (1.0.6-7) ... 85s Setting up cloud-init-base (25.4~1gcb12e00e-0ubuntu1) ... 85s Encountered debconf setting for cloud-init-base/datasources. 87s Setting up libfdisk1:arm64 (2.41.2-4ubuntu1) ... 87s Setting up mount (2.41.2-4ubuntu1) ... 87s Setting up uuid-runtime (2.41.2-4ubuntu1) ... 88s uuidd.service is a disabled or a static unit not running, not starting it. 88s Setting up libefiboot1t64:arm64 (39-2) ... 88s Setting up libapt-pkg7.0:arm64 (3.1.11) ... 88s Setting up util-linux-extra (2.41.2-4ubuntu1) ... 88s Setting up python3-cffi-backend:arm64 (2.0.0-2) ... 88s Setting up login (1:4.16.0-2+really2.41.2-4ubuntu1) ... 88s Setting up python3-blinker (1.9.0-2) ... 88s Setting up apt (3.1.11) ... 88s Installing new version of config file /etc/apt/apt.conf.d/01-vendor-ubuntu ... 88s Setting up cloud-init (25.4~1gcb12e00e-0ubuntu1) ... 88s Setting up fdisk (2.41.2-4ubuntu1) ... 88s Processing triggers for rsyslog (8.2504.0-1ubuntu2) ... 89s Processing triggers for man-db (2.13.1-1) ... 90s Processing triggers for libc-bin (2.42-0ubuntu3) ... 91s autopkgtest [07:14:00]: upgrading testbed (apt dist-upgrade and autopurge) 92s Reading package lists... 92s Building dependency tree... 92s Reading state information... 92s Calculating upgrade... 93s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s Solving dependencies... 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 94s autopkgtest [07:14:03]: rebooting testbed after setup commands that affected boot 120s autopkgtest [07:14:29]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 22 09:50:31 UTC 2025 123s autopkgtest [07:14:32]: @@@@@@@@@@@@@@@@@@@@ apt-source pdb2pqr 128s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (dsc) [1860 B] 128s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (tar) [7570 kB] 128s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (diff) [9876 B] 128s gpgv: Signature made Mon Jun 12 17:36:50 2023 UTC 128s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 128s gpgv: Can't check signature: No public key 128s dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found 129s autopkgtest [07:14:38]: testing package pdb2pqr version 3.6.1+dfsg-1 129s autopkgtest [07:14:38]: build not needed 132s autopkgtest [07:14:41]: test installation-test: preparing testbed 132s Reading package lists... 132s Building dependency tree... 132s Reading state information... 132s Solving dependencies... 133s The following NEW packages will be installed: 133s docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr python3-docutils 133s python3-numpy python3-numpy-dev python3-pdb2pqr python3-pdbx python3-propka 133s python3-roman sgml-base xml-core 133s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 133s Need to get 7931 kB of archives. 133s After this operation, 34.3 MB of additional disk space will be used. 133s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1ubuntu1 [146 kB] 133s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 libblas3 arm64 3.12.1-6build1 [186 kB] 134s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 libgfortran5 arm64 15.2.0-5ubuntu1 [450 kB] 134s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 liblapack3 arm64 3.12.1-6build1 [2340 kB] 135s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-numpy arm64 1:2.2.4+ds-1ubuntu1 [3986 kB] 137s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 sgml-base all 1.31+nmu1 [11.0 kB] 137s Get:7 http://ftpmaster.internal/ubuntu resolute/main arm64 xml-core all 0.19 [20.3 kB] 137s Get:8 http://ftpmaster.internal/ubuntu resolute/main arm64 docutils-common all 0.21.2+dfsg-2 [131 kB] 137s Get:9 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-roman all 5.1-1 [10.6 kB] 137s Get:10 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-docutils all 0.21.2+dfsg-2 [409 kB] 137s Get:11 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pdbx all 2.0.1-2 [16.5 kB] 137s Get:12 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-propka all 3.5.1-2 [70.1 kB] 137s Get:13 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pdb2pqr all 3.6.1+dfsg-1 [145 kB] 137s Get:14 http://ftpmaster.internal/ubuntu resolute/universe arm64 pdb2pqr all 3.6.1+dfsg-1 [10.4 kB] 138s Fetched 7931 kB in 4s (1847 kB/s) 138s Selecting previously unselected package python3-numpy-dev:arm64. 138s (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 ... 83457 files and directories currently installed.) 138s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 138s Unpacking python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 138s Selecting previously unselected package libblas3:arm64. 138s Preparing to unpack .../01-libblas3_3.12.1-6build1_arm64.deb ... 138s Unpacking libblas3:arm64 (3.12.1-6build1) ... 138s Selecting previously unselected package libgfortran5:arm64. 138s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_arm64.deb ... 138s Unpacking libgfortran5:arm64 (15.2.0-5ubuntu1) ... 138s Selecting previously unselected package liblapack3:arm64. 138s Preparing to unpack .../03-liblapack3_3.12.1-6build1_arm64.deb ... 138s Unpacking liblapack3:arm64 (3.12.1-6build1) ... 138s Selecting previously unselected package python3-numpy. 138s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_arm64.deb ... 138s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 138s Selecting previously unselected package sgml-base. 138s Preparing to unpack .../05-sgml-base_1.31+nmu1_all.deb ... 138s Unpacking sgml-base (1.31+nmu1) ... 138s Selecting previously unselected package xml-core. 138s Preparing to unpack .../06-xml-core_0.19_all.deb ... 138s Unpacking xml-core (0.19) ... 138s Selecting previously unselected package docutils-common. 138s Preparing to unpack .../07-docutils-common_0.21.2+dfsg-2_all.deb ... 138s Unpacking docutils-common (0.21.2+dfsg-2) ... 138s Selecting previously unselected package python3-roman. 138s Preparing to unpack .../08-python3-roman_5.1-1_all.deb ... 138s Unpacking python3-roman (5.1-1) ... 138s Selecting previously unselected package python3-docutils. 138s Preparing to unpack .../09-python3-docutils_0.21.2+dfsg-2_all.deb ... 138s Unpacking python3-docutils (0.21.2+dfsg-2) ... 138s Selecting previously unselected package python3-pdbx. 138s Preparing to unpack .../10-python3-pdbx_2.0.1-2_all.deb ... 138s Unpacking python3-pdbx (2.0.1-2) ... 138s Selecting previously unselected package python3-propka. 138s Preparing to unpack .../11-python3-propka_3.5.1-2_all.deb ... 138s Unpacking python3-propka (3.5.1-2) ... 138s Selecting previously unselected package python3-pdb2pqr. 138s Preparing to unpack .../12-python3-pdb2pqr_3.6.1+dfsg-1_all.deb ... 138s Unpacking python3-pdb2pqr (3.6.1+dfsg-1) ... 139s Selecting previously unselected package pdb2pqr. 139s Preparing to unpack .../13-pdb2pqr_3.6.1+dfsg-1_all.deb ... 139s Unpacking pdb2pqr (3.6.1+dfsg-1) ... 139s Setting up python3-propka (3.5.1-2) ... 139s Setting up python3-pdbx (2.0.1-2) ... 139s Setting up python3-roman (5.1-1) ... 139s Setting up libblas3:arm64 (3.12.1-6build1) ... 139s 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 139s Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1ubuntu1) ... 139s Setting up libgfortran5:arm64 (15.2.0-5ubuntu1) ... 139s Setting up sgml-base (1.31+nmu1) ... 139s Setting up liblapack3:arm64 (3.12.1-6build1) ... 139s 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 139s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 141s Setting up xml-core (0.19) ... 141s Processing triggers for libc-bin (2.42-0ubuntu3) ... 141s Processing triggers for man-db (2.13.1-1) ... 142s Processing triggers for sgml-base (1.31+nmu1) ... 142s Setting up docutils-common (0.21.2+dfsg-2) ... 142s Processing triggers for sgml-base (1.31+nmu1) ... 142s Setting up python3-docutils (0.21.2+dfsg-2) ... 143s Setting up python3-pdb2pqr (3.6.1+dfsg-1) ... 143s Setting up pdb2pqr (3.6.1+dfsg-1) ... 144s autopkgtest [07:14:53]: test installation-test: [----------------------- 144s Run pdb2pqr... 144s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 144s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 144s 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). 144s INFO:Checking and transforming input arguments. 144s INFO:Loading topology files. 144s INFO:Loading molecule: examples/1a1p/1a1p.pdb 144s INFO:Setting up molecule. 144s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 144s INFO:Created biomolecule object with 14 residues and 208 atoms. 144s INFO:Setting termini states for biomolecule chains. 144s INFO:Loading forcefield. 144s INFO:Loading hydrogen topology definitions. 144s INFO:This biomolecule is clean. No repair needed. 144s INFO:Updating disulfide bridges. 144s INFO:Debumping biomolecule. 144s INFO:Adding hydrogens to biomolecule. 144s INFO:Debumping biomolecule (again). 144s INFO:Optimizing hydrogen bonds 144s INFO:Applying force field to biomolecule states. 144s INFO:Regenerating headers. 144s INFO:Regenerating PDB lines. 144s WARNING:Ignoring 852 header lines in output. 144s WARNING:Ignoring 3 missing lines in output. 145s autopkgtest [07:14:54]: test installation-test: -----------------------] 145s autopkgtest [07:14:54]: test installation-test: - - - - - - - - - - results - - - - - - - - - - 145s installation-test PASS 146s autopkgtest [07:14:55]: test pdb2pka-test: preparing testbed 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 146s Solving dependencies... 147s The following NEW packages will be installed: 147s fonts-font-awesome fonts-lato libjs-jquery libjs-sphinxdoc libjs-underscore 147s pdb2pqr-doc sphinx-rtd-theme-common 147s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 147s Need to get 5035 kB of archives. 147s After this operation, 20.0 MB of additional disk space will be used. 147s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-lato all 2.015-1 [2781 kB] 148s Get:2 http://ftpmaster.internal/ubuntu resolute/main arm64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 149s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main arm64 libjs-jquery all 3.7.1+dfsg+~3.5.33-1build1 [321 kB] 149s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 149s Get:5 http://ftpmaster.internal/ubuntu resolute/main arm64 libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 149s Get:6 http://ftpmaster.internal/ubuntu resolute/main arm64 sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 149s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 pdb2pqr-doc all 3.6.1+dfsg-1 [258 kB] 149s Fetched 5035 kB in 2s (2455 kB/s) 149s Selecting previously unselected package fonts-lato. 149s (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 ... 84958 files and directories currently installed.) 149s Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... 149s Unpacking fonts-lato (2.015-1) ... 149s Selecting previously unselected package fonts-font-awesome. 149s Preparing to unpack .../1-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 149s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 150s Selecting previously unselected package libjs-jquery. 150s Preparing to unpack .../2-libjs-jquery_3.7.1+dfsg+~3.5.33-1build1_all.deb ... 150s Unpacking libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 150s Selecting previously unselected package libjs-underscore. 150s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 150s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 150s Selecting previously unselected package libjs-sphinxdoc. 150s Preparing to unpack .../4-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 150s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 150s Selecting previously unselected package sphinx-rtd-theme-common. 150s Preparing to unpack .../5-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 150s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 150s Selecting previously unselected package pdb2pqr-doc. 150s Preparing to unpack .../6-pdb2pqr-doc_3.6.1+dfsg-1_all.deb ... 150s Unpacking pdb2pqr-doc (3.6.1+dfsg-1) ... 150s Setting up fonts-lato (2.015-1) ... 150s Setting up libjs-jquery (3.7.1+dfsg+~3.5.33-1build1) ... 150s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 150s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 150s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 150s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 150s Setting up pdb2pqr-doc (3.6.1+dfsg-1) ... 151s autopkgtest [07:15:00]: test pdb2pka-test: [----------------------- 151s Run pdb2pqr... 152s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 152s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 152s 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). 152s INFO:Checking and transforming input arguments. 152s INFO:Loading topology files. 152s INFO:Loading molecule: 1a1p/1a1p.pdb 152s INFO:Setting up molecule. 152s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 152s INFO:Created biomolecule object with 14 residues and 208 atoms. 152s INFO:Setting termini states for biomolecule chains. 152s INFO:Loading forcefield. 152s INFO:Loading hydrogen topology definitions. 152s INFO:This biomolecule is clean. No repair needed. 152s INFO:Updating disulfide bridges. 152s INFO:Debumping biomolecule. 152s INFO:Adding hydrogens to biomolecule. 152s INFO:Debumping biomolecule (again). 152s INFO:Optimizing hydrogen bonds 152s INFO:Applying force field to biomolecule states. 152s INFO:Regenerating headers. 152s INFO:Regenerating PDB lines. 152s WARNING:Ignoring 852 header lines in output. 152s WARNING:Ignoring 3 missing lines in output. 152s autopkgtest [07:15:01]: test pdb2pka-test: -----------------------] 153s pdb2pka-test PASS 153s autopkgtest [07:15:02]: test pdb2pka-test: - - - - - - - - - - results - - - - - - - - - - 153s autopkgtest [07:15:02]: test command1: preparing testbed 153s Reading package lists... 153s Building dependency tree... 153s Reading state information... 154s Solving dependencies... 154s The following NEW packages will be installed: 154s python3-dateutil python3-iniconfig python3-packaging python3-pandas 154s python3-pandas-lib python3-pluggy python3-pytest python3-pytz 154s python3-testfixtures 155s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 155s Need to get 10.5 MB of archives. 155s After this operation, 64.4 MB of additional disk space will be used. 155s Get:1 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-dateutil all 2.9.0-4 [80.3 kB] 155s Get:2 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 155s Get:3 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-packaging all 25.0-1 [52.8 kB] 155s Get:4 http://ftpmaster.internal/ubuntu resolute/main arm64 python3-pytz all 2025.2-4 [32.3 kB] 155s Get:5 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas-lib arm64 2.3.3+dfsg-1ubuntu1 [6979 kB] 157s Get:6 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pandas all 2.3.3+dfsg-1ubuntu1 [2948 kB] 157s Get:7 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pluggy all 1.6.0-1 [21.0 kB] 157s Get:8 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-pytest all 8.3.5-2 [252 kB] 157s Get:9 http://ftpmaster.internal/ubuntu resolute/universe arm64 python3-testfixtures all 9.2.0-1 [79.2 kB] 157s Fetched 10.5 MB in 3s (3542 kB/s) 157s Selecting previously unselected package python3-dateutil. 157s (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 ... 85293 files and directories currently installed.) 157s Preparing to unpack .../0-python3-dateutil_2.9.0-4_all.deb ... 157s Unpacking python3-dateutil (2.9.0-4) ... 157s Selecting previously unselected package python3-iniconfig. 157s Preparing to unpack .../1-python3-iniconfig_1.1.1-2_all.deb ... 157s Unpacking python3-iniconfig (1.1.1-2) ... 157s Selecting previously unselected package python3-packaging. 157s Preparing to unpack .../2-python3-packaging_25.0-1_all.deb ... 157s Unpacking python3-packaging (25.0-1) ... 157s Selecting previously unselected package python3-pytz. 157s Preparing to unpack .../3-python3-pytz_2025.2-4_all.deb ... 157s Unpacking python3-pytz (2025.2-4) ... 158s Selecting previously unselected package python3-pandas-lib:arm64. 158s Preparing to unpack .../4-python3-pandas-lib_2.3.3+dfsg-1ubuntu1_arm64.deb ... 158s Unpacking python3-pandas-lib:arm64 (2.3.3+dfsg-1ubuntu1) ... 158s Selecting previously unselected package python3-pandas. 158s Preparing to unpack .../5-python3-pandas_2.3.3+dfsg-1ubuntu1_all.deb ... 158s Unpacking python3-pandas (2.3.3+dfsg-1ubuntu1) ... 158s Selecting previously unselected package python3-pluggy. 158s Preparing to unpack .../6-python3-pluggy_1.6.0-1_all.deb ... 158s Unpacking python3-pluggy (1.6.0-1) ... 158s Selecting previously unselected package python3-pytest. 158s Preparing to unpack .../7-python3-pytest_8.3.5-2_all.deb ... 158s Unpacking python3-pytest (8.3.5-2) ... 158s Selecting previously unselected package python3-testfixtures. 158s Preparing to unpack .../8-python3-testfixtures_9.2.0-1_all.deb ... 158s Unpacking python3-testfixtures (9.2.0-1) ... 158s Setting up python3-iniconfig (1.1.1-2) ... 158s Setting up python3-pandas-lib:arm64 (2.3.3+dfsg-1ubuntu1) ... 158s Setting up python3-testfixtures (9.2.0-1) ... 158s Setting up python3-pytz (2025.2-4) ... 158s Setting up python3-packaging (25.0-1) ... 159s Setting up python3-pluggy (1.6.0-1) ... 159s Setting up python3-dateutil (2.9.0-4) ... 159s Setting up python3-pytest (8.3.5-2) ... 159s Setting up python3-pandas (2.3.3+dfsg-1ubuntu1) ... 164s Processing triggers for man-db (2.13.1-1) ... 166s autopkgtest [07:15:15]: test command1: pytest-3 166s autopkgtest [07:15:15]: test command1: [----------------------- 167s ============================= test session starts ============================== 167s platform linux -- Python 3.13.9, pytest-8.3.5, pluggy-1.6.0 167s rootdir: /tmp/autopkgtest.6b2DY2/build.Xh2/src 167s configfile: pytest.ini 167s plugins: typeguard-4.4.2 167s 167s ----------------------------- live log collection ------------------------------ 167s WARNING py.warnings:warnings.py:110 /tmp/autopkgtest.6b2DY2/build.Xh2/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 167s @pytest.mark.long_test 167s 167s ERROR regression_test:regression_test.py:173 Need to reinstate the --apbs-input test with a temporary directory as path 167s collected 316 items 167s 167s tests/core_test.py::test_short_pdb[1FAS] SKIPPED (not running tests ...) [ 0%] 167s tests/core_test.py::test_short_pdb[5D8V] SKIPPED (not running tests ...) [ 0%] 167s tests/core_test.py::test_short_pdb[7BNA] SKIPPED (not running tests ...) [ 0%] 167s tests/core_test.py::test_short_pdb[4E8M] SKIPPED (not running tests ...) [ 1%] 167s tests/core_test.py::test_short_pdb[1K1I] SKIPPED (not running tests ...) [ 1%] 167s tests/core_test.py::test_short_pdb[1AQO] SKIPPED (not running tests ...) [ 1%] 167s tests/core_test.py::test_short_pdb[4UN3] SKIPPED (not running tests ...) [ 2%] 167s tests/core_test.py::test_short_pdb[1NAJ] SKIPPED (not running tests ...) [ 2%] 167s tests/core_test.py::test_basic_cif[1FAS] SKIPPED (not running tests ...) [ 2%] 167s tests/core_test.py::test_basic_cif[5D8V] SKIPPED (not running tests ...) [ 3%] 167s tests/core_test.py::test_basic_cif[7BNA] SKIPPED (not running tests ...) [ 3%] 167s tests/core_test.py::test_basic_cif[4E8M] SKIPPED (not running tests ...) [ 3%] 167s tests/core_test.py::test_basic_cif[1K1I] SKIPPED (not running tests ...) [ 4%] 167s tests/core_test.py::test_basic_cif[1AQO] SKIPPED (not running tests ...) [ 4%] 167s tests/core_test.py::test_basic_cif[4UN3] SKIPPED (not running tests ...) [ 4%] 167s tests/core_test.py::test_basic_cif[1NAJ] SKIPPED (not running tests ...) [ 5%] 167s tests/core_test.py::test_long_pdb[2QR3] SKIPPED (not running tests r...) [ 5%] 167s tests/core_test.py::test_long_pdb[2JCP] SKIPPED (not running tests r...) [ 5%] 167s tests/core_test.py::test_long_pdb[3KZD] SKIPPED (not running tests r...) 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[ 9%] 167s tests/core_test.py::test_long_pdb[2NSN] SKIPPED (not running tests r...) [ 9%] 167s tests/core_test.py::test_long_pdb[1SJV] SKIPPED (not running tests r...) [ 10%] 167s tests/core_test.py::test_long_pdb[4HTI] SKIPPED (not running tests r...) [ 10%] 167s tests/core_test.py::test_long_pdb[1USE] SKIPPED (not running tests r...) [ 10%] 167s tests/core_test.py::test_long_pdb[1YZM] SKIPPED (not running tests r...) [ 11%] 167s tests/core_test.py::test_long_pdb[1AFS] SKIPPED (not running tests r...) [ 11%] 167s tests/core_test.py::test_long_pdb[4IL7] SKIPPED (not running tests r...) [ 11%] 167s tests/core_test.py::test_long_pdb[3ONJ] SKIPPED (not running tests r...) [ 12%] 167s tests/core_test.py::test_long_pdb[2OCH] SKIPPED (not running tests r...) [ 12%] 167s tests/core_test.py::test_long_pdb[3ISU] SKIPPED (not running tests r...) [ 12%] 167s tests/core_test.py::test_long_pdb[2CKX] SKIPPED (not running tests r...) 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[ 65%] 167s tests/core_test.py::test_long_pdb[3US6] SKIPPED (not running tests r...) [ 65%] 167s tests/core_test.py::test_long_pdb[1WOU] SKIPPED (not running tests r...) [ 65%] 167s tests/core_test.py::test_long_pdb[4GMQ] SKIPPED (not running tests r...) [ 66%] 167s tests/core_test.py::test_broken_backbone[3U7T] 167s -------------------------------- live log call --------------------------------- 167s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_3U7T_0/3U7T.log 167s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 167s 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). 167s 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). 167s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 167s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 167s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T 198s XFAIL [ 66%] 198s tests/core_test.py::test_broken_backbone[1EJG] 198s -------------------------------- live log call --------------------------------- 198s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_1EJG_0/1EJG.log 198s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 198s 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). 198s 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). 198s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 198s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 199s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG 230s XFAIL [ 66%] 230s tests/core_test.py::test_broken_backbone[2V75] 230s -------------------------------- live log call --------------------------------- 230s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_2V75_0/2V75.log 230s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 230s 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). 230s 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). 230s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 230s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 230s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 231s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 231s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 231s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 90 residues and 687 atoms. 231s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 231s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 231s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 231s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 8 missing atoms in biomolecule. 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 231s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 231s 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 231s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 231s XFAIL [ 67%] 231s tests/core_test.py::test_broken_backbone[4MGP] 231s -------------------------------- live log call --------------------------------- 231s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_4MGP_0/4MGP.log 231s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 231s 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). 231s 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). 231s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 231s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 231s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP 232s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 232s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 232s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 23 residues and 163 atoms. 232s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in MET A 21. 232s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in MET A 21. 232s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in MET A 21. 232s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: SD in MET A 21. 232s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE in MET A 21. 232s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in MET A 21. At least one of the instances is being ignored. 232s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 232s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 232s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 232s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 12 missing atoms in biomolecule. 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 232s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 11 at coordinates 1.430, -1.683, -11.529 232s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 11 at coordinates 1.940, -0.315, -11.800 232s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CG to residue LYS A 14 at coordinates -1.600, -8.819, -6.913 232s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CD to residue LYS A 14 at coordinates -2.056, -8.844, -8.361 232s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 14 at coordinates -3.548, -9.031, -8.498 232s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 14 at coordinates -3.947, -9.048, -9.928 232s 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 232s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 232s XFAIL [ 67%] 232s tests/core_test.py::test_protonated_terminals[C-terminal HID] 232s -------------------------------- live log call --------------------------------- 232s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_protonated_terminals_C_te0/cterm_hid.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/cterm_hid.pdb 232s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 232s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms. 232s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 232s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 232s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 232s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule. 232s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 232s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402 232s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 232s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 232s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 232s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 232s 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:707 Applying custom naming scheme (amber). 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 464 header lines in output. 232s INFO common:common.py:198 0 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 [ 67%] 232s tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 232s -------------------------------- live log call --------------------------------- 232s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.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/5vav_cyclic_peptide.pdb 232s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 232s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms. 232s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 232s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 232s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 232s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 232s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 232s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 232s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 232s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 232s 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:707 Applying custom naming scheme (amber). 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 464 header lines in output. 232s INFO common:common.py:198 0 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 [ 68%] 233s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 68%] 233s tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 68%] 233s tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 68%] 233s tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 69%] 233s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 69%] 233s 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 [ 69%] 233s tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 70%] 233s tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 70%] 233s tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 70%] 233s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 71%] 233s tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 71%] 233s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 71%] 233s tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 72%] 233s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 72%] 233s tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 72%] 233s tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 73%] 233s tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 73%] 233s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 73%] 233s tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 74%] 233s tests/io_test.py::test_read_qcd PASSED [ 74%] 233s tests/io_test.py::test_dx2cube 233s -------------------------------- live log call --------------------------------- 233s INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... 233s INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... 233s INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 234s INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 234s INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... 235s INFO io_test:io_test.py:68 No differences found in output 235s PASSED [ 74%] 235s tests/ligand_test.py::test_peoe_charges 235s -------------------------------- live log call --------------------------------- 235s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 235s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 235s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 235s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 235s PASSED [ 75%] 236s tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 236s -------------------------------- live log call --------------------------------- 236s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 236s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 236s PASSED [ 75%] 236s tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 236s -------------------------------- live log call --------------------------------- 236s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 236s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 236s PASSED [ 75%] 236s tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 236s -------------------------------- live log call --------------------------------- 236s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 236s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 236s PASSED [ 75%] 236s tests/ligand_test.py::test_assign_parameters[acetate.mol2] 236s -------------------------------- live log call --------------------------------- 236s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 236s PASSED [ 76%] 236s tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 236s -------------------------------- live log call --------------------------------- 236s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 236s PASSED [ 76%] 236s tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 236s -------------------------------- live log call --------------------------------- 236s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 236s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 236s PASSED [ 76%] 236s tests/ligand_test.py::test_assign_parameters[adp.mol2] 236s -------------------------------- live log call --------------------------------- 236s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 236s INFO ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00 236s PASSED [ 77%] 236s tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 236s -------------------------------- live log call --------------------------------- 236s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 236s PASSED [ 77%] 236s tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 236s -------------------------------- live log call --------------------------------- 236s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 236s PASSED [ 77%] 236s tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 236s -------------------------------- live log call --------------------------------- 236s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 236s PASSED [ 78%] 236s tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 236s -------------------------------- live log call --------------------------------- 236s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 236s PASSED [ 78%] 236s tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 236s -------------------------------- live log call --------------------------------- 236s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 236s PASSED [ 78%] 236s tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 236s -------------------------------- live log call --------------------------------- 236s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 236s PASSED [ 79%] 236s tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 236s -------------------------------- live log call --------------------------------- 236s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 236s PASSED [ 79%] 236s tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 236s -------------------------------- live log call --------------------------------- 236s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 236s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 236s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 236s PASSED [ 79%] 237s tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 237s -------------------------------- live log call --------------------------------- 237s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 237s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 237s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 237s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 237s PASSED [ 80%] 237s tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 237s -------------------------------- live log call --------------------------------- 237s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 237s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 237s PASSED [ 80%] 237s tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 237s -------------------------------- live log call --------------------------------- 237s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 237s PASSED [ 80%] 237s tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED [ 81%] 237s tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED [ 81%] 237s tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 237s -------------------------------- live log call --------------------------------- 237s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 237s PASSED [ 81%] 237s tests/ligand_test.py::test_formal_charge[adp.mol2] 237s -------------------------------- live log call --------------------------------- 237s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 237s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 237s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 237s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 237s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 237s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 237s PASSED [ 81%] 237s tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED [ 82%] 237s tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED [ 82%] 237s tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED [ 82%] 237s tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED [ 83%] 237s tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED [ 83%] 238s tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED [ 83%] 238s tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED [ 84%] 238s tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 238s -------------------------------- live log call --------------------------------- 238s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 238s PASSED [ 84%] 238s tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED [ 84%] 238s tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED [ 85%] 238s tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED [ 85%] 238s tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED [ 85%] 238s tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED [ 86%] 238s tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED [ 86%] 238s tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED [ 86%] 239s tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED [ 87%] 239s tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED [ 87%] 239s tests/ligand_test.py::test_rings[acetate.mol2] PASSED [ 87%] 239s tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED [ 87%] 239s tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED [ 88%] 239s tests/ligand_test.py::test_rings[adp.mol2] PASSED [ 88%] 239s tests/ligand_test.py::test_rings[anthracene.mol2] PASSED [ 88%] 239s tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED [ 89%] 239s tests/ligand_test.py::test_rings[ethanol.mol2] PASSED [ 89%] 239s tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED [ 89%] 239s tests/ligand_test.py::test_rings[glycerol.mol2] PASSED [ 90%] 239s tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED [ 90%] 239s tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED [ 90%] 239s tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED [ 91%] 239s tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%] 239s tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%] 239s tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%] 239s tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%] 239s tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%] 239s tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%] 239s tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%] 239s tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%] 239s tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%] 239s tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%] 239s tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%] 239s tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] 239s tests/regression_test.py::test_basic[1AFS basic local] 239s -------------------------------- live log call --------------------------------- 239s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_basic_1AFS_basic_local_0/output.log 239s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 239s 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). 239s 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). 239s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 239s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 239s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 239s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 239s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 239s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 239s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 239s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 239s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 239s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 239s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 239s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 239s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 239s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 239s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 239s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 239s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 239s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 239s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 239s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 239s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 239s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 239s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 239s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 240s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 240s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 241s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 241s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 241s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 241s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 241s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 241s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 241s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 241s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 241s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 241s WARNING pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages 243s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 243s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 243s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 243s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 243s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 243s WARNING common:common.py:186 6 atoms have position differences > 0 243s INFO common:common.py:198 0 atoms have position differences > 0.01 243s INFO common:common.py:198 0 atoms have charge differences > 0 243s INFO common:common.py:198 0 atoms have charge differences > 0.01 243s INFO common:common.py:198 0 atoms have radius differences > 0 243s INFO common:common.py:198 0 atoms have radius differences > 0.01 243s PASSED [ 95%] 243s tests/regression_test.py::test_forcefields[1AFS whitespace AMBER] 243s -------------------------------- live log call --------------------------------- 243s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa0/output.log 243s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 243s 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). 243s 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). 243s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 243s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 243s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 243s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 243s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 243s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 243s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 243s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 243s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 243s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 243s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 243s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 243s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 243s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 243s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 243s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 243s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 243s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 243s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 243s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 243s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 243s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 243s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 243s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 244s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 244s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 247s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 247s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 247s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 247s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 247s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 247s WARNING common:common.py:186 6 atoms have position differences > 0 247s INFO common:common.py:198 0 atoms have position differences > 0.01 247s INFO common:common.py:198 0 atoms have charge differences > 0 247s INFO common:common.py:198 0 atoms have charge differences > 0.01 247s INFO common:common.py:198 0 atoms have radius differences > 0 247s INFO common:common.py:198 0 atoms have radius differences > 0.01 247s PASSED [ 95%] 247s tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] 247s -------------------------------- live log call --------------------------------- 247s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa1/output.log 247s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 247s 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). 247s 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). 247s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 247s 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 WARNING pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages 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. 248s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 248s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 249s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 251s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 251s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 251s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 251s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 251s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 252s WARNING common:common.py:186 5 atoms have position differences > 0 252s INFO common:common.py:198 0 atoms have position differences > 0.01 252s INFO common:common.py:198 0 atoms have charge differences > 0 252s INFO common:common.py:198 0 atoms have charge differences > 0.01 252s INFO common:common.py:198 0 atoms have radius differences > 0 252s INFO common:common.py:198 0 atoms have radius differences > 0.01 252s PASSED [ 95%] 252s tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] 252s -------------------------------- live log call --------------------------------- 252s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa2/output.log 252s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 252s 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). 252s 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). 252s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 252s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 252s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 252s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 252s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 252s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 252s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 252s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 252s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 252s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 252s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 252s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 252s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 252s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 252s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 252s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 252s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 252s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 252s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 252s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 252s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 253s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 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 5424 header lines in output. 256s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 256s WARNING common:common.py:186 6 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 [ 96%] 256s tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] 256s -------------------------------- live log call --------------------------------- 256s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa3/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. 257s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 257s 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 5426 header lines in output. 260s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 260s WARNING common:common.py:186 6 atoms have position differences > 0 260s INFO common:common.py:198 0 atoms have position differences > 0.01 260s INFO common:common.py:198 0 atoms have charge differences > 0 260s INFO common:common.py:198 0 atoms have charge differences > 0.01 260s INFO common:common.py:198 0 atoms have radius differences > 0 260s INFO common:common.py:198 0 atoms have radius differences > 0.01 260s PASSED [ 96%] 260s tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] 260s -------------------------------- live log call --------------------------------- 260s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa4/output.log 260s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 260s 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). 260s 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). 260s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 260s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 260s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 260s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 260s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 260s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 260s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 260s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 260s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 260s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 260s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 260s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 260s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 260s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 260s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 260s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 260s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 260s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 260s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 260s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 261s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 262s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 264s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 264s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 264s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 264s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output. 264s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 265s WARNING common:common.py:186 6 atoms have position differences > 0 265s INFO common:common.py:198 0 atoms have position differences > 0.01 265s INFO common:common.py:198 0 atoms have charge differences > 0 265s INFO common:common.py:198 0 atoms have charge differences > 0.01 265s INFO common:common.py:198 0 atoms have radius differences > 0 265s INFO common:common.py:198 0 atoms have radius differences > 0.01 265s PASSED [ 96%] 265s tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] 265s -------------------------------- live log call --------------------------------- 265s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa5/output.log 265s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 265s 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). 265s 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). 265s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 265s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 265s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 265s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 265s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 265s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 265s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 265s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 265s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 265s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 265s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 265s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 265s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 265s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 265s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 265s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 265s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 265s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 265s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 265s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 265s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 266s 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 [ 97%] 269s tests/regression_test.py::test_other_options[1AFS whitespace clean] 269s -------------------------------- live log call --------------------------------- 269s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_whites0/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:778 Arguments specified cleaning only; skipping remaining steps. 269s INFO common:common.py:198 0 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 [ 97%] 269s tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] 269s -------------------------------- live log call --------------------------------- 269s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_assign0/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/1A1P.pdb 269s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 269s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 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 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 852 header lines in output. 269s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 269s INFO common:common.py:198 0 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 [ 97%] 269s tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] 269s -------------------------------- live log call --------------------------------- 269s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_nodebu0/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/1A1P.pdb 269s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 269s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 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 INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 269s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 269s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 269s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 269s INFO pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization... 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 852 header lines in output. 269s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 269s INFO common:common.py:198 0 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 [ 98%] 269s tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] 269s -------------------------------- live log call --------------------------------- 269s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_chain_0/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 273s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 273s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 273s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 273s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 273s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 274s WARNING common:common.py:186 6 atoms have position differences > 0 274s INFO common:common.py:198 0 atoms have position differences > 0.01 274s INFO common:common.py:198 0 atoms have charge differences > 0 274s INFO common:common.py:198 0 atoms have charge differences > 0.01 274s INFO common:common.py:198 0 atoms have radius differences > 0 274s INFO common:common.py:198 0 atoms have radius differences > 0.01 274s PASSED [ 98%] 274s tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] 274s -------------------------------- live log call --------------------------------- 274s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_neutra0/output.log 274s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 274s 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). 274s 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). 274s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 274s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 274s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 274s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 274s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 274s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 274s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 274s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 274s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 274s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 274s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 274s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 274s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 274s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 274s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 274s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 274s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 274s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 274s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 274s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 274s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 275s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 278s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 278s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 278s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 278s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 278s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 278s WARNING common:common.py:186 6 atoms have position differences > 0 278s INFO common:common.py:198 0 atoms have position differences > 0.01 278s INFO common:common.py:198 0 atoms have charge differences > 0 278s INFO common:common.py:198 0 atoms have charge differences > 0.01 278s INFO common:common.py:198 0 atoms have radius differences > 0 278s INFO common:common.py:198 0 atoms have radius differences > 0.01 278s PASSED [ 98%] 278s tests/regression_test.py::test_other_options[1AFS drop-water AMBER] 278s -------------------------------- live log call --------------------------------- 278s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_drop_w0/output.log 278s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 278s 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). 278s 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). 278s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 278s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 278s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 278s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 278s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 278s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms. 278s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 278s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 278s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 278s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 278s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 278s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 278s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 278s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 278s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 278s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 278s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 278s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 278s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 278s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 278s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 278s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 279s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 281s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 281s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 281s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 281s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 281s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 281s WARNING common:common.py:186 6 atoms have position differences > 0 281s INFO common:common.py:198 0 atoms have position differences > 0.01 281s INFO common:common.py:198 0 atoms have charge differences > 0 281s INFO common:common.py:198 0 atoms have charge differences > 0.01 281s INFO common:common.py:198 0 atoms have radius differences > 0 281s INFO common:common.py:198 0 atoms have radius differences > 0.01 281s PASSED [ 99%] 281s tests/regression_test.py::test_other_options[1AFS userff usernames whitespace] 281s -------------------------------- live log call --------------------------------- 281s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_userff0/output.log 281s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 281s 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). 281s 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). 281s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 281s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 281s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 281s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 281s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 281s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 281s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 281s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 281s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 281s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 281s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 281s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 281s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 281s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 281s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 281s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 281s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 281s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 281s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 281s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 282s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 282s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 285s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 285s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 285s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 285s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 285s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 285s WARNING common:common.py:186 6 atoms have position differences > 0 285s INFO common:common.py:198 0 atoms have position differences > 0.01 285s INFO common:common.py:198 0 atoms have charge differences > 0 285s INFO common:common.py:198 0 atoms have charge differences > 0.01 285s INFO common:common.py:198 0 atoms have radius differences > 0 285s INFO common:common.py:198 0 atoms have radius differences > 0.01 285s PASSED [ 99%] 285s tests/test_version.py::test_version_exists PASSED [ 99%] 285s tests/test_version.py::test_version PASSED [100%] 285s 285s ============ 92 passed, 220 skipped, 4 xfailed in 119.00s (0:01:59) ============ 286s autopkgtest [07:17:15]: test command1: -----------------------] 286s command1 PASS 286s autopkgtest [07:17:15]: test command1: - - - - - - - - - - results - - - - - - - - - - 287s autopkgtest [07:17:16]: @@@@@@@@@@@@@@@@@@@@ summary 287s installation-test PASS 287s pdb2pka-test PASS 287s command1 PASS