0s autopkgtest [22:16:24]: starting date and time: 2025-10-20 22:16:24+0000 0s autopkgtest [22:16:24]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [22:16:24]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.rnuo940c/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:pytest,src:python-pluggy --apt-upgrade pdb2pqr --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.4.2-1 python-pluggy/1.6.0-1' -- lxd -r lxd-armhf-10.145.243.85 lxd-armhf-10.145.243.85:autopkgtest/ubuntu/resolute/armhf 22s autopkgtest [22:16:46]: testbed dpkg architecture: armhf 24s autopkgtest [22:16:48]: testbed apt version: 3.1.6ubuntu2 28s autopkgtest [22:16:52]: @@@@@@@@@@@@@@@@@@@@ test bed setup 30s autopkgtest [22:16:54]: testbed release detected to be: None 37s autopkgtest [22:17:01]: updating testbed package index (apt update) 39s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 39s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [83.3 kB] 40s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 40s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 40s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 40s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [15.0 kB] 40s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [683 kB] 40s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [63.1 kB] 40s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [109 kB] 40s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted armhf Packages [940 B] 40s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [429 kB] 40s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [3200 B] 40s Get:13 http://ftpmaster.internal/ubuntu resolute/restricted Sources [14.4 kB] 40s Get:14 http://ftpmaster.internal/ubuntu resolute/main Sources [1413 kB] 40s Get:15 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.1 MB] 41s Get:16 http://ftpmaster.internal/ubuntu resolute/multiverse Sources [307 kB] 41s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1357 kB] 41s Get:18 http://ftpmaster.internal/ubuntu resolute/restricted armhf Packages [1672 B] 41s Get:19 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.3 MB] 42s Get:20 http://ftpmaster.internal/ubuntu resolute/multiverse armhf Packages [182 kB] 45s Fetched 41.1 MB in 5s (7638 kB/s) 46s Reading package lists... 52s autopkgtest [22:17:16]: upgrading testbed (apt dist-upgrade and autopurge) 53s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s Calculating upgrade... 55s The following packages will be upgraded: 55s apparmor apt base-files binutils binutils-arm-linux-gnueabihf 55s binutils-common cloud-init cloud-init-base distro-info-data dpkg dpkg-dev 55s gcc-15-base gir1.2-girepository-2.0 libapparmor1 libapt-pkg7.0 libatomic1 55s libaudit-common libaudit1 libbinutils libbrotli1 libcap-ng0 libctf-nobfd0 55s libctf0 libdpkg-perl libgcc-s1 libgirepository-1.0-1 libjson-c5 libnewt0.52 55s libnftables1 libp11-kit0 libseccomp2 libselinux1 libsemanage-common 55s libsemanage2 libsframe2 libstdc++6 lto-disabled-list nftables 55s python-apt-common python3-apt python3-cffi-backend python3-inflect 55s python3-markupsafe python3-oauthlib python3-zipp sudo-rs whiptail 55s 47 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s Need to get 11.8 MB of archives. 55s After this operation, 694 kB of additional disk space will be used. 55s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf base-files armhf 14ubuntu4 [75.4 kB] 56s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libatomic1 armhf 15.2.0-5ubuntu1 [7942 B] 56s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf gcc-15-base armhf 15.2.0-5ubuntu1 [58.1 kB] 56s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libgcc-s1 armhf 15.2.0-5ubuntu1 [40.6 kB] 56s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libstdc++6 armhf 15.2.0-5ubuntu1 [731 kB] 56s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libapt-pkg7.0 armhf 3.1.8ubuntu1 [1148 kB] 56s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf dpkg armhf 1.22.21ubuntu4 [1245 kB] 56s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf libseccomp2 armhf 2.6.0-2ubuntu3 [53.5 kB] 56s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf apt armhf 3.1.8ubuntu1 [1404 kB] 56s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf libaudit-common all 1:4.0.5-1build2 [6596 B] 56s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libcap-ng0 armhf 0.8.5-4build3 [14.0 kB] 56s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf libaudit1 armhf 1:4.0.5-1build2 [51.7 kB] 56s Get:13 http://ftpmaster.internal/ubuntu resolute/main armhf libselinux1 armhf 3.8.1-1build2 [81.3 kB] 56s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf libsemanage-common all 3.8.1-1build1 [7916 B] 56s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf libsemanage2 armhf 3.8.1-1build1 [89.2 kB] 56s Get:16 http://ftpmaster.internal/ubuntu resolute/main armhf distro-info-data all 0.68 [7378 B] 56s Get:17 http://ftpmaster.internal/ubuntu resolute/main armhf libgirepository-1.0-1 armhf 1.86.0-6 [111 kB] 56s Get:18 http://ftpmaster.internal/ubuntu resolute/main armhf gir1.2-girepository-2.0 armhf 1.86.0-6 [25.3 kB] 56s Get:19 http://ftpmaster.internal/ubuntu resolute/main armhf libapparmor1 armhf 5.0.0~alpha1-0ubuntu8.1 [52.9 kB] 56s Get:20 http://ftpmaster.internal/ubuntu resolute/main armhf libjson-c5 armhf 0.18+ds-1.1 [33.3 kB] 56s Get:21 http://ftpmaster.internal/ubuntu resolute/main armhf libnewt0.52 armhf 0.52.25-1ubuntu2 [39.9 kB] 56s Get:22 http://ftpmaster.internal/ubuntu resolute/main armhf libp11-kit0 armhf 0.25.9-2 [265 kB] 56s Get:23 http://ftpmaster.internal/ubuntu resolute/main armhf python-apt-common all 3.0.0ubuntu2 [21.7 kB] 56s Get:24 http://ftpmaster.internal/ubuntu resolute/main armhf python3-apt armhf 3.0.0ubuntu2 [189 kB] 56s Get:25 http://ftpmaster.internal/ubuntu resolute/main armhf python3-cffi-backend armhf 1.17.1-3build1 [98.4 kB] 56s Get:26 http://ftpmaster.internal/ubuntu resolute/main armhf sudo-rs armhf 0.2.8-1ubuntu5.1 [548 kB] 56s Get:27 http://ftpmaster.internal/ubuntu resolute/main armhf whiptail armhf 0.52.25-1ubuntu2 [17.1 kB] 56s Get:28 http://ftpmaster.internal/ubuntu resolute/main armhf apparmor armhf 5.0.0~alpha1-0ubuntu8.1 [631 kB] 56s Get:29 http://ftpmaster.internal/ubuntu resolute/main armhf nftables armhf 1.1.5-2 [73.2 kB] 56s Get:30 http://ftpmaster.internal/ubuntu resolute/main armhf libnftables1 armhf 1.1.5-2 [329 kB] 56s Get:31 http://ftpmaster.internal/ubuntu resolute/main armhf libctf0 armhf 2.45-7ubuntu2 [75.7 kB] 56s Get:32 http://ftpmaster.internal/ubuntu resolute/main armhf libctf-nobfd0 armhf 2.45-7ubuntu2 [79.1 kB] 56s Get:33 http://ftpmaster.internal/ubuntu resolute/main armhf binutils-arm-linux-gnueabihf armhf 2.45-7ubuntu2 [1022 kB] 56s Get:34 http://ftpmaster.internal/ubuntu resolute/main armhf libbinutils armhf 2.45-7ubuntu2 [411 kB] 56s Get:35 http://ftpmaster.internal/ubuntu resolute/main armhf binutils armhf 2.45-7ubuntu2 [3240 B] 56s Get:36 http://ftpmaster.internal/ubuntu resolute/main armhf binutils-common armhf 2.45-7ubuntu2 [220 kB] 57s Get:37 http://ftpmaster.internal/ubuntu resolute/main armhf libsframe2 armhf 2.45-7ubuntu2 [13.4 kB] 57s Get:38 http://ftpmaster.internal/ubuntu resolute/main armhf cloud-init-base all 25.3-0ubuntu1 [625 kB] 57s Get:39 http://ftpmaster.internal/ubuntu resolute/main armhf cloud-init all 25.3-0ubuntu1 [2106 B] 57s Get:40 http://ftpmaster.internal/ubuntu resolute/main armhf python3-oauthlib all 3.3.1-1 [93.5 kB] 57s Get:41 http://ftpmaster.internal/ubuntu resolute/main armhf dpkg-dev all 1.22.21ubuntu4 [1088 kB] 57s Get:42 http://ftpmaster.internal/ubuntu resolute/main armhf libdpkg-perl all 1.22.21ubuntu4 [280 kB] 57s Get:43 http://ftpmaster.internal/ubuntu resolute/main armhf lto-disabled-list all 71 [12.5 kB] 57s Get:44 http://ftpmaster.internal/ubuntu resolute/main armhf libbrotli1 armhf 1.1.0-2build6 [320 kB] 57s Get:45 http://ftpmaster.internal/ubuntu resolute/main armhf python3-inflect all 7.5.0-1 [33.9 kB] 57s Get:46 http://ftpmaster.internal/ubuntu resolute/main armhf python3-markupsafe armhf 2.1.5-1build5 [13.3 kB] 57s Get:47 http://ftpmaster.internal/ubuntu resolute/main armhf python3-zipp all 3.23.0-1 [10.4 kB] 57s Preconfiguring packages ... 58s Fetched 11.8 MB in 2s (7091 kB/s) 58s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61081 files and directories currently installed.) 58s Preparing to unpack .../base-files_14ubuntu4_armhf.deb ... 58s Unpacking base-files (14ubuntu4) over (14ubuntu3) ... 58s Setting up base-files (14ubuntu4) ... 58s Installing new version of config file /etc/issue ... 58s Installing new version of config file /etc/issue.net ... 58s Installing new version of config file /etc/lsb-release ... 59s motd-news.service is a disabled or a static unit not running, not starting it. 59s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61081 files and directories currently installed.) 59s Preparing to unpack .../libatomic1_15.2.0-5ubuntu1_armhf.deb ... 59s Unpacking libatomic1:armhf (15.2.0-5ubuntu1) over (15.2.0-4ubuntu4) ... 59s Preparing to unpack .../gcc-15-base_15.2.0-5ubuntu1_armhf.deb ... 59s Unpacking gcc-15-base:armhf (15.2.0-5ubuntu1) over (15.2.0-4ubuntu4) ... 59s Setting up gcc-15-base:armhf (15.2.0-5ubuntu1) ... 59s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61081 files and directories currently installed.) 59s Preparing to unpack .../libgcc-s1_15.2.0-5ubuntu1_armhf.deb ... 59s Unpacking libgcc-s1:armhf (15.2.0-5ubuntu1) over (15.2.0-4ubuntu4) ... 59s Setting up libgcc-s1:armhf (15.2.0-5ubuntu1) ... 59s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61081 files and directories currently installed.) 59s Preparing to unpack .../libstdc++6_15.2.0-5ubuntu1_armhf.deb ... 59s Unpacking libstdc++6:armhf (15.2.0-5ubuntu1) over (15.2.0-4ubuntu4) ... 59s Setting up libstdc++6:armhf (15.2.0-5ubuntu1) ... 59s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61081 files and directories currently installed.) 59s Preparing to unpack .../libapt-pkg7.0_3.1.8ubuntu1_armhf.deb ... 59s Unpacking libapt-pkg7.0:armhf (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 59s Setting up libapt-pkg7.0:armhf (3.1.8ubuntu1) ... 59s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61081 files and directories currently installed.) 59s Preparing to unpack .../dpkg_1.22.21ubuntu4_armhf.deb ... 59s Unpacking dpkg (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 60s Setting up dpkg (1.22.21ubuntu4) ... 60s (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 ... 61081 files and directories currently installed.) 60s Preparing to unpack .../libseccomp2_2.6.0-2ubuntu3_armhf.deb ... 60s Unpacking libseccomp2:armhf (2.6.0-2ubuntu3) over (2.6.0-2ubuntu2) ... 60s Setting up libseccomp2:armhf (2.6.0-2ubuntu3) ... 60s (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 ... 61081 files and directories currently installed.) 60s Preparing to unpack .../apt_3.1.8ubuntu1_armhf.deb ... 60s Unpacking apt (3.1.8ubuntu1) over (3.1.6ubuntu2) ... 60s Setting up apt (3.1.8ubuntu1) ... 61s (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 ... 61081 files and directories currently installed.) 61s Preparing to unpack .../libaudit-common_1%3a4.0.5-1build2_all.deb ... 61s Unpacking libaudit-common (1:4.0.5-1build2) over (1:4.0.5-1build1) ... 61s Setting up libaudit-common (1:4.0.5-1build2) ... 61s (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 ... 61081 files and directories currently installed.) 61s Preparing to unpack .../libcap-ng0_0.8.5-4build3_armhf.deb ... 61s Unpacking libcap-ng0:armhf (0.8.5-4build3) over (0.8.5-4build2) ... 61s Setting up libcap-ng0:armhf (0.8.5-4build3) ... 61s (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 ... 61081 files and directories currently installed.) 61s Preparing to unpack .../libaudit1_1%3a4.0.5-1build2_armhf.deb ... 61s Unpacking libaudit1:armhf (1:4.0.5-1build2) over (1:4.0.5-1build1) ... 61s Setting up libaudit1:armhf (1:4.0.5-1build2) ... 62s (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 ... 61081 files and directories currently installed.) 62s Preparing to unpack .../libselinux1_3.8.1-1build2_armhf.deb ... 62s Unpacking libselinux1:armhf (3.8.1-1build2) over (3.8.1-1build1) ... 62s Setting up libselinux1:armhf (3.8.1-1build2) ... 62s (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 ... 61081 files and directories currently installed.) 62s Preparing to unpack .../libsemanage-common_3.8.1-1build1_all.deb ... 62s Unpacking libsemanage-common (3.8.1-1build1) over (3.8.1-1) ... 62s Setting up libsemanage-common (3.8.1-1build1) ... 62s (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 ... 61081 files and directories currently installed.) 62s Preparing to unpack .../libsemanage2_3.8.1-1build1_armhf.deb ... 62s Unpacking libsemanage2:armhf (3.8.1-1build1) over (3.8.1-1) ... 62s Setting up libsemanage2:armhf (3.8.1-1build1) ... 62s (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 ... 61081 files and directories currently installed.) 62s Preparing to unpack .../00-distro-info-data_0.68_all.deb ... 62s Unpacking distro-info-data (0.68) over (0.66) ... 62s Preparing to unpack .../01-libgirepository-1.0-1_1.86.0-6_armhf.deb ... 62s Unpacking libgirepository-1.0-1:armhf (1.86.0-6) over (1.84.0-1) ... 62s Preparing to unpack .../02-gir1.2-girepository-2.0_1.86.0-6_armhf.deb ... 62s Unpacking gir1.2-girepository-2.0:armhf (1.86.0-6) over (1.84.0-1) ... 62s Preparing to unpack .../03-libapparmor1_5.0.0~alpha1-0ubuntu8.1_armhf.deb ... 62s Unpacking libapparmor1:armhf (5.0.0~alpha1-0ubuntu8.1) over (5.0.0~alpha1-0ubuntu8) ... 62s Preparing to unpack .../04-libjson-c5_0.18+ds-1.1_armhf.deb ... 62s Unpacking libjson-c5:armhf (0.18+ds-1.1) over (0.18+ds-1) ... 62s Preparing to unpack .../05-libnewt0.52_0.52.25-1ubuntu2_armhf.deb ... 62s Unpacking libnewt0.52:armhf (0.52.25-1ubuntu2) over (0.52.25-1ubuntu1) ... 62s Preparing to unpack .../06-libp11-kit0_0.25.9-2_armhf.deb ... 62s Unpacking libp11-kit0:armhf (0.25.9-2) over (0.25.5-3ubuntu1) ... 62s Preparing to unpack .../07-python-apt-common_3.0.0ubuntu2_all.deb ... 62s Unpacking python-apt-common (3.0.0ubuntu2) over (3.0.0ubuntu1) ... 62s Preparing to unpack .../08-python3-apt_3.0.0ubuntu2_armhf.deb ... 62s Unpacking python3-apt (3.0.0ubuntu2) over (3.0.0ubuntu1) ... 62s Preparing to unpack .../09-python3-cffi-backend_1.17.1-3build1_armhf.deb ... 62s Unpacking python3-cffi-backend:armhf (1.17.1-3build1) over (1.17.1-3) ... 62s Preparing to unpack .../10-sudo-rs_0.2.8-1ubuntu5.1_armhf.deb ... 63s Unpacking sudo-rs (0.2.8-1ubuntu5.1) over (0.2.8-1ubuntu5) ... 63s Preparing to unpack .../11-whiptail_0.52.25-1ubuntu2_armhf.deb ... 63s Unpacking whiptail (0.52.25-1ubuntu2) over (0.52.25-1ubuntu1) ... 63s Preparing to unpack .../12-apparmor_5.0.0~alpha1-0ubuntu8.1_armhf.deb ... 64s Unpacking apparmor (5.0.0~alpha1-0ubuntu8.1) over (5.0.0~alpha1-0ubuntu8) ... 65s Preparing to unpack .../13-nftables_1.1.5-2_armhf.deb ... 65s Unpacking nftables (1.1.5-2) over (1.1.5-1) ... 65s Preparing to unpack .../14-libnftables1_1.1.5-2_armhf.deb ... 65s Unpacking libnftables1:armhf (1.1.5-2) over (1.1.5-1) ... 65s Preparing to unpack .../15-libctf0_2.45-7ubuntu2_armhf.deb ... 65s Unpacking libctf0:armhf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 65s Preparing to unpack .../16-libctf-nobfd0_2.45-7ubuntu2_armhf.deb ... 65s Unpacking libctf-nobfd0:armhf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 65s Preparing to unpack .../17-binutils-arm-linux-gnueabihf_2.45-7ubuntu2_armhf.deb ... 65s Unpacking binutils-arm-linux-gnueabihf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 65s Preparing to unpack .../18-libbinutils_2.45-7ubuntu2_armhf.deb ... 65s Unpacking libbinutils:armhf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 65s Preparing to unpack .../19-binutils_2.45-7ubuntu2_armhf.deb ... 65s Unpacking binutils (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 66s Preparing to unpack .../20-binutils-common_2.45-7ubuntu2_armhf.deb ... 66s Unpacking binutils-common:armhf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 66s Preparing to unpack .../21-libsframe2_2.45-7ubuntu2_armhf.deb ... 66s Unpacking libsframe2:armhf (2.45-7ubuntu2) over (2.45-7ubuntu1) ... 66s Preparing to unpack .../22-cloud-init-base_25.3-0ubuntu1_all.deb ... 66s Unpacking cloud-init-base (25.3-0ubuntu1) over (25.3~2g890873f5-0ubuntu2) ... 66s Preparing to unpack .../23-cloud-init_25.3-0ubuntu1_all.deb ... 66s Unpacking cloud-init (25.3-0ubuntu1) over (25.3~2g890873f5-0ubuntu2) ... 66s Preparing to unpack .../24-python3-oauthlib_3.3.1-1_all.deb ... 67s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 67s Preparing to unpack .../25-dpkg-dev_1.22.21ubuntu4_all.deb ... 67s Unpacking dpkg-dev (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 67s Preparing to unpack .../26-libdpkg-perl_1.22.21ubuntu4_all.deb ... 67s Unpacking libdpkg-perl (1.22.21ubuntu4) over (1.22.21ubuntu3) ... 67s Preparing to unpack .../27-lto-disabled-list_71_all.deb ... 67s Unpacking lto-disabled-list (71) over (69) ... 67s Preparing to unpack .../28-libbrotli1_1.1.0-2build6_armhf.deb ... 67s Unpacking libbrotli1:armhf (1.1.0-2build6) over (1.1.0-2build5) ... 67s Preparing to unpack .../29-python3-inflect_7.5.0-1_all.deb ... 67s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 67s Preparing to unpack .../30-python3-markupsafe_2.1.5-1build5_armhf.deb ... 67s Unpacking python3-markupsafe (2.1.5-1build5) over (2.1.5-1build4) ... 67s Preparing to unpack .../31-python3-zipp_3.23.0-1_all.deb ... 67s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 68s Setting up lto-disabled-list (71) ... 68s Setting up libapparmor1:armhf (5.0.0~alpha1-0ubuntu8.1) ... 68s Setting up libnewt0.52:armhf (0.52.25-1ubuntu2) ... 68s Setting up libnftables1:armhf (1.1.5-2) ... 68s Setting up nftables (1.1.5-2) ... 68s Setting up distro-info-data (0.68) ... 68s Setting up libsframe2:armhf (2.45-7ubuntu2) ... 68s Setting up libbrotli1:armhf (1.1.0-2build6) ... 68s Setting up binutils-common:armhf (2.45-7ubuntu2) ... 68s Setting up libctf-nobfd0:armhf (2.45-7ubuntu2) ... 68s Setting up python3-zipp (3.23.0-1) ... 68s Setting up python3-markupsafe (2.1.5-1build5) ... 68s Setting up apparmor (5.0.0~alpha1-0ubuntu8.1) ... 68s Installing new version of config file /etc/apparmor.d/fusermount3 ... 69s apparmor_parser: Unable to replace "lsb_release". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s apparmor_parser: Unable to replace "kmod". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 69s apparmor_parser: Unable to replace "nvidia_modprobe". apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 69s 70s Reloading AppArmor profiles 70s /sbin/apparmor_parser: Unable to replace "1password". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "MongoDB Compass". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "Discord". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "balena-etcher". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "brave". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "buildah". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "cam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ch-checkns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ch-run". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "chrome". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "chromium". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "bwrap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "vscode". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "babeld". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "crun". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "bfdd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "devhelp". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "bgpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "alsamixer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "element-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "epiphany". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "evolution". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "flatpak". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "firefox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "foliate". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "geary". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "github-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "goldendict". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "eigrpd". /sbin/apparmor_parser: Unable to replace "dnstracer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "dig". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "fabricd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "hostname". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "iotop-c". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "kchmviewer". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "keybase". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lc-compliance". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "isisd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "libcamerify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "fusermount3". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "linux-sandbox". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "gs". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "john". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "loupe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ldpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "Xorg". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ipa_verify". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lxc-attach". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lxc-create". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lxc-destroy". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lxc-execute". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lxc-stop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lxc-unshare". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "irssi". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lxc-usernsexec". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "mmdebstrap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lsblk". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "msedge". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "compressor". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "locale". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "linux-boot-prober". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lsusb". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "notepadqq". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "lsb_release". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "mbsync". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "obsidian". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "opam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "nhrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "opera". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "mosquitto". /sbin/apparmor_parser: Unable to replace "nslookup". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "notify-send". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "pageedit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "nc.openbsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "kmod". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "nvidia_modprobe". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ospf6d". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "pbrd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "pim6d". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "os-prober". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "podman". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ospfd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "polypane". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "pathd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "privacybrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "QtWebEngineProcess". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "plasmashell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "qcam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "qutebrowser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "qmapshack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "rootlesskit". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "pimd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "rpm". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "rssguard". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "runc". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-abort". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ripngd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-adduser". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ripd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "qpdf". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-apt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-clean". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-createchroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-destroychroot". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-checkpackages". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-distupgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-shell". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-hold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-unhold". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-update". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "signal-desktop". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "scide". /sbin/apparmor_parser: Unable to replace "slirp4netns". /sbin/apparmor_parser: Unable to replace "slack". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "sbuild-upgrade". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "stress-ng". /sbin/apparmor_parser: Unable to replace "steam". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "surfshark". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ip". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "openvpn". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "thunderbird". /sbin/apparmor_parser: Unable to replace "systemd-coredump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "proftpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ssh-keyscan". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "trinity". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "staticd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "tuxedo-control-center". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "tup". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "systemd-detect-virt". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "tinyproxy". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "unprivileged_userns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "userbindmount". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "mx-extract". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "rygel". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "unix-chkpwd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_apt_news". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "/usr/bin/man". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "uwsgi-core". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "vdens". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "virtiofsd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "vivaldi-bin". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "vpnns". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "/usr/sbin/chronyd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "rsyslogd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "wg". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "vrrpd". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "wike". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "wpcom". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "cmds". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "tnftp". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "who". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "dumpcap". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 70s /sbin/apparmor_parser: Unable to replace "tshark". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 70s 71s /sbin/apparmor_parser: Unable to replace "ip". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 71s 71s /sbin/apparmor_parser: Unable to replace "wg-quick". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 71s 71s /sbin/apparmor_parser: Unable to replace "znc". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 71s 71s /sbin/apparmor_parser: Unable to replace "tcpdump". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 71s 71s /sbin/apparmor_parser: Unable to replace "transmission-cli". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 71s 71s /sbin/apparmor_parser: Unable to replace "apt_methods". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 71s 71s /sbin/apparmor_parser: Unable to replace "ubuntu_pro_esm_cache". /sbin/apparmor_parser: Access denied. You need policy admin privileges to manage profiles. 71s 71s Error: At least one profile failed to load 71s Setting up python3-inflect (7.5.0-1) ... 71s Setting up python3-oauthlib (3.3.1-1) ... 71s Setting up libp11-kit0:armhf (0.25.9-2) ... 71s Setting up libatomic1:armhf (15.2.0-5ubuntu1) ... 71s Setting up libdpkg-perl (1.22.21ubuntu4) ... 71s Setting up whiptail (0.52.25-1ubuntu2) ... 71s Setting up python-apt-common (3.0.0ubuntu2) ... 71s Setting up libgirepository-1.0-1:armhf (1.86.0-6) ... 71s Setting up libbinutils:armhf (2.45-7ubuntu2) ... 71s Setting up libjson-c5:armhf (0.18+ds-1.1) ... 71s Setting up sudo-rs (0.2.8-1ubuntu5.1) ... 71s Setting up python3-cffi-backend:armhf (1.17.1-3build1) ... 71s Setting up libctf0:armhf (2.45-7ubuntu2) ... 71s Setting up python3-apt (3.0.0ubuntu2) ... 72s Setting up cloud-init-base (25.3-0ubuntu1) ... 74s Setting up gir1.2-girepository-2.0:armhf (1.86.0-6) ... 74s Setting up binutils-arm-linux-gnueabihf (2.45-7ubuntu2) ... 74s Setting up cloud-init (25.3-0ubuntu1) ... 74s Setting up binutils (2.45-7ubuntu2) ... 74s Setting up dpkg-dev (1.22.21ubuntu4) ... 74s Processing triggers for procps (2:4.0.4-8ubuntu3) ... 74s Processing triggers for install-info (7.1.1-1ubuntu1) ... 74s Processing triggers for libc-bin (2.42-0ubuntu3) ... 74s Processing triggers for rsyslog (8.2504.0-1ubuntu2) ... 74s Processing triggers for systemd (257.9-0ubuntu2) ... 74s Processing triggers for man-db (2.13.1-1) ... 76s Processing triggers for plymouth-theme-ubuntu-text (24.004.60+git20250831.4a3c171d-0ubuntu1) ... 79s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Solving dependencies... 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s autopkgtest [22:17:47]: rebooting testbed after setup commands that affected boot 123s autopkgtest [22:18:27]: testbed running kernel: Linux 6.8.0-58-generic #60~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Mar 28 14:48:37 UTC 2 148s autopkgtest [22:18:52]: @@@@@@@@@@@@@@@@@@@@ apt-source pdb2pqr 166s Get:1 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (dsc) [1860 B] 166s Get:2 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (tar) [7570 kB] 166s Get:3 http://ftpmaster.internal/ubuntu resolute/universe pdb2pqr 3.6.1+dfsg-1 (diff) [9876 B] 166s gpgv: Signature made Mon Jun 12 17:36:50 2023 UTC 166s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 166s gpgv: Can't check signature: No public key 166s dpkg-source: warning: cannot verify inline signature for ./pdb2pqr_3.6.1+dfsg-1.dsc: no acceptable signature found 167s autopkgtest [22:19:11]: testing package pdb2pqr version 3.6.1+dfsg-1 169s autopkgtest [22:19:13]: build not needed 173s autopkgtest [22:19:17]: test installation-test: preparing testbed 174s Reading package lists... 175s Building dependency tree... 175s Reading state information... 175s Solving dependencies... 176s The following NEW packages will be installed: 176s docutils-common libblas3 libgfortran5 liblapack3 pdb2pqr python3-docutils 176s python3-numpy python3-numpy-dev python3-pdb2pqr python3-pdbx python3-propka 176s python3-roman sgml-base xml-core 176s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 176s Need to get 7246 kB of archives. 176s After this operation, 28.4 MB of additional disk space will be used. 176s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy-dev armhf 1:2.2.4+ds-1ubuntu1 [141 kB] 177s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-6build1 [133 kB] 177s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-5ubuntu1 [334 kB] 177s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-6build1 [2091 kB] 177s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy armhf 1:2.2.4+ds-1ubuntu1 [3724 kB] 177s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf sgml-base all 1.31+nmu1 [11.0 kB] 177s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf xml-core all 0.19 [20.3 kB] 177s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf docutils-common all 0.21.2+dfsg-2 [131 kB] 177s Get:9 http://ftpmaster.internal/ubuntu resolute/main armhf python3-roman all 5.1-1 [10.6 kB] 177s Get:10 http://ftpmaster.internal/ubuntu resolute/main armhf python3-docutils all 0.21.2+dfsg-2 [409 kB] 177s Get:11 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pdbx all 2.0.1-2 [16.5 kB] 177s Get:12 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-propka all 3.5.1-2 [70.1 kB] 177s Get:13 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pdb2pqr all 3.6.1+dfsg-1 [145 kB] 177s Get:14 http://ftpmaster.internal/ubuntu resolute/universe armhf pdb2pqr all 3.6.1+dfsg-1 [10.4 kB] 178s Fetched 7246 kB in 1s (5587 kB/s) 178s Selecting previously unselected package python3-numpy-dev:armhf. 178s (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 ... 61097 files and directories currently installed.) 178s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 178s Unpacking python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 178s Selecting previously unselected package libblas3:armhf. 178s Preparing to unpack .../01-libblas3_3.12.1-6build1_armhf.deb ... 178s Unpacking libblas3:armhf (3.12.1-6build1) ... 178s Selecting previously unselected package libgfortran5:armhf. 178s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_armhf.deb ... 178s Unpacking libgfortran5:armhf (15.2.0-5ubuntu1) ... 178s Selecting previously unselected package liblapack3:armhf. 178s Preparing to unpack .../03-liblapack3_3.12.1-6build1_armhf.deb ... 178s Unpacking liblapack3:armhf (3.12.1-6build1) ... 178s Selecting previously unselected package python3-numpy. 178s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 178s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 179s Selecting previously unselected package sgml-base. 179s Preparing to unpack .../05-sgml-base_1.31+nmu1_all.deb ... 179s Unpacking sgml-base (1.31+nmu1) ... 179s Selecting previously unselected package xml-core. 179s Preparing to unpack .../06-xml-core_0.19_all.deb ... 179s Unpacking xml-core (0.19) ... 179s Selecting previously unselected package docutils-common. 179s Preparing to unpack .../07-docutils-common_0.21.2+dfsg-2_all.deb ... 179s Unpacking docutils-common (0.21.2+dfsg-2) ... 179s Selecting previously unselected package python3-roman. 179s Preparing to unpack .../08-python3-roman_5.1-1_all.deb ... 179s Unpacking python3-roman (5.1-1) ... 179s Selecting previously unselected package python3-docutils. 179s Preparing to unpack .../09-python3-docutils_0.21.2+dfsg-2_all.deb ... 179s Unpacking python3-docutils (0.21.2+dfsg-2) ... 179s Selecting previously unselected package python3-pdbx. 179s Preparing to unpack .../10-python3-pdbx_2.0.1-2_all.deb ... 179s Unpacking python3-pdbx (2.0.1-2) ... 179s Selecting previously unselected package python3-propka. 179s Preparing to unpack .../11-python3-propka_3.5.1-2_all.deb ... 179s Unpacking python3-propka (3.5.1-2) ... 179s Selecting previously unselected package python3-pdb2pqr. 179s Preparing to unpack .../12-python3-pdb2pqr_3.6.1+dfsg-1_all.deb ... 179s Unpacking python3-pdb2pqr (3.6.1+dfsg-1) ... 179s Selecting previously unselected package pdb2pqr. 179s Preparing to unpack .../13-pdb2pqr_3.6.1+dfsg-1_all.deb ... 179s Unpacking pdb2pqr (3.6.1+dfsg-1) ... 179s Setting up python3-propka (3.5.1-2) ... 179s Setting up python3-pdbx (2.0.1-2) ... 179s Setting up python3-roman (5.1-1) ... 180s Setting up libblas3:armhf (3.12.1-6build1) ... 180s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 180s Setting up python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 180s Setting up libgfortran5:armhf (15.2.0-5ubuntu1) ... 180s Setting up sgml-base (1.31+nmu1) ... 180s Setting up liblapack3:armhf (3.12.1-6build1) ... 180s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 180s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 182s Setting up xml-core (0.19) ... 183s Processing triggers for libc-bin (2.42-0ubuntu3) ... 183s Processing triggers for man-db (2.13.1-1) ... 183s Processing triggers for sgml-base (1.31+nmu1) ... 183s Setting up docutils-common (0.21.2+dfsg-2) ... 183s Processing triggers for sgml-base (1.31+nmu1) ... 183s Setting up python3-docutils (0.21.2+dfsg-2) ... 184s Setting up python3-pdb2pqr (3.6.1+dfsg-1) ... 184s Setting up pdb2pqr (3.6.1+dfsg-1) ... 192s autopkgtest [22:19:36]: test installation-test: [----------------------- 194s Run pdb2pqr... 195s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 195s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 195s 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). 195s INFO:Checking and transforming input arguments. 195s INFO:Loading topology files. 195s INFO:Loading molecule: examples/1a1p/1a1p.pdb 195s INFO:Setting up molecule. 195s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 195s INFO:Created biomolecule object with 14 residues and 208 atoms. 195s INFO:Setting termini states for biomolecule chains. 195s INFO:Loading forcefield. 195s INFO:Loading hydrogen topology definitions. 195s INFO:This biomolecule is clean. No repair needed. 195s INFO:Updating disulfide bridges. 195s INFO:Debumping biomolecule. 195s INFO:Adding hydrogens to biomolecule. 195s INFO:Debumping biomolecule (again). 195s INFO:Optimizing hydrogen bonds 195s INFO:Applying force field to biomolecule states. 195s INFO:Regenerating headers. 195s INFO:Regenerating PDB lines. 195s WARNING:Ignoring 852 header lines in output. 195s WARNING:Ignoring 3 missing lines in output. 195s autopkgtest [22:19:39]: test installation-test: -----------------------] 199s autopkgtest [22:19:43]: test installation-test: - - - - - - - - - - results - - - - - - - - - - 199s installation-test PASS 203s autopkgtest [22:19:47]: test pdb2pka-test: preparing testbed 205s Reading package lists... 205s Building dependency tree... 205s Reading state information... 205s Solving dependencies... 206s The following NEW packages will be installed: 206s fonts-font-awesome fonts-lato libjs-jquery libjs-sphinxdoc libjs-underscore 206s pdb2pqr-doc sphinx-rtd-theme-common 206s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 206s Need to get 5041 kB of archives. 206s After this operation, 20.0 MB of additional disk space will be used. 206s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-lato all 2.015-1 [2781 kB] 208s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB] 208s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 208s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 208s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf libjs-sphinxdoc all 8.2.3-1ubuntu2 [28.0 kB] 208s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf sphinx-rtd-theme-common all 3.0.2+dfsg-3 [1013 kB] 208s Get:7 http://ftpmaster.internal/ubuntu resolute/universe armhf pdb2pqr-doc all 3.6.1+dfsg-1 [258 kB] 209s Fetched 5041 kB in 2s (2575 kB/s) 209s Selecting previously unselected package fonts-lato. 209s (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 ... 62599 files and directories currently installed.) 209s Preparing to unpack .../0-fonts-lato_2.015-1_all.deb ... 209s Unpacking fonts-lato (2.015-1) ... 209s Selecting previously unselected package fonts-font-awesome. 209s Preparing to unpack .../1-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... 209s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 209s Selecting previously unselected package libjs-jquery. 209s Preparing to unpack .../2-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 209s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 209s Selecting previously unselected package libjs-underscore. 209s Preparing to unpack .../3-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 209s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 209s Selecting previously unselected package libjs-sphinxdoc. 209s Preparing to unpack .../4-libjs-sphinxdoc_8.2.3-1ubuntu2_all.deb ... 209s Unpacking libjs-sphinxdoc (8.2.3-1ubuntu2) ... 209s Selecting previously unselected package sphinx-rtd-theme-common. 209s Preparing to unpack .../5-sphinx-rtd-theme-common_3.0.2+dfsg-3_all.deb ... 209s Unpacking sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 209s Selecting previously unselected package pdb2pqr-doc. 209s Preparing to unpack .../6-pdb2pqr-doc_3.6.1+dfsg-1_all.deb ... 209s Unpacking pdb2pqr-doc (3.6.1+dfsg-1) ... 209s Setting up fonts-lato (2.015-1) ... 209s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 209s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... 209s Setting up sphinx-rtd-theme-common (3.0.2+dfsg-3) ... 209s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 209s Setting up libjs-sphinxdoc (8.2.3-1ubuntu2) ... 209s Setting up pdb2pqr-doc (3.6.1+dfsg-1) ... 221s autopkgtest [22:20:05]: test pdb2pka-test: [----------------------- 223s Run pdb2pqr... 223s INFO:PDB2PQR v3.6.1: biomolecular structure conversion software. 223s INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018). 223s 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). 223s INFO:Checking and transforming input arguments. 223s INFO:Loading topology files. 223s INFO:Loading molecule: 1a1p/1a1p.pdb 223s INFO:Setting up molecule. 223s WARNING:Unable to find amino or nucleic acid definition for NH2. Parsing as new residue. 223s INFO:Created biomolecule object with 14 residues and 208 atoms. 223s INFO:Setting termini states for biomolecule chains. 223s INFO:Loading forcefield. 223s INFO:Loading hydrogen topology definitions. 223s INFO:This biomolecule is clean. No repair needed. 223s INFO:Updating disulfide bridges. 223s INFO:Debumping biomolecule. 223s INFO:Adding hydrogens to biomolecule. 223s INFO:Debumping biomolecule (again). 223s INFO:Optimizing hydrogen bonds 223s INFO:Applying force field to biomolecule states. 223s INFO:Regenerating headers. 223s INFO:Regenerating PDB lines. 223s WARNING:Ignoring 852 header lines in output. 223s WARNING:Ignoring 3 missing lines in output. 224s autopkgtest [22:20:08]: test pdb2pka-test: -----------------------] 228s autopkgtest [22:20:12]: test pdb2pka-test: - - - - - - - - - - results - - - - - - - - - - 228s pdb2pka-test PASS 232s autopkgtest [22:20:16]: test command1: preparing testbed 234s Reading package lists... 234s Building dependency tree... 234s Reading state information... 234s Solving dependencies... 235s The following NEW packages will be installed: 235s python3-dateutil python3-iniconfig python3-packaging python3-pandas 235s python3-pandas-lib python3-pluggy python3-pytest python3-pytz 235s python3-testfixtures 235s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 235s Need to get 8663 kB of archives. 235s After this operation, 43.1 MB of additional disk space will be used. 235s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf python3-dateutil all 2.9.0-4 [80.3 kB] 235s Get:2 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 235s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf python3-packaging all 25.0-1 [52.8 kB] 235s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf python3-pytz all 2025.2-3 [163 kB] 236s Get:5 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-9 [4884 kB] 237s Get:6 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pandas all 2.2.3+dfsg-9 [3112 kB] 237s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf python3-pluggy all 1.6.0-1 [21.0 kB] 237s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf python3-pytest all 8.4.2-1 [268 kB] 237s Get:9 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-testfixtures all 8.3.0-2 [75.6 kB] 238s Fetched 8663 kB in 2s (3761 kB/s) 238s Selecting previously unselected package python3-dateutil. 238s (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 ... 62934 files and directories currently installed.) 238s Preparing to unpack .../0-python3-dateutil_2.9.0-4_all.deb ... 238s Unpacking python3-dateutil (2.9.0-4) ... 238s Selecting previously unselected package python3-iniconfig. 238s Preparing to unpack .../1-python3-iniconfig_1.1.1-2_all.deb ... 238s Unpacking python3-iniconfig (1.1.1-2) ... 238s Selecting previously unselected package python3-packaging. 238s Preparing to unpack .../2-python3-packaging_25.0-1_all.deb ... 238s Unpacking python3-packaging (25.0-1) ... 238s Selecting previously unselected package python3-pytz. 238s Preparing to unpack .../3-python3-pytz_2025.2-3_all.deb ... 238s Unpacking python3-pytz (2025.2-3) ... 238s Selecting previously unselected package python3-pandas-lib:armhf. 238s Preparing to unpack .../4-python3-pandas-lib_2.2.3+dfsg-9_armhf.deb ... 238s Unpacking python3-pandas-lib:armhf (2.2.3+dfsg-9) ... 238s Selecting previously unselected package python3-pandas. 238s Preparing to unpack .../5-python3-pandas_2.2.3+dfsg-9_all.deb ... 238s Unpacking python3-pandas (2.2.3+dfsg-9) ... 239s Selecting previously unselected package python3-pluggy. 239s Preparing to unpack .../6-python3-pluggy_1.6.0-1_all.deb ... 239s Unpacking python3-pluggy (1.6.0-1) ... 239s Selecting previously unselected package python3-pytest. 239s Preparing to unpack .../7-python3-pytest_8.4.2-1_all.deb ... 239s Unpacking python3-pytest (8.4.2-1) ... 239s Selecting previously unselected package python3-testfixtures. 239s Preparing to unpack .../8-python3-testfixtures_8.3.0-2_all.deb ... 239s Unpacking python3-testfixtures (8.3.0-2) ... 239s Setting up python3-iniconfig (1.1.1-2) ... 239s Setting up python3-pandas-lib:armhf (2.2.3+dfsg-9) ... 239s Setting up python3-testfixtures (8.3.0-2) ... 239s Setting up python3-pytz (2025.2-3) ... 240s Setting up python3-packaging (25.0-1) ... 240s Setting up python3-pluggy (1.6.0-1) ... 240s Setting up python3-dateutil (2.9.0-4) ... 240s Setting up python3-pytest (8.4.2-1) ... 241s Setting up python3-pandas (2.2.3+dfsg-9) ... 247s Processing triggers for man-db (2.13.1-1) ... 259s autopkgtest [22:20:43]: test command1: pytest-3 259s autopkgtest [22:20:43]: test command1: [----------------------- 262s ============================= test session starts ============================== 262s platform linux -- Python 3.13.7, pytest-8.4.2, pluggy-1.6.0 262s rootdir: /tmp/autopkgtest.Jf4e2W/build.wO4/src 262s configfile: pytest.ini 262s plugins: typeguard-4.4.2 262s 262s ----------------------------- live log collection ------------------------------ 262s WARNING py.warnings:warnings.py:110 /tmp/autopkgtest.Jf4e2W/build.wO4/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 262s @pytest.mark.long_test 262s 262s ERROR regression_test:regression_test.py:173 Need to reinstate the --apbs-input test with a temporary directory as path 262s collected 316 items 262s 262s tests/core_test.py::test_short_pdb[1AQO] SKIPPED (not running tests ...) [ 0%] 262s tests/core_test.py::test_short_pdb[7BNA] SKIPPED (not running tests ...) [ 0%] 262s tests/core_test.py::test_short_pdb[1NAJ] SKIPPED (not running tests ...) [ 0%] 262s tests/core_test.py::test_short_pdb[4E8M] SKIPPED (not running tests ...) [ 1%] 262s tests/core_test.py::test_short_pdb[4UN3] SKIPPED (not running tests ...) [ 1%] 262s tests/core_test.py::test_short_pdb[1FAS] SKIPPED (not running tests ...) [ 1%] 262s tests/core_test.py::test_short_pdb[1K1I] SKIPPED (not running tests ...) [ 2%] 262s tests/core_test.py::test_short_pdb[5D8V] SKIPPED (not running tests ...) 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[ 44%] 262s tests/core_test.py::test_long_pdb[4AXT] SKIPPED (not running tests r...) [ 44%] 262s tests/core_test.py::test_long_pdb[1NXO] SKIPPED (not running tests r...) [ 44%] 262s tests/core_test.py::test_long_pdb[1OA4] SKIPPED (not running tests r...) [ 45%] 262s tests/core_test.py::test_long_pdb[1OPS] SKIPPED (not running tests r...) [ 45%] 262s tests/core_test.py::test_long_pdb[2CWR] SKIPPED (not running tests r...) [ 45%] 262s tests/core_test.py::test_long_pdb[3V1A] SKIPPED (not running tests r...) [ 46%] 262s tests/core_test.py::test_long_pdb[4PGR] SKIPPED (not running tests r...) [ 46%] 262s tests/core_test.py::test_long_pdb[3ZHI] SKIPPED (not running tests r...) [ 46%] 262s tests/core_test.py::test_long_pdb[4S11] SKIPPED (not running tests r...) [ 47%] 262s tests/core_test.py::test_long_pdb[3I1G] SKIPPED (not running tests r...) [ 47%] 262s tests/core_test.py::test_long_pdb[2ZQE] SKIPPED (not running tests r...) [ 47%] 262s tests/core_test.py::test_long_pdb[3CSR] SKIPPED (not running tests r...) [ 48%] 262s tests/core_test.py::test_long_pdb[2ERA] SKIPPED (not running tests r...) [ 48%] 262s tests/core_test.py::test_long_pdb[1DF4] SKIPPED (not running tests r...) [ 48%] 262s tests/core_test.py::test_long_pdb[3T1S] SKIPPED (not running tests r...) [ 49%] 262s tests/core_test.py::test_long_pdb[4I2T] SKIPPED (not running tests r...) [ 49%] 262s tests/core_test.py::test_long_pdb[1X6J] SKIPPED (not running tests r...) [ 49%] 262s tests/core_test.py::test_long_pdb[4POY] SKIPPED (not running tests r...) [ 50%] 262s tests/core_test.py::test_long_pdb[1DUP] SKIPPED (not running tests r...) [ 50%] 262s tests/core_test.py::test_long_pdb[3ZSL] SKIPPED (not running tests r...) [ 50%] 262s tests/core_test.py::test_long_pdb[3DVI] SKIPPED (not running tests r...) [ 50%] 262s tests/core_test.py::test_long_pdb[1TQG] SKIPPED (not running tests r...) [ 51%] 262s tests/core_test.py::test_long_pdb[2FI9] SKIPPED (not running tests r...) [ 51%] 262s tests/core_test.py::test_long_pdb[1AIL] SKIPPED (not running tests r...) [ 51%] 262s tests/core_test.py::test_long_pdb[1I2T] SKIPPED (not running tests r...) [ 52%] 262s tests/core_test.py::test_long_pdb[4HS2] SKIPPED (not running tests r...) [ 52%] 262s tests/core_test.py::test_long_pdb[3JTE] SKIPPED (not running tests r...) [ 52%] 262s tests/core_test.py::test_long_pdb[2SGA] SKIPPED (not running tests r...) [ 53%] 262s tests/core_test.py::test_long_pdb[4IL7] SKIPPED (not running tests r...) [ 53%] 262s tests/core_test.py::test_long_pdb[1TUD] SKIPPED (not running tests r...) [ 53%] 262s tests/core_test.py::test_long_pdb[1OPC] SKIPPED (not running tests r...) [ 54%] 262s tests/core_test.py::test_long_pdb[3H0X] SKIPPED (not running tests r...) [ 54%] 262s tests/core_test.py::test_long_pdb[2OO2] SKIPPED (not running tests r...) [ 54%] 262s tests/core_test.py::test_long_pdb[1FAS] SKIPPED (not running tests r...) [ 55%] 262s tests/core_test.py::test_long_pdb[1Z0P] SKIPPED (not running tests r...) [ 55%] 262s tests/core_test.py::test_long_pdb[2R6Q] SKIPPED (not running tests r...) [ 55%] 262s tests/core_test.py::test_long_pdb[1USM] SKIPPED (not running tests r...) [ 56%] 262s tests/core_test.py::test_long_pdb[3LAA] SKIPPED (not running tests r...) [ 56%] 262s tests/core_test.py::test_long_pdb[2HP7] SKIPPED (not running tests r...) [ 56%] 262s tests/core_test.py::test_long_pdb[3ONJ] SKIPPED (not running tests r...) [ 56%] 262s tests/core_test.py::test_long_pdb[1BM8] SKIPPED (not running tests r...) [ 57%] 262s tests/core_test.py::test_long_pdb[1RJ1] SKIPPED (not running tests r...) [ 57%] 262s tests/core_test.py::test_long_pdb[1SJV] SKIPPED (not running tests r...) [ 57%] 262s tests/core_test.py::test_long_pdb[1LN4] SKIPPED (not running tests r...) [ 58%] 262s tests/core_test.py::test_long_pdb[2IBL] SKIPPED (not running tests r...) [ 58%] 262s tests/core_test.py::test_long_pdb[4EO0] SKIPPED (not running tests r...) [ 58%] 262s tests/core_test.py::test_long_pdb[1P9I] SKIPPED (not running tests r...) [ 59%] 262s tests/core_test.py::test_long_pdb[4GMQ] SKIPPED (not running tests r...) [ 59%] 262s tests/core_test.py::test_long_pdb[3RFI] SKIPPED (not running tests r...) [ 59%] 262s tests/core_test.py::test_long_pdb[1WOU] SKIPPED (not running tests r...) [ 60%] 262s tests/core_test.py::test_long_pdb[2NSN] SKIPPED (not running tests r...) [ 60%] 262s tests/core_test.py::test_long_pdb[1L2P] SKIPPED (not running tests r...) [ 60%] 262s tests/core_test.py::test_long_pdb[4NPN] SKIPPED (not running tests r...) [ 61%] 262s tests/core_test.py::test_long_pdb[2IWN] SKIPPED (not running tests r...) [ 61%] 262s tests/core_test.py::test_long_pdb[5DV8] SKIPPED (not running tests r...) [ 61%] 262s tests/core_test.py::test_long_pdb[1HOE] SKIPPED (not running tests r...) [ 62%] 262s tests/core_test.py::test_long_pdb[3CP1] SKIPPED (not running tests r...) [ 62%] 262s tests/core_test.py::test_long_pdb[1JQ0] SKIPPED (not running tests r...) [ 62%] 262s tests/core_test.py::test_long_pdb[2FWG] SKIPPED (not running tests r...) [ 62%] 262s tests/core_test.py::test_long_pdb[2QBV] SKIPPED (not running tests r...) [ 63%] 262s tests/core_test.py::test_long_pdb[4G3O] SKIPPED (not running tests r...) [ 63%] 262s tests/core_test.py::test_long_pdb[3HRN] SKIPPED (not running tests r...) [ 63%] 262s tests/core_test.py::test_long_pdb[2CKX] SKIPPED (not running tests r...) [ 64%] 262s tests/core_test.py::test_long_pdb[2CJJ] SKIPPED (not running tests r...) [ 64%] 262s tests/core_test.py::test_long_pdb[3SO2] SKIPPED (not running tests r...) [ 64%] 262s tests/core_test.py::test_long_pdb[5EE2] SKIPPED (not running tests r...) [ 65%] 262s tests/core_test.py::test_long_pdb[2J6B] SKIPPED (not running tests r...) [ 65%] 262s tests/core_test.py::test_long_pdb[4Q2Q] SKIPPED (not running tests r...) [ 65%] 262s tests/core_test.py::test_long_pdb[2ERW] SKIPPED (not running tests r...) [ 66%] 262s tests/core_test.py::test_broken_backbone[4MGP] 262s -------------------------------- live log call --------------------------------- 262s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_4MGP_0/4MGP.log 262s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 262s 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). 262s 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). 262s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 262s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 262s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 4MGP 263s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 263s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 263s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 23 residues and 163 atoms. 263s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in MET A 21. 263s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in MET A 21. 263s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in MET A 21. 263s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: SD in MET A 21. 263s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE in MET A 21. 263s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in MET A 21. At least one of the instances is being ignored. 263s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 263s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 263s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 263s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 12 missing atoms in biomolecule. 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 11 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 11 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue LYS A 14 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CD in residue LYS A 14 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CE in residue LYS A 14 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom NZ in residue LYS A 14 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue SER A 23 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue SER A 23 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue SER A 23 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue SER A 23 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OG in residue SER A 23 263s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue SER A 23 263s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 11 at coordinates 1.430, -1.683, -11.529 263s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 11 at coordinates 1.940, -0.315, -11.800 263s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CG to residue LYS A 14 at coordinates -1.600, -8.819, -6.913 263s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CD to residue LYS A 14 at coordinates -2.056, -8.844, -8.361 263s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom CE to residue LYS A 14 at coordinates -3.548, -9.031, -8.498 263s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom NZ to residue LYS A 14 at coordinates -3.947, -9.048, -9.928 263s 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 263s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 263s XFAIL [ 66%] 263s tests/core_test.py::test_broken_backbone[3U7T] 263s -------------------------------- live log call --------------------------------- 263s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_3U7T_0/3U7T.log 263s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 263s 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). 263s 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). 263s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 263s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 263s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 3U7T 264s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 264s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 264s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 652 atoms. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in PRO A 22. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in PRO A 22. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in PRO A 22. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in PRO A 22. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 22. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in PRO A 22. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in PRO A 22. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 22. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 22. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in PRO A 22. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 22. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in PRO A 22. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 22. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 22. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 22. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 22. 264s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 22. At least one of the instances is being ignored. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in LEU A 25. 264s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in LEU A 25. At least one of the instances is being ignored. 264s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 264s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 264s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 264s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 264s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 264s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 264s CRITICAL PDB2PQR3.6.1:main.py:800 Unable to debump biomolecule. Biomolecular structure is incomplete: Found gap in biomolecule structure for atom ATOM 313 OG PRO 22 -13.108 -5.696 -15.739 0.0000 0.0000 264s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 264s XFAIL [ 66%] 264s tests/core_test.py::test_broken_backbone[1EJG] 264s -------------------------------- live log call --------------------------------- 264s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_1EJG_0/1EJG.log 264s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 264s 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). 264s 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). 264s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 264s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 264s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 1EJG 265s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 265s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 265s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 46 residues and 650 atoms. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in THR A 1. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 1. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 1. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 1. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 1. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H1 in THR A 1. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H2 in THR A 1. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H3 in THR A 1. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 1. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 1. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 1. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 1. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 1. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 1. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 1. At least one of the instances is being ignored. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in THR A 2. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 2. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 2. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 2. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in THR A 2. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 2. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG1 in THR A 2. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 2. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 2. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 2. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 2. At least one of the instances is being ignored. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 7. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 7. At least one of the instances is being ignored. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in VAL A 8. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in VAL A 8. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in VAL A 8. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in VAL A 8. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in VAL A 8. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in VAL A 8. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in VAL A 8. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in VAL A 8. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG11 in VAL A 8. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in VAL A 8. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in VAL A 8. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in VAL A 8. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in VAL A 8. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in VAL A 8. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in VAL A 8. At least one of the instances is being ignored. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NE in ARG A 10. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in ARG A 10. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH1 in ARG A 10. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: NH2 in ARG A 10. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE in ARG A 10. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH11 in ARG A 10. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH12 in ARG A 10. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH21 in ARG A 10. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH22 in ARG A 10. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ARG A 10. At least one of the instances is being ignored. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ASN A 12. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASN A 12. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 12. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 12. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 12. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ASN A 12. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASN A 12. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASN A 12. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 12. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 12. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 12. At least one of the instances is being ignored. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PHE A 13. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in PHE A 13. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in PHE A 13. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in PHE A 13. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in PHE A 13. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in PHE A 13. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in PHE A 13. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PHE A 13. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in PHE A 13. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in PHE A 13. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HZ in PHE A 13. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PHE A 13. At least one of the instances is being ignored. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 19. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 19. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 19. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 19. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 19. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in PRO A 19. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in PRO A 19. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 19. At least one of the instances is being ignored. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in SER A 22. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in SER A 22. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in SER A 22. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in SER A 22. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in SER A 22. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in SER A 22. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in SER A 22. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in SER A 22. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in SER A 22. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in SER A 22. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in SER A 22. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in SER A 22. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD3 in SER A 22. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG in SER A 22. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in SER A 22. At least one of the instances is being ignored. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in GLU A 23. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD in GLU A 23. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE1 in GLU A 23. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OE2 in GLU A 23. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in GLU A 23. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in GLU A 23. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in GLU A 23. At least one of the instances is being ignored. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: N in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CA in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: C in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: O in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: H in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HA in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD23 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 25. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 25. At least one of the instances is being ignored. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in TYR A 29. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in TYR A 29. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD2 in TYR A 29. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE1 in TYR A 29. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CE2 in TYR A 29. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CZ in TYR A 29. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OH in TYR A 29. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD1 in TYR A 29. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD2 in TYR A 29. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE1 in TYR A 29. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HE2 in TYR A 29. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HH in TYR A 29. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in TYR A 29. At least one of the instances is being ignored. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ILE A 34. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG1 in ILE A 34. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in ILE A 34. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CD1 in ILE A 34. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in ILE A 34. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG12 in ILE A 34. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG13 in ILE A 34. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in ILE A 34. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in ILE A 34. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in ILE A 34. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD11 in ILE A 34. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD12 in ILE A 34. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD13 in ILE A 34. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ILE A 34. At least one of the instances is being ignored. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in PRO A 36. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in PRO A 36. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in PRO A 36. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in PRO A 36. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG2 in PRO A 36. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG3 in PRO A 36. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in PRO A 36. At least one of the instances is being ignored. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in THR A 39. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OG1 in THR A 39. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG2 in THR A 39. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB in THR A 39. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG21 in THR A 39. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG22 in THR A 39. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HG23 in THR A 39. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in THR A 39. At least one of the instances is being ignored. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CB in ASP A 43. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASP A 43. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASP A 43. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD2 in ASP A 43. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB2 in ASP A 43. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HB3 in ASP A 43. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASP A 43. At least one of the instances is being ignored. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: CG in ASN A 46. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: OD1 in ASN A 46. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: ND2 in ASN A 46. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD21 in ASN A 46. 265s WARNING PDB2PQR3.6.1:main.py:418 Multiple occupancies found: HD22 in ASN A 46. 265s WARNING PDB2PQR3.6.1:main.py:424 Multiple occupancies found in ASN A 46. At least one of the instances is being ignored. 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 INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 265s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 265s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 265s CRITICAL PDB2PQR3.6.1:main.py:800 Unable to debump biomolecule. Biomolecular structure is incomplete: Found gap in biomolecule structure for atom ATOM 405 CG SER 22 4.661 14.854 -4.058 0.0000 0.0000 265s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 265s XFAIL [ 67%] 265s tests/core_test.py::test_broken_backbone[2V75] 265s -------------------------------- live log call --------------------------------- 265s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_broken_backbone_2V75_0/2V75.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. 266s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: 2V75 266s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 266s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 266s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 90 residues and 687 atoms. 266s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 266s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 266s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 266s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 266s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 266s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 266s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 267s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 8 missing atoms in biomolecule. 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CA in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom C in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom O in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CB in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom CG in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OD1 in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom ND2 in residue ASN A 95 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue ASN A 95 267s 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 267s CRITICAL PDB2PQR3.6.1:main.py:801 Giving up. 267s XFAIL [ 67%] 267s tests/core_test.py::test_protonated_terminals[C-terminal HID] 267s -------------------------------- live log call --------------------------------- 267s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_protonated_terminals_C_te0/cterm_hid.log 267s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 267s 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). 267s 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). 267s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 267s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 267s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/cterm_hid.pdb 267s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 267s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 115 atoms. 267s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 267s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 267s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 267s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 1 missing atoms in biomolecule. 267s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue HIS B 209 267s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue HIS B 209 at coordinates -25.652, 1.939, 26.402 267s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 267s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 267s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 267s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 267s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 267s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 267s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 267s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 267s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 267s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 267s INFO common:common.py:198 0 atoms have position differences > 0 267s INFO common:common.py:198 0 atoms have position differences > 0.01 267s INFO common:common.py:198 0 atoms have charge differences > 0 267s INFO common:common.py:198 0 atoms have charge differences > 0.01 267s INFO common:common.py:198 0 atoms have radius differences > 0 267s INFO common:common.py:198 0 atoms have radius differences > 0.01 267s PASSED [ 67%] 267s tests/core_test.py::test_cyclic_peptide[Cyclic peptide] 267s -------------------------------- live log call --------------------------------- 267s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_cyclic_peptide_Cyclic_pep0/5vav_cyclic_peptide.log 267s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 267s 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). 267s 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). 267s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 267s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 267s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/5vav_cyclic_peptide.pdb 267s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 267s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 209 atoms. 267s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 267s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 267s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 267s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 267s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 267s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 267s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 267s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 267s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 267s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 267s INFO PDB2PQR3.6.1:main.py:707 Applying custom naming scheme (amber). 267s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 267s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 267s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 464 header lines in output. 267s INFO common:common.py:198 0 atoms have position differences > 0 267s INFO common:common.py:198 0 atoms have position differences > 0.01 267s INFO common:common.py:198 0 atoms have charge differences > 0 267s INFO common:common.py:198 0 atoms have charge differences > 0.01 267s INFO common:common.py:198 0 atoms have radius differences > 0 267s INFO common:common.py:198 0 atoms have radius differences > 0.01 267s PASSED [ 68%] 267s tests/io_test.py::test_read_pqr[tests/data/dx2cube.pqr] PASSED [ 68%] 267s tests/io_test.py::test_read_pqr[tests/data/cterm_hid_out.pqr] PASSED [ 68%] 267s tests/io_test.py::test_read_pqr[tests/data/5vav_cyclic_peptide_out.pqr] PASSED [ 68%] 267s 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%] 267s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=TYL06.pqr] PASSED [ 69%] 267s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=SWANSON.pqr] PASSED [ 69%] 267s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PEOEPB.pqr] PASSED [ 70%] 267s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=PARSE.pqr] PASSED [ 70%] 267s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=CHARMM.pqr] PASSED [ 70%] 267s tests/io_test.py::test_read_pqr[tests/data/1AFS_whitespace_ff=AMBER.pqr] PASSED [ 71%] 267s tests/io_test.py::test_read_pqr[tests/data/1AFS_userff_usernames_whitespace.pqr] PASSED [ 71%] 267s tests/io_test.py::test_read_pqr[tests/data/1AFS_nodebump_noopt_whitespace_ff=AMBER.pqr] PASSED [ 71%] 267s tests/io_test.py::test_read_pqr[tests/data/1AFS_neutralc_neutraln_whitespace_ff=PARSE.pqr] PASSED [ 72%] 267s tests/io_test.py::test_read_pqr[tests/data/1AFS_ff=AMBER.pqr] PASSED [ 72%] 267s tests/io_test.py::test_read_pqr[tests/data/1AFS_drop-water_ff=AMBER.pqr] PASSED [ 72%] 267s tests/io_test.py::test_read_pqr[tests/data/1AFS_clean_whitespace.pqr] PASSED [ 73%] 268s tests/io_test.py::test_read_pqr[tests/data/1AFS_chain_whitespace_ff=AMBER.pqr] PASSED [ 73%] 268s tests/io_test.py::test_read_pqr[tests/data/1AFS_apbs-input_include-header_whitespace_ff=AMBER.pqr] PASSED [ 73%] 268s tests/io_test.py::test_read_pqr[tests/data/1A1P_assign-only_whitespace_ff=AMBER.pqr] PASSED [ 74%] 268s tests/io_test.py::test_read_qcd PASSED [ 74%] 268s tests/io_test.py::test_dx2cube 268s -------------------------------- live log call --------------------------------- 268s INFO io_test:io_test.py:44 Reading PQR from tests/data/dx2cube.pqr... 268s INFO io_test:io_test.py:47 Reading DX from tests/data/dx2cube.dx... 268s INFO io_test:io_test.py:50 Writing Cube to /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 269s INFO io_test:io_test.py:53 Reading this cube from /tmp/pytest-of-ubuntu/pytest-0/test_dx2cube0/test.cube... 269s INFO io_test:io_test.py:55 Reading test cube from tests/data/dx2cube.cube... 269s INFO io_test:io_test.py:68 No differences found in output 270s PASSED [ 74%] 270s tests/ligand_test.py::test_peoe_charges 270s -------------------------------- live log call --------------------------------- 270s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 270s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 270s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 270s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 270s PASSED [ 75%] 271s tests/ligand_test.py::test_assign_parameters[1HPX-ligand.mol2] 271s -------------------------------- live log call --------------------------------- 271s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 271s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 271s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 271s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 271s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 271s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 271s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 271s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 271s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 271s PASSED [ 75%] 271s tests/ligand_test.py::test_assign_parameters[1QBS-ligand.mol2] 271s -------------------------------- live log call --------------------------------- 271s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 271s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 271s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 271s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 271s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 271s PASSED [ 75%] 271s tests/ligand_test.py::test_assign_parameters[1US0-ligand.mol2] 271s -------------------------------- live log call --------------------------------- 271s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 271s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 271s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 272s PASSED [ 75%] 272s tests/ligand_test.py::test_assign_parameters[acetate.mol2] 272s -------------------------------- live log call --------------------------------- 272s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 272s PASSED [ 76%] 272s tests/ligand_test.py::test_assign_parameters[acetonitrile.mol2] 272s -------------------------------- live log call --------------------------------- 272s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 272s PASSED [ 76%] 272s tests/ligand_test.py::test_assign_parameters[acetylcholine.mol2] 272s -------------------------------- live log call --------------------------------- 272s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 272s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 272s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 272s PASSED [ 76%] 272s tests/ligand_test.py::test_assign_parameters[adp.mol2] 272s -------------------------------- live log call --------------------------------- 272s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 272s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 272s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 272s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 272s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 272s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 272s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 272s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 272s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 272s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 272s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 272s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 272s INFO ligand_test:ligand_test.py:73 Total charge: -2.00 -> -2.00 272s PASSED [ 77%] 272s tests/ligand_test.py::test_assign_parameters[anthracene.mol2] 272s -------------------------------- live log call --------------------------------- 272s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 272s PASSED [ 77%] 272s tests/ligand_test.py::test_assign_parameters[cyclohexane.mol2] 272s -------------------------------- live log call --------------------------------- 272s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 272s PASSED [ 77%] 272s tests/ligand_test.py::test_assign_parameters[ethanol.mol2] 272s -------------------------------- live log call --------------------------------- 272s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 272s PASSED [ 78%] 272s tests/ligand_test.py::test_assign_parameters[fatty-acid.mol2] 272s -------------------------------- live log call --------------------------------- 272s INFO ligand_test:ligand_test.py:73 Total charge: -1.00 -> -1.00 272s PASSED [ 78%] 272s tests/ligand_test.py::test_assign_parameters[glycerol.mol2] 272s -------------------------------- live log call --------------------------------- 272s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 272s PASSED [ 78%] 272s tests/ligand_test.py::test_assign_parameters[naphthalene.mol2] 272s -------------------------------- live log call --------------------------------- 272s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> -0.00 272s PASSED [ 79%] 272s tests/ligand_test.py::test_assign_parameters[pyrrole.mol2] 272s -------------------------------- live log call --------------------------------- 272s INFO ligand_test:ligand_test.py:73 Total charge: 0.00 -> 0.00 272s PASSED [ 79%] 272s tests/ligand_test.py::test_assign_parameters[tetramethylammonium.mol2] 272s -------------------------------- live log call --------------------------------- 272s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 272s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 272s INFO ligand_test:ligand_test.py:73 Total charge: 1.00 -> 1.00 272s PASSED [ 79%] 272s tests/ligand_test.py::test_formal_charge[1HPX-ligand.mol2] 272s -------------------------------- live log call --------------------------------- 272s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 272s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 272s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 272s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 272s PASSED [ 80%] 273s tests/ligand_test.py::test_formal_charge[1QBS-ligand.mol2] 273s -------------------------------- live log call --------------------------------- 273s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 273s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 273s PASSED [ 80%] 273s tests/ligand_test.py::test_formal_charge[1US0-ligand.mol2] 273s -------------------------------- live log call --------------------------------- 273s WARNING pdb2pqr.ligand.mol2:mol2.py:245 Correcting planar/amide bond order. 273s PASSED [ 80%] 273s tests/ligand_test.py::test_formal_charge[acetate.mol2] PASSED [ 81%] 273s tests/ligand_test.py::test_formal_charge[acetonitrile.mol2] PASSED [ 81%] 273s tests/ligand_test.py::test_formal_charge[acetylcholine.mol2] 273s -------------------------------- live log call --------------------------------- 273s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 273s PASSED [ 81%] 273s tests/ligand_test.py::test_formal_charge[adp.mol2] 273s -------------------------------- live log call --------------------------------- 273s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 273s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 273s WARNING pdb2pqr.ligand.mol2:mol2.py:295 Correcting phosphate bond order. 273s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 273s WARNING pdb2pqr.ligand.mol2:mol2.py:253 Correcting aromatic nitrogen bond order. 273s WARNING pdb2pqr.ligand.mol2:mol2.py:261 Correcting aromatic carbon bond order. 273s PASSED [ 81%] 273s tests/ligand_test.py::test_formal_charge[anthracene.mol2] PASSED [ 82%] 273s tests/ligand_test.py::test_formal_charge[cyclohexane.mol2] PASSED [ 82%] 273s tests/ligand_test.py::test_formal_charge[ethanol.mol2] PASSED [ 82%] 273s tests/ligand_test.py::test_formal_charge[fatty-acid.mol2] PASSED [ 83%] 273s tests/ligand_test.py::test_formal_charge[glycerol.mol2] PASSED [ 83%] 273s tests/ligand_test.py::test_formal_charge[naphthalene.mol2] PASSED [ 83%] 273s tests/ligand_test.py::test_formal_charge[pyrrole.mol2] PASSED [ 84%] 273s tests/ligand_test.py::test_formal_charge[tetramethylammonium.mol2] 273s -------------------------------- live log call --------------------------------- 273s WARNING pdb2pqr.ligand.mol2:mol2.py:283 Correcting ammonium atom type. 273s PASSED [ 84%] 273s tests/ligand_test.py::test_torsions[acetylcholine.mol2] PASSED [ 84%] 273s tests/ligand_test.py::test_torsions[ethanol.mol2] PASSED [ 85%] 273s tests/ligand_test.py::test_torsions[pyrrole.mol2] PASSED [ 85%] 273s tests/ligand_test.py::test_torsions[tetramethylammonium.mol2] PASSED [ 85%] 273s tests/ligand_test.py::test_torsions[glycerol.mol2] PASSED [ 86%] 273s tests/ligand_test.py::test_torsions[cyclohexane.mol2] PASSED [ 86%] 274s tests/ligand_test.py::test_rings[1HPX-ligand.mol2] PASSED [ 86%] 275s tests/ligand_test.py::test_rings[1QBS-ligand.mol2] PASSED [ 87%] 275s tests/ligand_test.py::test_rings[1US0-ligand.mol2] PASSED [ 87%] 275s tests/ligand_test.py::test_rings[acetate.mol2] PASSED [ 87%] 275s tests/ligand_test.py::test_rings[acetonitrile.mol2] PASSED [ 87%] 275s tests/ligand_test.py::test_rings[acetylcholine.mol2] PASSED [ 88%] 275s tests/ligand_test.py::test_rings[adp.mol2] PASSED [ 88%] 275s tests/ligand_test.py::test_rings[anthracene.mol2] PASSED [ 88%] 275s tests/ligand_test.py::test_rings[cyclohexane.mol2] PASSED [ 89%] 275s tests/ligand_test.py::test_rings[ethanol.mol2] PASSED [ 89%] 275s tests/ligand_test.py::test_rings[fatty-acid.mol2] PASSED [ 89%] 275s tests/ligand_test.py::test_rings[glycerol.mol2] PASSED [ 90%] 275s tests/ligand_test.py::test_rings[naphthalene.mol2] PASSED [ 90%] 275s tests/ligand_test.py::test_rings[pyrrole.mol2] PASSED [ 90%] 275s tests/ligand_test.py::test_rings[tetramethylammonium.mol2] PASSED [ 91%] 275s tests/ligand_test.py::test_ligand_biomolecule[1HPX] SKIPPED (not run...) [ 91%] 275s tests/logging_test.py::test_log_output_in_pqr_location[1A1P.pdb-1A1P_assign-only_whitespace_ff=AMBER_log.pqr] PASSED [ 91%] 275s tests/propka_test.py::test_propka_apo[1K1I] SKIPPED (not running tes...) [ 92%] 275s tests/propka_test.py::test_propka_apo[1AFS] SKIPPED (not running tes...) [ 92%] 275s tests/propka_test.py::test_propka_apo[1FAS] SKIPPED (not running tes...) [ 92%] 275s tests/propka_test.py::test_propka_apo[5DV8] SKIPPED (not running tes...) [ 93%] 275s tests/propka_test.py::test_propka_apo[5D8V] SKIPPED (not running tes...) [ 93%] 275s tests/propka_test.py::test_propka_pka[1K1I] SKIPPED (not running tes...) [ 93%] 275s tests/propka_test.py::test_propka_pka[1AFS] SKIPPED (not running tes...) [ 93%] 275s tests/propka_test.py::test_propka_pka[1FAS] SKIPPED (not running tes...) [ 94%] 275s tests/propka_test.py::test_propka_pka[5DV8] SKIPPED (not running tes...) [ 94%] 275s tests/propka_test.py::test_propka_pka[5D8V] SKIPPED (not running tes...) [ 94%] 275s tests/regression_test.py::test_basic[1AFS basic local] 275s -------------------------------- live log call --------------------------------- 275s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_basic_1AFS_basic_local_0/output.log 275s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 275s 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). 275s 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). 275s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 275s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 275s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 275s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 275s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 275s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 275s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 275s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 275s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 275s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 275s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 275s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 275s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 275s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 275s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 275s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 275s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 275s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 275s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 275s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 275s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 275s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 275s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 275s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 276s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 277s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 278s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 278s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 278s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 278s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 278s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 278s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 278s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H1 in HOH A 333 skipped when optimizing H2 in HOH A 334 278s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 278s WARNING pdb2pqr.debump:debump.py:354 Skipped atom during water optimization: H2 in HOH A 334 skipped when optimizing H2 in HOH A 333 278s WARNING pdb2pqr.io:io.py:40 Suppressing further "Skipped atom during water optimization" messages 280s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 280s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 280s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 280s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 280s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 280s WARNING common:common.py:186 6 atoms have position differences > 0 280s INFO common:common.py:198 0 atoms have position differences > 0.01 280s INFO common:common.py:198 0 atoms have charge differences > 0 280s INFO common:common.py:198 0 atoms have charge differences > 0.01 280s INFO common:common.py:198 0 atoms have radius differences > 0 280s INFO common:common.py:198 0 atoms have radius differences > 0.01 280s PASSED [ 95%] 280s tests/regression_test.py::test_forcefields[1AFS whitespace AMBER] 280s -------------------------------- live log call --------------------------------- 280s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa0/output.log 280s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 280s 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). 280s 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). 280s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 280s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 280s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 280s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 280s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 280s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 280s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for NAP. Parsing as new residue. 280s WARNING pdb2pqr.biomolecule:biomolecule.py:992 Unable to find amino or nucleic acid definition for TES. Parsing as new residue. 280s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 280s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 280s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 280s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 280s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 280s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 280s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 280s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 280s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 280s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 280s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 281s 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 [ 95%] 285s tests/regression_test.py::test_forcefields[1AFS whitespace CHARMM] 285s -------------------------------- live log call --------------------------------- 285s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa1/output.log 285s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 285s 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). 285s 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). 285s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 285s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 285s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 285s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 285s WARNING pdb2pqr.io:io.py:40 Suppressing further "Unable to find amino or nucleic acid definition for" messages 285s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 285s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 285s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 285s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 285s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 285s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 285s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 285s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 285s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 285s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 285s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 285s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 285s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 285s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 285s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 286s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 286s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 287s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 290s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 290s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 290s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 290s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 290s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 290s WARNING common:common.py:186 5 atoms have position differences > 0 290s INFO common:common.py:198 0 atoms have position differences > 0.01 290s INFO common:common.py:198 0 atoms have charge differences > 0 290s INFO common:common.py:198 0 atoms have charge differences > 0.01 290s INFO common:common.py:198 0 atoms have radius differences > 0 290s INFO common:common.py:198 0 atoms have radius differences > 0.01 290s PASSED [ 95%] 290s tests/regression_test.py::test_forcefields[1AFS whitespace PARSE] 290s -------------------------------- live log call --------------------------------- 290s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa2/output.log 290s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 290s 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). 290s 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). 290s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 290s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 290s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 291s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 291s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 291s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 291s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 291s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 291s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 291s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 291s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 291s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 291s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 291s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 291s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 291s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 291s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 291s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 291s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 291s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 291s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 292s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 295s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 295s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 295s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 295s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 295s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 295s WARNING common:common.py:186 6 atoms have position differences > 0 295s INFO common:common.py:198 0 atoms have position differences > 0.01 295s INFO common:common.py:198 0 atoms have charge differences > 0 295s INFO common:common.py:198 0 atoms have charge differences > 0.01 295s INFO common:common.py:198 0 atoms have radius differences > 0 295s INFO common:common.py:198 0 atoms have radius differences > 0.01 295s PASSED [ 96%] 295s tests/regression_test.py::test_forcefields[1AFS whitespace PEOEPB] 295s -------------------------------- live log call --------------------------------- 295s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa3/output.log 295s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 296s 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). 296s 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). 296s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 296s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 296s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 296s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 296s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 296s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 296s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 296s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 296s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 296s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 296s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 296s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 296s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 296s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 296s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 296s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 296s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 296s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 296s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 296s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 296s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 297s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 300s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 300s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 300s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 300s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5426 header lines in output. 300s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 301s WARNING common:common.py:186 6 atoms have position differences > 0 301s INFO common:common.py:198 0 atoms have position differences > 0.01 301s INFO common:common.py:198 0 atoms have charge differences > 0 301s INFO common:common.py:198 0 atoms have charge differences > 0.01 301s INFO common:common.py:198 0 atoms have radius differences > 0 301s INFO common:common.py:198 0 atoms have radius differences > 0.01 301s PASSED [ 96%] 301s tests/regression_test.py::test_forcefields[1AFS whitespace SWANSON] 301s -------------------------------- live log call --------------------------------- 301s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa4/output.log 301s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 301s 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). 301s 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). 301s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 301s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 301s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 301s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 301s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 301s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 301s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 301s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 301s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 301s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 301s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 301s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 301s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 301s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 301s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 301s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 301s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 301s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 301s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 301s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 302s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 302s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 306s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 306s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 306s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 306s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5428 header lines in output. 306s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 306s WARNING common:common.py:186 6 atoms have position differences > 0 306s INFO common:common.py:198 0 atoms have position differences > 0.01 306s INFO common:common.py:198 0 atoms have charge differences > 0 306s INFO common:common.py:198 0 atoms have charge differences > 0.01 306s INFO common:common.py:198 0 atoms have radius differences > 0 306s INFO common:common.py:198 0 atoms have radius differences > 0.01 306s PASSED [ 96%] 306s tests/regression_test.py::test_forcefields[1AFS whitespace TYL06] 306s -------------------------------- live log call --------------------------------- 306s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_forcefields_1AFS_whitespa5/output.log 306s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 306s 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). 306s 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). 306s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 306s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 306s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 306s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 306s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 306s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 306s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 306s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 306s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 306s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 306s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 306s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 306s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 306s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 306s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 306s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 306s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 306s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 306s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 306s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 307s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 308s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 311s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 311s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 311s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 311s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 311s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 311s WARNING common:common.py:186 6 atoms have position differences > 0 311s INFO common:common.py:198 0 atoms have position differences > 0.01 311s INFO common:common.py:198 0 atoms have charge differences > 0 311s INFO common:common.py:198 0 atoms have charge differences > 0.01 311s INFO common:common.py:198 0 atoms have radius differences > 0 311s INFO common:common.py:198 0 atoms have radius differences > 0.01 311s PASSED [ 97%] 311s tests/regression_test.py::test_other_options[1AFS whitespace clean] 311s -------------------------------- live log call --------------------------------- 311s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_whites0/output.log 311s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 311s 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). 311s 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). 311s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 311s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 311s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 311s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 311s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 311s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 311s INFO PDB2PQR3.6.1:main.py:778 Arguments specified cleaning only; skipping remaining steps. 311s INFO common:common.py:198 0 atoms have position differences > 0 311s INFO common:common.py:198 0 atoms have position differences > 0.01 311s INFO common:common.py:198 0 atoms have charge differences > 0 311s INFO common:common.py:198 0 atoms have charge differences > 0.01 311s INFO common:common.py:198 0 atoms have radius differences > 0 311s INFO common:common.py:198 0 atoms have radius differences > 0.01 311s PASSED [ 97%] 311s tests/regression_test.py::test_other_options[1A1P assign-only whitespace AMBER] 311s -------------------------------- live log call --------------------------------- 311s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_assign0/output.log 311s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 311s 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). 311s 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). 311s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 311s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 312s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 312s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 312s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 312s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 312s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 312s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 312s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 312s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 312s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 312s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 312s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 312s INFO common:common.py:198 0 atoms have position differences > 0 312s INFO common:common.py:198 0 atoms have position differences > 0.01 312s INFO common:common.py:198 0 atoms have charge differences > 0 312s INFO common:common.py:198 0 atoms have charge differences > 0.01 312s INFO common:common.py:198 0 atoms have radius differences > 0 312s INFO common:common.py:198 0 atoms have radius differences > 0.01 312s PASSED [ 97%] 312s tests/regression_test.py::test_other_options[1A1P nodebump noopt whitespace AMBER] 312s -------------------------------- live log call --------------------------------- 312s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1A1P_nodebu0/output.log 312s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 312s 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). 312s 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). 312s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 312s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 312s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1A1P.pdb 312s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 312s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 14 residues and 208 atoms. 312s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 312s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 312s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 312s INFO PDB2PQR3.6.1:main.py:459 This biomolecule is clean. No repair needed. 312s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 312s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 312s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 312s INFO pdb2pqr.hydrogens:__init__.py:370 Initializing water bonding optimization... 312s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 312s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 312s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 312s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 852 header lines in output. 312s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 3 missing lines in output. 312s INFO common:common.py:198 0 atoms have position differences > 0 312s INFO common:common.py:198 0 atoms have position differences > 0.01 312s INFO common:common.py:198 0 atoms have charge differences > 0 312s INFO common:common.py:198 0 atoms have charge differences > 0.01 312s INFO common:common.py:198 0 atoms have radius differences > 0 312s INFO common:common.py:198 0 atoms have radius differences > 0.01 312s PASSED [ 98%] 312s tests/regression_test.py::test_other_options[1AFS chain whitespace AMBER] 312s -------------------------------- live log call --------------------------------- 312s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_chain_0/output.log 312s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 312s 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). 312s 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). 312s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 312s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 312s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 312s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 312s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 312s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 312s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 312s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 312s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 312s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 312s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 312s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 312s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 312s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 312s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 312s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 312s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 312s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 312s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 312s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 313s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 314s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 317s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 317s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 317s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 317s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 317s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 317s WARNING common:common.py:186 6 atoms have position differences > 0 317s INFO common:common.py:198 0 atoms have position differences > 0.01 317s INFO common:common.py:198 0 atoms have charge differences > 0 317s INFO common:common.py:198 0 atoms have charge differences > 0.01 317s INFO common:common.py:198 0 atoms have radius differences > 0 317s INFO common:common.py:198 0 atoms have radius differences > 0.01 317s PASSED [ 98%] 317s tests/regression_test.py::test_other_options[1AFS neutralc neutraln PARSE] 317s -------------------------------- live log call --------------------------------- 317s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_neutra0/output.log 317s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 317s 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). 317s 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). 317s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 317s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 317s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 317s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 317s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 317s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 317s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 317s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 317s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 317s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 318s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 318s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 318s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 318s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 318s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 318s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 318s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 318s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 318s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 318s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 318s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 319s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 322s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 322s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 322s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 322s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 322s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 323s WARNING common:common.py:186 6 atoms have position differences > 0 323s INFO common:common.py:198 0 atoms have position differences > 0.01 323s INFO common:common.py:198 0 atoms have charge differences > 0 323s INFO common:common.py:198 0 atoms have charge differences > 0.01 323s INFO common:common.py:198 0 atoms have radius differences > 0 323s INFO common:common.py:198 0 atoms have radius differences > 0.01 323s PASSED [ 98%] 323s tests/regression_test.py::test_other_options[1AFS drop-water AMBER] 323s -------------------------------- live log call --------------------------------- 323s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_drop_w0/output.log 323s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 323s 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). 323s 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). 323s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 323s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 323s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 323s INFO PDB2PQR3.6.1:main.py:768 Dropping water from structure. 323s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 323s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 642 residues and 5300 atoms. 323s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 323s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 323s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 323s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 323s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 323s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 323s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 323s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 323s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 323s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 323s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 323s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 323s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 323s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 323s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 323s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 324s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 326s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 326s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 326s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 326s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 326s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 327s WARNING common:common.py:186 6 atoms have position differences > 0 327s INFO common:common.py:198 0 atoms have position differences > 0.01 327s INFO common:common.py:198 0 atoms have charge differences > 0 327s INFO common:common.py:198 0 atoms have charge differences > 0.01 327s INFO common:common.py:198 0 atoms have radius differences > 0 327s INFO common:common.py:198 0 atoms have radius differences > 0.01 327s PASSED [ 99%] 327s tests/regression_test.py::test_other_options[1AFS userff usernames whitespace] 327s -------------------------------- live log call --------------------------------- 327s INFO pdb2pqr.io:io.py:514 Logs stored: /tmp/pytest-of-ubuntu/pytest-0/test_other_options_1AFS_userff0/output.log 327s INFO PDB2PQR3.6.1:main.py:240 PDB2PQR v3.6.1: biomolecular structure conversion software. 327s 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). 327s 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). 327s INFO PDB2PQR3.6.1:main.py:759 Checking and transforming input arguments. 327s INFO PDB2PQR3.6.1:main.py:763 Loading topology files. 327s INFO PDB2PQR3.6.1:main.py:765 Loading molecule: tests/data/1AFS.pdb 327s INFO PDB2PQR3.6.1:main.py:770 Setting up molecule. 327s INFO PDB2PQR3.6.1:main.py:408 Created biomolecule object with 700 residues and 5358 atoms. 327s INFO PDB2PQR3.6.1:main.py:774 Setting termini states for biomolecule chains. 327s INFO PDB2PQR3.6.1:main.py:604 Loading forcefield. 327s INFO PDB2PQR3.6.1:main.py:608 Loading hydrogen topology definitions. 327s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 327s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 327s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 327s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 327s INFO PDB2PQR3.6.1:main.py:618 Attempting to repair 2 missing atoms in biomolecule. 327s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE A 319 327s WARNING pdb2pqr.biomolecule:biomolecule.py:157 Missing atom OXT in residue PHE B 319 327s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE A 319 at coordinates -20.664, 13.168, 13.288 327s INFO pdb2pqr.biomolecule:biomolecule.py:1077 Added atom OXT to residue PHE B 319 at coordinates -20.299, 64.352, -34.928 327s INFO PDB2PQR3.6.1:main.py:623 Updating disulfide bridges. 327s INFO PDB2PQR3.6.1:main.py:626 Debumping biomolecule. 327s INFO PDB2PQR3.6.1:main.py:649 Adding hydrogens to biomolecule. 328s INFO PDB2PQR3.6.1:main.py:652 Debumping biomolecule (again). 329s INFO PDB2PQR3.6.1:main.py:654 Optimizing hydrogen bonds 332s INFO PDB2PQR3.6.1:main.py:666 Applying force field to biomolecule states. 332s INFO PDB2PQR3.6.1:main.py:713 Regenerating headers. 332s INFO PDB2PQR3.6.1:main.py:738 Regenerating PDB lines. 332s WARNING PDB2PQR3.6.1:main.py:311 Ignoring 5424 header lines in output. 332s WARNING PDB2PQR3.6.1:main.py:315 Ignoring 138 missing lines in output. 332s WARNING common:common.py:186 6 atoms have position differences > 0 332s INFO common:common.py:198 0 atoms have position differences > 0.01 332s INFO common:common.py:198 0 atoms have charge differences > 0 332s INFO common:common.py:198 0 atoms have charge differences > 0.01 332s INFO common:common.py:198 0 atoms have radius differences > 0 332s INFO common:common.py:198 0 atoms have radius differences > 0.01 332s PASSED [ 99%] 332s tests/test_version.py::test_version_exists PASSED [ 99%] 333s tests/test_version.py::test_version PASSED [100%] 333s 333s ============ 92 passed, 220 skipped, 4 xfailed in 71.04s (0:01:11) ============= 333s autopkgtest [22:21:57]: test command1: -----------------------] 337s autopkgtest [22:22:01]: test command1: - - - - - - - - - - results - - - - - - - - - - 337s command1 PASS 341s autopkgtest [22:22:05]: @@@@@@@@@@@@@@@@@@@@ summary 341s installation-test PASS 341s pdb2pka-test PASS 341s command1 PASS