Test: linux.clang.integration.release_debug_no_symbols 「view this page in B3 βῆτα server」
Branch: rosetta:commits 「revision: №20668」
Test files: 「file-system-view」 「file-list-view」
Daemon: hojo-2     Started at: 2025-03-25 14:46:49     Run time: 1:12:06      State: failed

Failed sub-tests (click for more details):
features include_cc_check ligand_motif_discovery ligand_motif_identification real_motif_analysis remove_duplicate_motifs

Compiling: find bin -type l ! -name ".*" -exec rm {} \; ; /home/benchmark/prefix/hojo-2/linux/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9 ./scons.py bin mode=release_debug_no_symbols cxx=clang extras= -j24 Running: unset __PYVENV_LAUNCHER__ && . /home/benchmark/prefix/hojo-2/linux/python_virtual_environments/python-3.9/df3055f6f81b525b8050290cef45e968/bin/activate && cd /home/benchmark/rosetta/tests/integration && python ./integration.py --mode=release_debug_no_symbols --compiler=clang --extras= --timeout=3600 -j24 --skip-comparison --additional_flags "-in:path:database_cache_dir /home/benchmark/rosetta/.database-binaries/linuxclangrelease_debug_no_symbols" Running integration script... Command line: unset __PYVENV_LAUNCHER__ && . /home/benchmark/prefix/hojo-2/linux/python_virtual_environments/python-3.9/df3055f6f81b525b8050290cef45e968/bin/activate && cd /home/benchmark/rosetta/tests/integration && python ./integration.py --mode=release_debug_no_symbols --compiler=clang --extras= --timeout=3600 -j24 --skip-comparison --additional_flags "-in:path:database_cache_dir /home/benchmark/rosetta/.database-binaries/linuxclangrelease_debug_no_symbols" Using Rosetta source dir at: /home/benchmark/rosetta/source Using Rosetta database dir at:/home/benchmark/rosetta/database Current Versions Tested: MAIN: 7ff170db059b0ec642ec65933626395bfc321c4e TOOLS: b0af2521cbed1f2bde597ef1c5406efa376a6f85 DEMOS: 48c9239db73b9a8c828954d9215c983b9f144c92 Python: `/home/benchmark/prefix/hojo-2/linux/python_virtual_environments/python-3.9/df3055f6f81b525b8050290cef45e968/bin/python` Outdir: new No correct command.sh file found for test_rosetta_thread_manager_basic_API. Skipping. No correct command.sh file found for test_rosetta_thread_manager_advanced_API. Skipping. Running Test remove_duplicate_motifs ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/remove_duplicate_motifs/command.sh No correct command.sh file found for proteinMPNN_model_perplexity. Skipping. No correct command.sh file found for multithreaded_packrotamersmover. Skipping. No correct command.sh file found for multithreaded_interaction_graph_accuracy_symm. Skipping. No correct command.sh file found for multithreaded_interaction_graph_accuracy. Skipping. No correct command.sh file found for multithreaded_fixbb. Skipping. No correct command.sh file found for multithreaded_fastdesign. Skipping. Running Test real_motif_analysis ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/real_motif_analysis/command.sh No correct command.sh file found for bcl_fragment_mutate. Skipping. No correct command.sh file found for antibody_cc. Skipping. No correct command.sh file found for replica_docking. Skipping. No correct command.sh file found for abinitio_with_trRosetta. Skipping. No correct command.sh file found for trRosetta_test_predict_ubiquitin_init_by_bins. Skipping. No correct command.sh file found for trRosettaProtocolMover. Skipping. No correct command.sh file found for trRosetta_test_predict. Skipping. No correct command.sh file found for smart_annealer. Skipping. No correct command.sh file found for PTMPrediction. Skipping. Running Test mp_f19_relax ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_f19_relax/command.sh No correct command.sh file found for mpi_simple_cycpep_predict_computing_pnear_to_all. Skipping. No correct command.sh file found for recon_design_mpi. Skipping. No correct command.sh file found for mpi_simple_cycpep_predict_4level. Skipping. No correct command.sh file found for mpi_simple_cycpep_predict. Skipping. No correct command.sh file found for features_pdb_mpi. Skipping. Running Test app_exception_handling ulimit -t 7200 && bash /home/benchmark/rosetta/tests/integration/new/app_exception_handling/command.sh Running Test dgdp_script ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/dgdp_script/command.sh Running Test simple_cycpep_predict_square_pyramidal_metal ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_square_pyramidal_metal/command.sh Running Test auto-drrafter_setup_run_R2 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/auto-drrafter_setup_run_R2/command.sh Running Test dgdp_aio ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/dgdp_aio/command.sh Running Test database_md5 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/database_md5/command.sh Running Test ddG_of_mutation ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ddG_of_mutation/command.sh Running Test antibody_H3 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/antibody_H3/command.sh Running Test fast_relax_scripts ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/fast_relax_scripts/command.sh Running Test cyclization ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cyclization/command.sh Running Test ccd_ends_graft_mover_rs ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ccd_ends_graft_mover_rs/command.sh Running Test glycopeptidedocking_diglyco_long ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/glycopeptidedocking_diglyco_long/command.sh Running Test bundlegridsampler_composition_energy ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/bundlegridsampler_composition_energy/command.sh Running Test add_helix_sequence_constraints ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/add_helix_sequence_constraints/command.sh Running Test glycan_tree_relax ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/glycan_tree_relax/command.sh Running Test crosslinkermover_octahedral ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_octahedral/command.sh Running Test ligand_dock_ensemble ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ligand_dock_ensemble/command.sh Running Test nonideal_rtmin ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/nonideal_rtmin/command.sh Running Test ga_ligand_dock ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ga_ligand_dock/command.sh Running Test ddG_sym ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ddG_sym/command.sh Running Test buried_unsat_voids_hbnet_design_symm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/buried_unsat_voids_hbnet_design_symm/command.sh Encounter error while executing: ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/remove_duplicate_motifs/command.sh *** Test remove_duplicate_motifs did not run! Check your --mode flag and paths. [2025-03-25 14:48:52.452048] Finished remove_duplicate_motifs in 4 seconds [~ 47 test (5.831265508684863%) started, 759 in queue, 24 running] Running Test add_helix_sequence_constraints_advanced_setup ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/add_helix_sequence_constraints_advanced_setup/command.sh Encounter error while executing: ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/real_motif_analysis/command.sh *** Test real_motif_analysis did not run! Check your --mode flag and paths. [2025-03-25 14:49:00.134340] Finished real_motif_analysis in 12 seconds [~ 48 test (5.955334987593052%) started, 758 in queue, 24 running] Running Test auto-drrafter_setup_run_R1 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/auto-drrafter_setup_run_R1/command.sh Finished database_md5 in 51 seconds [~ 49 test (6.079404466501241%) started, 757 in queue, 24 running] Running Test crosslinkermover_tma ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_tma/command.sh Finished app_exception_handling in 112 seconds [~ 50 test (6.20347394540943%) started, 756 in queue, 24 running] Running Test ppi_v3_suiteC ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ppi_v3_suiteC/command.sh Finished buried_unsat_voids_hbnet_design_symm in 270 seconds [~ 51 test (6.327543424317618%) started, 755 in queue, 24 running] Running Test peptiderive ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/peptiderive/command.sh Finished ddG_sym in 360 seconds [~ 52 test (6.451612903225806%) started, 754 in queue, 24 running] Running Test drrafter_run ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/drrafter_run/command.sh Finished auto-drrafter_setup_run_R1 in 376 seconds [~ 53 test (6.575682382133995%) started, 753 in queue, 24 running] Running Test rna_denovo_lariat ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_lariat/command.sh Finished ga_ligand_dock in 394 seconds [~ 54 test (6.699751861042183%) started, 752 in queue, 24 running] Running Test voids_penalty_energy_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/voids_penalty_energy_design/command.sh Finished fast_relax_scripts in 398 seconds [~ 55 test (6.823821339950372%) started, 751 in queue, 24 running] Running Test swm_dna_bridge ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_dna_bridge/command.sh Finished nonideal_rtmin in 418 seconds [~ 56 test (6.947890818858561%) started, 750 in queue, 24 running] Running Test flexpepdock ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/flexpepdock/command.sh Finished add_helix_sequence_constraints_advanced_setup in 426 seconds [~ 57 test (7.07196029776675%) started, 749 in queue, 24 running] Running Test swm_rna_srl_triplet ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_rna_srl_triplet/command.sh Finished auto-drrafter_setup_run_R2 in 445 seconds [~ 58 test (7.196029776674938%) started, 748 in queue, 24 running] Running Test ga_ligand_dock_macrocycle ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ga_ligand_dock_macrocycle/command.sh Finished crosslinkermover_tma in 400 seconds [~ 59 test (7.320099255583126%) started, 747 in queue, 24 running] Running Test validate_database ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/validate_database/command.sh Finished ccd_ends_graft_mover_rs in 463 seconds [~ 60 test (7.444168734491315%) started, 746 in queue, 24 running] Running Test swa_protein_CCDclose ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_protein_CCDclose/command.sh Finished bundlegridsampler_composition_energy in 464 seconds [~ 61 test (7.568238213399503%) started, 745 in queue, 24 running] Running Test ddG_ensemble ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ddG_ensemble/command.sh Finished crosslinkermover_octahedral in 468 seconds [~ 62 test (7.6923076923076925%) started, 744 in queue, 24 running] Running Test coupled_moves ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/coupled_moves/command.sh Finished ppi_v3_suiteC in 404 seconds [~ 63 test (7.816377171215881%) started, 743 in queue, 24 running] Running Test job_definition_script_vars ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/job_definition_script_vars/command.sh Finished add_helix_sequence_constraints in 519 seconds [~ 64 test (7.94044665012407%) started, 742 in queue, 24 running] Running Test swm_rna_base_pair_constraints ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_rna_base_pair_constraints/command.sh Finished cyclization in 522 seconds [~ 65 test (8.064516129032258%) started, 741 in queue, 24 running] Running Test rnp_ddg_relax_command_2 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rnp_ddg_relax_command_2/command.sh Finished ddG_of_mutation in 543 seconds [~ 66 test (8.188585607940446%) started, 740 in queue, 24 running] Running Test test1_benchmark ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/test1_benchmark/command.sh Finished dgdp_aio in 549 seconds [~ 67 test (8.312655086848634%) started, 739 in queue, 24 running] Running Test ppi_v3_suiteF ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ppi_v3_suiteF/command.sh Finished drrafter_run in 231 seconds [~ 68 test (8.436724565756824%) started, 738 in queue, 24 running] Running Test glycan_relax ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/glycan_relax/command.sh Finished glycan_tree_relax in 618 seconds [~ 69 test (8.560794044665013%) started, 737 in queue, 24 running] Running Test docking_ensemble_prepack ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/docking_ensemble_prepack/command.sh Finished flexpepdock in 204 seconds [~ 70 test (8.6848635235732%) started, 736 in queue, 24 running] Running Test simple_cycpep_predict_trigonal_pyramidal_metal ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_trigonal_pyramidal_metal/command.sh Finished glycopeptidedocking_diglyco_long in 641 seconds [~ 71 test (8.808933002481389%) started, 735 in queue, 24 running] No correct command.sh file found for esm_model_perplexity. Skipping. Running Test auto-drrafter_setup_run_R3 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/auto-drrafter_setup_run_R3/command.sh Finished dgdp_script in 654 seconds [~ 73 test (9.057071960297767%) started, 733 in queue, 24 running] Running Test antibody_designer ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/antibody_designer/command.sh Finished antibody_H3 in 667 seconds [~ 74 test (9.181141439205955%) started, 732 in queue, 24 running] Running Test rna_denovo_dna_bridge ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_dna_bridge/command.sh Finished job_definition_script_vars in 219 seconds [~ 75 test (9.305210918114144%) started, 731 in queue, 24 running] Running Test count_cycpep_sequences ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/count_cycpep_sequences/command.sh Finished ga_ligand_dock_macrocycle in 302 seconds [~ 76 test (9.429280397022332%) started, 730 in queue, 24 running] Running Test rnp_ddg_calc_mut ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rnp_ddg_calc_mut/command.sh Finished voids_penalty_energy_design in 369 seconds [~ 77 test (9.553349875930522%) started, 729 in queue, 24 running] Running Test helical_bundle_predict_psipred_with_helix_globals ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/helical_bundle_predict_psipred_with_helix_globals/command.sh Finished swm_dna_bridge in 371 seconds [~ 78 test (9.67741935483871%) started, 728 in queue, 24 running] Running Test simple_metrics_per_residue ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_metrics_per_residue/command.sh Finished rna_denovo_lariat in 382 seconds [~ 79 test (9.801488833746898%) started, 727 in queue, 24 running] Running Test composition_energy_layers ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/composition_energy_layers/command.sh Finished swa_protein_CCDclose in 328 seconds [~ 80 test (9.925558312655086%) started, 726 in queue, 24 running] Running Test glycopeptidedocking ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/glycopeptidedocking/command.sh Finished ddG_ensemble in 333 seconds [~ 81 test (10.049627791563275%) started, 725 in queue, 24 running] Running Test helical_bundle_predict_psipred ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/helical_bundle_predict_psipred/command.sh Finished peptiderive in 540 seconds [~ 82 test (10.173697270471465%) started, 724 in queue, 24 running] Running Test SnugDock ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/SnugDock/command.sh Finished mp_f19_relax in 814 seconds [~ 83 test (10.297766749379653%) started, 723 in queue, 24 running] Running Test swm_dna_loop ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_dna_loop/command.sh Finished validate_database in 368 seconds [~ 84 test (10.421836228287841%) started, 722 in queue, 24 running] Running Test rosetta_scripts_loops ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rosetta_scripts_loops/command.sh Finished auto-drrafter_setup_run_R3 in 205 seconds [~ 85 test (10.54590570719603%) started, 721 in queue, 24 running] Running Test antibody_designer_xml ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/antibody_designer_xml/command.sh Finished test1_benchmark in 305 seconds [~ 86 test (10.66997518610422%) started, 720 in queue, 24 running] Running Test hbnet_asymm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hbnet_asymm/command.sh Finished simple_cycpep_predict_trigonal_pyramidal_metal in 226 seconds [~ 87 test (10.794044665012407%) started, 719 in queue, 24 running] Running Test voids_penalty_energy_design_symmetry ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/voids_penalty_energy_design_symmetry/command.sh Finished swm_rna_srl_triplet in 431 seconds [~ 88 test (10.918114143920596%) started, 718 in queue, 24 running] Running Test hydrate_relax ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hydrate_relax/command.sh Finished count_cycpep_sequences in 136 seconds [~ 89 test (11.042183622828784%) started, 717 in queue, 24 running] Running Test hbnet_energy ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hbnet_energy/command.sh Finished ppi_v3_suiteF in 326 seconds [~ 90 test (11.166253101736972%) started, 716 in queue, 24 running] Running Test docking_ensemble ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/docking_ensemble/command.sh Finished antibody_designer in 246 seconds [~ 91 test (11.290322580645162%) started, 715 in queue, 24 running] Running Test crosslinkermover_square_pyramidal ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_square_pyramidal/command.sh Finished coupled_moves in 442 seconds [~ 92 test (11.41439205955335%) started, 714 in queue, 24 running] Running Test bundlegridsampler_copy_pitch ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/bundlegridsampler_copy_pitch/command.sh Finished ligand_dock_ensemble in 913 seconds [~ 93 test (11.538461538461538%) started, 713 in queue, 24 running] Running Test dna_interface_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/dna_interface_design/command.sh Finished simple_cycpep_predict_square_pyramidal_metal in 926 seconds [~ 94 test (11.662531017369727%) started, 712 in queue, 24 running] Running Test crosslinkermover_1_4_bbmb_s2_symm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_1_4_bbmb_s2_symm/command.sh Finished docking_ensemble_prepack in 309 seconds [~ 95 test (11.786600496277917%) started, 711 in queue, 24 running] Running Test crosslinkermover_tetrahedral_metal_d2_symmetry ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_tetrahedral_metal_d2_symmetry/command.sh Finished swm_rna_base_pair_constraints in 410 seconds [~ 96 test (11.910669975186105%) started, 710 in queue, 24 running] Running Test vip ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/vip/command.sh Finished hbnet_asymm in 142 seconds [~ 97 test (12.034739454094293%) started, 709 in queue, 24 running] Running Test swa_rna_gagu_09_sample_virtual_ribose ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_09_sample_virtual_ribose/command.sh Finished helical_bundle_predict_psipred_with_helix_globals in 249 seconds [~ 98 test (12.158808933002481%) started, 708 in queue, 24 running] Finished simple_metrics_per_residue in 244 seconds [~ 98 test (12.158808933002481%) started, 708 in queue, 23 running] Running Test fiber_diffraction_fad ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/fiber_diffraction_fad/command.sh Running Test supercharge ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/supercharge/command.sh Finished rna_denovo_dna_bridge in 371 seconds [~ 100 test (12.40694789081886%) started, 706 in queue, 24 running] Running Test molfile_to_params_polymer ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/molfile_to_params_polymer/command.sh Finished hydrate_relax in 193 seconds [~ 101 test (12.531017369727047%) started, 705 in queue, 24 running] Running Test PolarDesign2019 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/PolarDesign2019/command.sh Finished helical_bundle_predict_psipred in 275 seconds [~ 102 test (12.655086848635236%) started, 704 in queue, 24 running] Running Test simple_glycosylation ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_glycosylation/command.sh Finished composition_energy_layers in 303 seconds [~ 103 test (12.779156327543424%) started, 703 in queue, 24 running] Running Test jd2test_mmCIFin_PDBout ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/jd2test_mmCIFin_PDBout/command.sh Finished rnp_ddg_relax_command_2 in 553 seconds [~ 104 test (12.903225806451612%) started, 702 in queue, 24 running] Running Test jd2test_mmCIFIO ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/jd2test_mmCIFIO/command.sh Finished voids_penalty_energy_design_symmetry in 243 seconds [~ 105 test (13.027295285359802%) started, 701 in queue, 24 running] Running Test helical_bundle_predict ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/helical_bundle_predict/command.sh Finished docking_ensemble in 219 seconds [~ 106 test (13.15136476426799%) started, 700 in queue, 24 running] Running Test crosslinkermover_square_planar ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_square_planar/command.sh Finished antibody_designer_xml in 256 seconds [~ 107 test (13.275434243176178%) started, 699 in queue, 24 running] Running Test bundlegridsampler_composition_energy_fract_range ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/bundlegridsampler_composition_energy_fract_range/command.sh Finished swm_dna_loop in 288 seconds [~ 108 test (13.399503722084367%) started, 698 in queue, 24 running] Running Test LoopAnalyzer ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/LoopAnalyzer/command.sh Finished dna_interface_design in 202 seconds [~ 109 test (13.523573200992557%) started, 697 in queue, 24 running] Running Test relax_w_allatom_cst ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/relax_w_allatom_cst/command.sh Finished glycan_relax in 539 seconds [~ 110 test (13.647642679900745%) started, 696 in queue, 24 running] Running Test helical_bundle_predict_skipping_residues ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/helical_bundle_predict_skipping_residues/command.sh Finished rosetta_scripts_loops in 313 seconds [~ 111 test (13.771712158808933%) started, 695 in queue, 24 running] Running Test hbnet_energy_rosettascripts_linear ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hbnet_energy_rosettascripts_linear/command.sh Finished glycopeptidedocking in 345 seconds [~ 112 test (13.895781637717121%) started, 694 in queue, 24 running] Finished crosslinkermover_1_4_bbmb_s2_symm in 212 seconds [~ 112 test (13.895781637717121%) started, 694 in queue, 23 running] Running Test d_workflow ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/d_workflow/command.sh Running Test control_flow_rs ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/control_flow_rs/command.sh Finished molfile_to_params_polymer in 105 seconds [~ 114 test (14.1439205955335%) started, 692 in queue, 24 running] Running Test simple_metrics ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_metrics/command.sh Finished crosslinkermover_square_pyramidal in 250 seconds [~ 115 test (14.267990074441688%) started, 691 in queue, 24 running] Running Test crosslinkermover_tma_symm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_tma_symm/command.sh Finished crosslinkermover_tetrahedral_metal_d2_symmetry in 226 seconds [~ 116 test (14.392059553349876%) started, 690 in queue, 24 running] Running Test rna_denovo_base_pair_constraints ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_base_pair_constraints/command.sh Finished hbnet_energy in 292 seconds [~ 117 test (14.516129032258064%) started, 689 in queue, 24 running] Running Test hotspot_hashing ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hotspot_hashing/command.sh Finished vip in 244 seconds [~ 118 test (14.640198511166252%) started, 688 in queue, 24 running] Running Test helical_bundle_predict_sequence ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/helical_bundle_predict_sequence/command.sh Finished swa_rna_gagu_09_sample_virtual_ribose in 186 seconds [~ 119 test (14.764267990074442%) started, 687 in queue, 24 running] Running Test design_glycans ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/design_glycans/command.sh Finished bundlegridsampler_copy_pitch in 282 seconds [~ 120 test (14.88833746898263%) started, 686 in queue, 24 running] Running Test ligand_water_docking ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ligand_water_docking/command.sh Finished fiber_diffraction_fad in 190 seconds [~ 121 test (15.012406947890819%) started, 685 in queue, 24 running] Running Test fiber_diffraction ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/fiber_diffraction/command.sh Finished SnugDock in 433 seconds [~ 122 test (15.136476426799007%) started, 684 in queue, 24 running] Running Test beta_strand_homodimer ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/beta_strand_homodimer/command.sh Finished rnp_ddg_calc_mut in 506 seconds [~ 123 test (15.260545905707197%) started, 683 in queue, 24 running] Running Test polyaramid_test_trivial ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/polyaramid_test_trivial/command.sh Finished supercharge in 244 seconds [~ 124 test (15.384615384615385%) started, 682 in queue, 24 running] Running Test crosslinkermover_1_4_bbmb_asymm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_1_4_bbmb_asymm/command.sh Finished LoopAnalyzer in 165 seconds [~ 125 test (15.508684863523573%) started, 681 in queue, 24 running] Running Test mr_protocols ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mr_protocols/command.sh Finished control_flow_rs in 165 seconds [~ 126 test (15.632754342431761%) started, 680 in queue, 24 running] Running Test simple_cycpep_predict_cartesian ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_cartesian/command.sh Finished helical_bundle_predict in 220 seconds [~ 127 test (15.75682382133995%) started, 679 in queue, 24 running] Running Test AlterSpecDisruption ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/AlterSpecDisruption/command.sh Finished simple_metrics in 174 seconds [~ 128 test (15.88089330024814%) started, 678 in queue, 24 running] Running Test mp_domain_assembly_FtsQ ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_domain_assembly_FtsQ/command.sh Finished relax_w_allatom_cst in 215 seconds [~ 129 test (16.004962779156326%) started, 677 in queue, 24 running] Running Test glycomutagenesis ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/glycomutagenesis/command.sh Finished bundlegridsampler_composition_energy_fract_range in 230 seconds [~ 130 test (16.129032258064516%) started, 676 in queue, 24 running] Running Test backrub ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/backrub/command.sh Finished d_workflow in 195 seconds [~ 131 test (16.253101736972706%) started, 675 in queue, 24 running] Running Test autoNOE_rosetta ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/autoNOE_rosetta/command.sh Finished jd2test_mmCIFIO in 268 seconds [~ 132 test (16.377171215880892%) started, 674 in queue, 24 running] Running Test antibody_H3_camelid ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/antibody_H3_camelid/command.sh Finished crosslinkermover_square_planar in 248 seconds [~ 133 test (16.501240694789082%) started, 673 in queue, 24 running] Running Test simple_cycpep_predict ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict/command.sh Finished crosslinkermover_tma_symm in 192 seconds [~ 134 test (16.62531017369727%) started, 672 in queue, 24 running] Running Test pertmin ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/pertmin/command.sh Finished jd2test_mmCIFin_PDBout in 270 seconds [~ 135 test (16.74937965260546%) started, 671 in queue, 24 running] Running Test crosslinkermover_tetrahedral_metal_c2_symmetry ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_tetrahedral_metal_c2_symmetry/command.sh Finished PolarDesign2019 in 305 seconds [~ 136 test (16.87344913151365%) started, 670 in queue, 24 running] Running Test rs_loophash ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rs_loophash/command.sh Finished helical_bundle_predict_skipping_residues in 249 seconds [~ 137 test (16.997518610421835%) started, 669 in queue, 24 running] Running Test rnp_ddg_calc_wt ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rnp_ddg_calc_wt/command.sh Finished ligand_water_docking in 187 seconds [~ 138 test (17.121588089330025%) started, 668 in queue, 24 running] Running Test hybridization ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hybridization/command.sh Finished hbnet_energy_rosettascripts_linear in 260 seconds [~ 139 test (17.245657568238215%) started, 667 in queue, 24 running] Running Test hts_io ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hts_io/command.sh Finished helical_bundle_predict_sequence in 228 seconds [~ 140 test (17.3697270471464%) started, 666 in queue, 24 running] Running Test swa_protein_prepack ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_protein_prepack/command.sh Finished simple_glycosylation in 359 seconds [~ 141 test (17.49379652605459%) started, 665 in queue, 24 running] Running Test swa_protein_loop_sampler ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_protein_loop_sampler/command.sh Finished design_glycans in 257 seconds [~ 142 test (17.617866004962778%) started, 664 in queue, 24 running] Running Test crosslinkermover_square_planar_d2_symm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_square_planar_d2_symm/command.sh Finished mr_protocols in 183 seconds [~ 143 test (17.741935483870968%) started, 663 in queue, 24 running] Running Test simple_cycpep_predict_anglelength ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_anglelength/command.sh Finished simple_cycpep_predict_cartesian in 164 seconds [~ 144 test (17.866004962779158%) started, 662 in queue, 24 running] Running Test rosetta_scripts_jd3 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rosetta_scripts_jd3/command.sh Finished polyaramid_test_trivial in 213 seconds [~ 145 test (17.990074441687344%) started, 661 in queue, 24 running] Running Test ligand_database_io ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ligand_database_io/command.sh Finished beta_strand_homodimer in 224 seconds [~ 146 test (18.114143920595534%) started, 660 in queue, 24 running] Running Test simple_cycpep_predict_setting ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_setting/command.sh Finished hotspot_hashing in 305 seconds [~ 147 test (18.23821339950372%) started, 659 in queue, 24 running] Running Test netcharge_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/netcharge_design/command.sh Finished crosslinkermover_1_4_bbmb_asymm in 216 seconds [~ 148 test (18.36228287841191%) started, 658 in queue, 24 running] Running Test fast_relax ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/fast_relax/command.sh Finished autoNOE_rosetta in 148 seconds [~ 149 test (18.4863523573201%) started, 657 in queue, 24 running] Running Test pmut_scan ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/pmut_scan/command.sh Finished backrub in 163 seconds [~ 150 test (18.610421836228287%) started, 656 in queue, 24 running] Running Test hbnet ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hbnet/command.sh Finished AlterSpecDisruption in 186 seconds [~ 151 test (18.734491315136477%) started, 655 in queue, 24 running] Running Test simple_cycpep_predict_tetrahedral_metal ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_tetrahedral_metal/command.sh Finished simple_cycpep_predict in 158 seconds [~ 152 test (18.858560794044664%) started, 654 in queue, 24 running] Running Test simple_cycpep_predict_angle ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_angle/command.sh Finished hts_io in 116 seconds [~ 153 test (18.982630272952854%) started, 653 in queue, 24 running] Running Test remodel_disulfides_rosettascripts ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/remodel_disulfides_rosettascripts/command.sh Finished mp_domain_assembly_FtsQ in 198 seconds [~ 154 test (19.106699751861044%) started, 652 in queue, 24 running] Running Test mirror_symm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mirror_symm/command.sh Finished crosslinkermover_tetrahedral_metal_c2_symmetry in 178 seconds [~ 155 test (19.23076923076923%) started, 651 in queue, 24 running] Running Test swa_rna_erraser ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_erraser/command.sh Finished hybridization in 149 seconds [~ 156 test (19.35483870967742%) started, 650 in queue, 24 running] Running Test rna_denovo_fragment_homology_exclusion ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_fragment_homology_exclusion/command.sh Finished rs_loophash in 177 seconds [~ 157 test (19.478908188585606%) started, 649 in queue, 24 running] Running Test perturb_helical_bundle_copying_pitch ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/perturb_helical_bundle_copying_pitch/command.sh Finished simple_cycpep_predict_setting in 72 seconds [~ 158 test (19.602977667493796%) started, 648 in queue, 24 running] Running Test batch_relax ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/batch_relax/command.sh Finished glycomutagenesis in 220 seconds [~ 159 test (19.727047146401986%) started, 647 in queue, 24 running] Running Test swm_l_rna ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_l_rna/command.sh Finished antibody_H3_camelid in 208 seconds [~ 160 test (19.851116625310173%) started, 646 in queue, 24 running] Running Test rna_puzzle5_P15P3P8_noP4P6_4RB_G208phosphate_ligation ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_puzzle5_P15P3P8_noP4P6_4RB_G208phosphate_ligation/command.sh Finished crosslinkermover_square_planar_d2_symm in 153 seconds [~ 161 test (19.975186104218363%) started, 645 in queue, 24 running] Running Test seed_ensemble_JD2_JI ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/seed_ensemble_JD2_JI/command.sh Finished pertmin in 246 seconds [~ 162 test (20.09925558312655%) started, 644 in queue, 24 running] Finished swa_protein_loop_sampler in 157 seconds [~ 162 test (20.09925558312655%) started, 644 in queue, 23 running] Running Test simple_cycpep_predict_trigonal_planar_metal ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_trigonal_planar_metal/command.sh Running Test symm_disulfidize ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/symm_disulfidize/command.sh Finished swa_protein_prepack in 197 seconds [~ 164 test (20.34739454094293%) started, 642 in queue, 24 running] Running Test ligand_dock_script ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ligand_dock_script/command.sh Finished simple_cycpep_predict_angle in 127 seconds [~ 165 test (20.471464019851116%) started, 641 in queue, 24 running] Running Test simple_cycpep_predict_tbmb ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_tbmb/command.sh Finished hbnet in 136 seconds [~ 166 test (20.595533498759306%) started, 640 in queue, 24 running] Running Test mp_dock_ensemble ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_dock_ensemble/command.sh Finished rna_denovo_base_pair_constraints in 480 seconds [~ 167 test (20.719602977667495%) started, 639 in queue, 24 running] Running Test farnesyl ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/farnesyl/command.sh Finished swa_rna_erraser in 112 seconds [~ 168 test (20.843672456575682%) started, 638 in queue, 24 running] Running Test range_relax_w_cst ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/range_relax_w_cst/command.sh Finished fast_relax in 167 seconds [~ 169 test (20.967741935483872%) started, 637 in queue, 24 running] Running Test motif_dna_packer_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/motif_dna_packer_design/command.sh Finished ligand_database_io in 176 seconds [~ 170 test (21.09181141439206%) started, 636 in queue, 24 running] Running Test crosslinkermover_octahedral_s2_symm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_octahedral_s2_symm/command.sh Finished pmut_scan in 164 seconds [~ 171 test (21.21588089330025%) started, 635 in queue, 24 running] Finished simple_cycpep_predict_tetrahedral_metal in 146 seconds [~ 171 test (21.21588089330025%) started, 635 in queue, 23 running] Running Test test_degreaser ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/test_degreaser/command.sh Running Test KIC_with_fragments ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/KIC_with_fragments/command.sh Finished rna_denovo_fragment_homology_exclusion in 117 seconds [~ 173 test (21.464019851116625%) started, 633 in queue, 24 running] Running Test repeat_relax ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/repeat_relax/command.sh Finished netcharge_design in 181 seconds [~ 174 test (21.588089330024815%) started, 632 in queue, 24 running] Running Test remodel_helical_repeat ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/remodel_helical_repeat/command.sh Finished simple_cycpep_predict_anglelength in 210 seconds [~ 175 test (21.712158808933%) started, 631 in queue, 24 running] Running Test next_generation_KIC ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/next_generation_KIC/command.sh Finished rosetta_scripts_jd3 in 203 seconds [~ 176 test (21.83622828784119%) started, 630 in queue, 24 running] Running Test splice_out_H3_longer ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/splice_out_H3_longer/command.sh Finished perturb_helical_bundle_copying_pitch in 145 seconds [~ 177 test (21.96029776674938%) started, 629 in queue, 24 running] Running Test simple_cycpep_predict_tma ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_tma/command.sh Finished remodel_disulfides_rosettascripts in 186 seconds [~ 178 test (22.084367245657567%) started, 628 in queue, 24 running] Running Test rna_puzzle12_P5P6P7_DMS ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_puzzle12_P5P6P7_DMS/command.sh Finished batch_relax in 157 seconds [~ 179 test (22.208436724565757%) started, 627 in queue, 24 running] Running Test docking_local_refine ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/docking_local_refine/command.sh Finished mirror_symm in 181 seconds [~ 180 test (22.332506203473944%) started, 626 in queue, 24 running] Running Test rna_denovo_symm_hack ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_symm_hack/command.sh Finished swm_l_rna in 149 seconds [~ 181 test (22.456575682382134%) started, 625 in queue, 24 running] Running Test cycpep_rigid_body_permutation_mover ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cycpep_rigid_body_permutation_mover/command.sh Finished rnp_ddg_calc_wt in 332 seconds [~ 182 test (22.580645161290324%) started, 624 in queue, 24 running] Running Test zinc_heterodimer ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/zinc_heterodimer/command.sh Finished mp_dock_ensemble in 81 seconds [~ 183 test (22.70471464019851%) started, 623 in queue, 24 running] Running Test sdf_reader ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/sdf_reader/command.sh Finished symm_disulfidize in 138 seconds [~ 184 test (22.8287841191067%) started, 622 in queue, 24 running] Running Test crankshaft_flip ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crankshaft_flip/command.sh Finished seed_ensemble_JD2_JI in 152 seconds [~ 185 test (22.952853598014887%) started, 621 in queue, 24 running] Running Test AlignPDBInfoToSequences ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/AlignPDBInfoToSequences/command.sh Finished next_generation_KIC in 100 seconds [~ 186 test (23.076923076923077%) started, 620 in queue, 24 running] Running Test ga_ligand_dock_amino_acid ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ga_ligand_dock_amino_acid/command.sh Finished test_degreaser in 117 seconds [~ 187 test (23.200992555831267%) started, 619 in queue, 24 running] Running Test simple_cycpep_predict_octahedral_metal ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_octahedral_metal/command.sh Finished remodel_helical_repeat in 116 seconds [~ 188 test (23.325062034739453%) started, 618 in queue, 24 running] Running Test mp_relax ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_relax/command.sh Finished ligand_dock_script in 171 seconds [~ 189 test (23.449131513647643%) started, 617 in queue, 24 running] Running Test ppi_v3_suiteB ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ppi_v3_suiteB/command.sh Finished crosslinkermover_octahedral_s2_symm in 134 seconds [~ 190 test (23.573200992555833%) started, 616 in queue, 24 running] Running Test mp_find_interface ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_find_interface/command.sh Finished repeat_relax in 131 seconds [~ 191 test (23.69727047146402%) started, 615 in queue, 24 running] Running Test hotspot_graft ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hotspot_graft/command.sh Finished rna_puzzle5_P15P3P8_noP4P6_4RB_G208phosphate_ligation in 229 seconds [~ 192 test (23.82133995037221%) started, 614 in queue, 24 running] Running Test fixbb ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/fixbb/command.sh Finished fiber_diffraction in 579 seconds [~ 193 test (23.945409429280396%) started, 613 in queue, 24 running] Running Test hbs_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hbs_design/command.sh Finished range_relax_w_cst in 150 seconds [~ 194 test (24.069478908188586%) started, 612 in queue, 24 running] Running Test disulfidize_beta_cys ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/disulfidize_beta_cys/command.sh Finished simple_cycpep_predict_trigonal_planar_metal in 196 seconds [~ 195 test (24.193548387096776%) started, 611 in queue, 24 running] Running Test buried_unsat_voids_hbnet_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/buried_unsat_voids_hbnet_design/command.sh Finished motif_dna_packer_design in 149 seconds [~ 196 test (24.317617866004962%) started, 610 in queue, 24 running] Running Test bundlegridsampler_epsilon ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/bundlegridsampler_epsilon/command.sh Finished KIC_with_fragments in 151 seconds [~ 197 test (24.441687344913152%) started, 609 in queue, 24 running] Running Test TryDisulfPermutations ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/TryDisulfPermutations/command.sh Finished simple_cycpep_predict_tbmb in 168 seconds [~ 198 test (24.56575682382134%) started, 608 in queue, 24 running] Running Test swa_protein_combine_loops ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_protein_combine_loops/command.sh Finished splice_out_H3_longer in 129 seconds [~ 199 test (24.68982630272953%) started, 607 in queue, 24 running] Running Test mp_symdock ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_symdock/command.sh Finished simple_cycpep_predict_tma in 129 seconds [~ 200 test (24.81389578163772%) started, 606 in queue, 24 running] Running Test enzdes ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/enzdes/command.sh Finished farnesyl in 184 seconds [~ 201 test (24.937965260545905%) started, 605 in queue, 24 running] Running Test entropy_correction ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/entropy_correction/command.sh Finished rna_denovo_symm_hack in 126 seconds [~ 202 test (25.062034739454095%) started, 604 in queue, 24 running] Running Test bundlereporter_filter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/bundlereporter_filter/command.sh Finished crankshaft_flip in 97 seconds [~ 203 test (25.18610421836228%) started, 603 in queue, 24 running] Running Test secondary_structure_output ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/secondary_structure_output/command.sh Finished cycpep_rigid_body_permutation_mover in 129 seconds [~ 204 test (25.31017369727047%) started, 602 in queue, 24 running] Running Test rna_denovo_new_FT_RNP_2prot_dens ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_new_FT_RNP_2prot_dens/command.sh Finished sdf_reader in 120 seconds [~ 205 test (25.43424317617866%) started, 601 in queue, 24 running] Running Test mp_domain_assembly ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_domain_assembly/command.sh Finished rna_puzzle12_P5P6P7_DMS in 142 seconds [~ 206 test (25.558312655086848%) started, 600 in queue, 24 running] Running Test generate_6Dloopclose ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/generate_6Dloopclose/command.sh Finished AlignPDBInfoToSequences in 100 seconds [~ 207 test (25.682382133995038%) started, 599 in queue, 24 running] Running Test explicit_membrane ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/explicit_membrane/command.sh Finished docking_local_refine in 159 seconds [~ 208 test (25.806451612903224%) started, 598 in queue, 24 running] Running Test docking_distance_constraints ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/docking_distance_constraints/command.sh Finished zinc_heterodimer in 149 seconds [~ 209 test (25.930521091811414%) started, 597 in queue, 24 running] Running Test UBQ_E2_thioester_extra_bodies ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/UBQ_E2_thioester_extra_bodies/command.sh Finished ga_ligand_dock_amino_acid in 109 seconds [~ 210 test (26.054590570719604%) started, 596 in queue, 24 running] Running Test simple_cycpep_predict_bondangle_bondlength ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_bondangle_bondlength/command.sh Finished hotspot_graft in 98 seconds [~ 211 test (26.17866004962779%) started, 595 in queue, 24 running] Running Test mhc_epitope ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mhc_epitope/command.sh Finished disulfidize_beta_cys in 94 seconds [~ 212 test (26.30272952853598%) started, 594 in queue, 24 running] Running Test small_molecule_lattice_dock ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/small_molecule_lattice_dock/command.sh Finished TryDisulfPermutations in 85 seconds [~ 213 test (26.426799007444167%) started, 593 in queue, 24 running] Running Test rna_denovo_RNP_refine_native ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_RNP_refine_native/command.sh Finished simple_cycpep_predict_octahedral_metal in 121 seconds [~ 214 test (26.550868486352357%) started, 592 in queue, 24 running] Running Test oop_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/oop_design/command.sh Finished rna_denovo_new_FT_RNP_2prot_dens in 56 seconds [~ 215 test (26.674937965260547%) started, 591 in queue, 24 running] Running Test make_symmdef_file ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/make_symmdef_file/command.sh Finished mp_relax in 122 seconds [~ 216 test (26.799007444168733%) started, 590 in queue, 24 running] Running Test crosslinkermover_1_4_bbmb_c2_symmetry ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_1_4_bbmb_c2_symmetry/command.sh Finished mp_find_interface in 121 seconds [~ 217 test (26.923076923076923%) started, 589 in queue, 24 running] No correct command.sh file found for trRosetta. Skipping. Running Test SID_ERMS_prediction ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/SID_ERMS_prediction/command.sh Finished buried_unsat_voids_hbnet_design in 114 seconds [~ 219 test (27.1712158808933%) started, 587 in queue, 24 running] Running Test rna_denovo_RNP_low_res ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_RNP_low_res/command.sh Finished ppi_v3_suiteB in 133 seconds [~ 220 test (27.29528535980149%) started, 586 in queue, 24 running] Running Test ppi_v3_suiteE ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ppi_v3_suiteE/command.sh Finished bundlereporter_filter in 86 seconds [~ 221 test (27.419354838709676%) started, 585 in queue, 24 running] Running Test ppi_v3_suiteA ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ppi_v3_suiteA/command.sh Finished mp_symdock in 113 seconds [~ 222 test (27.543424317617866%) started, 584 in queue, 24 running] Running Test kinematic_looprelax ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/kinematic_looprelax/command.sh Finished fixbb in 131 seconds [~ 223 test (27.667493796526056%) started, 583 in queue, 24 running] Running Test hbnet_energy_symm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hbnet_energy_symm/command.sh Finished bundlegridsampler_epsilon in 123 seconds [~ 224 test (27.791563275434243%) started, 582 in queue, 24 running] Running Test evolution ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/evolution/command.sh Finished hbs_design in 134 seconds [~ 225 test (27.915632754342433%) started, 581 in queue, 24 running] Running Test UBQ_E2_thioester ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/UBQ_E2_thioester/command.sh Finished secondary_structure_output in 95 seconds [~ 226 test (28.03970223325062%) started, 580 in queue, 24 running] Running Test simple_cycpep_predict_terminal_disulfide_tails_2 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_terminal_disulfide_tails_2/command.sh Finished swa_protein_combine_loops in 125 seconds [~ 227 test (28.16377171215881%) started, 579 in queue, 24 running] Running Test homodimer_fnd_ref2015_memb ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/homodimer_fnd_ref2015_memb/command.sh Finished generate_6Dloopclose in 101 seconds [~ 228 test (28.287841191067%) started, 578 in queue, 24 running] Running Test docking_site_constraints ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/docking_site_constraints/command.sh Finished enzdes in 127 seconds [~ 229 test (28.411910669975185%) started, 577 in queue, 24 running] Running Test cycpep_rdkit_metric ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cycpep_rdkit_metric/command.sh Finished mhc_epitope in 65 seconds [~ 230 test (28.535980148883375%) started, 576 in queue, 24 running] Running Test cycpep_design_pipeline ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cycpep_design_pipeline/command.sh Finished entropy_correction in 130 seconds [~ 231 test (28.66004962779156%) started, 575 in queue, 24 running] Running Test rna_denovo_new_libs ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_new_libs/command.sh Finished mp_domain_assembly in 114 seconds [~ 232 test (28.78411910669975%) started, 574 in queue, 24 running] Running Test ligand_dock_cholesterol ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ligand_dock_cholesterol/command.sh Finished small_molecule_lattice_dock in 80 seconds [~ 233 test (28.90818858560794%) started, 573 in queue, 24 running] Running Test dock_glycans ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/dock_glycans/command.sh Finished simple_cycpep_predict_bondangle_bondlength in 89 seconds [~ 234 test (29.032258064516128%) started, 572 in queue, 24 running] Running Test AnchoredDesign ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/AnchoredDesign/command.sh Finished make_symmdef_file in 82 seconds [~ 235 test (29.156327543424318%) started, 571 in queue, 24 running] Running Test symm_rotamer_boltzmann ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/symm_rotamer_boltzmann/command.sh Finished docking_distance_constraints in 119 seconds [~ 236 test (29.280397022332505%) started, 570 in queue, 24 running] Running Test rna_farfar_block_stack ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_farfar_block_stack/command.sh Finished crosslinkermover_1_4_bbmb_c2_symmetry in 88 seconds [~ 237 test (29.404466501240694%) started, 569 in queue, 24 running] Running Test bundlegridsampler ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/bundlegridsampler/command.sh Finished SID_ERMS_prediction in 86 seconds [~ 238 test (29.528535980148884%) started, 568 in queue, 24 running] Running Test rna_denovo_new_FT_2in_dens ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_new_FT_2in_dens/command.sh Finished rna_denovo_RNP_low_res in 96 seconds [~ 239 test (29.65260545905707%) started, 567 in queue, 24 running] Running Test mixed_monte_carlo ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mixed_monte_carlo/command.sh Finished ppi_v3_suiteE in 94 seconds [~ 240 test (29.77667493796526%) started, 566 in queue, 24 running] Running Test features_parallel ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/features_parallel/command.sh Finished homodimer_fnd_ref2015_memb in 78 seconds [~ 241 test (29.90074441687345%) started, 565 in queue, 24 running] Running Test splice_out_L3_longer ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/splice_out_L3_longer/command.sh Finished explicit_membrane in 160 seconds [~ 242 test (30.024813895781637%) started, 564 in queue, 24 running] Running Test splice_out_H1_H2_longer ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/splice_out_H1_H2_longer/command.sh Finished simple_cycpep_predict_terminal_disulfide_tails_2 in 81 seconds [~ 243 test (30.148883374689827%) started, 563 in queue, 24 running] Running Test simple_cycpep_predict_beta_thioether_lariat ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_beta_thioether_lariat/command.sh Finished oop_design in 118 seconds [~ 244 test (30.272952853598014%) started, 562 in queue, 24 running] Running Test rotamer_probability ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rotamer_probability/command.sh Finished rna_denovo_RNP_refine_native in 122 seconds [~ 245 test (30.397022332506204%) started, 561 in queue, 24 running] Running Test iphold ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/iphold/command.sh Finished kinematic_looprelax in 95 seconds [~ 246 test (30.521091811414394%) started, 560 in queue, 24 running] Running Test interaction_graph_summary_metric ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/interaction_graph_summary_metric/command.sh Finished hbnet_energy_symm in 107 seconds [~ 247 test (30.64516129032258%) started, 559 in queue, 24 running] Running Test genkic_sugars ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/genkic_sugars/command.sh Finished ppi_v3_suiteA in 108 seconds [~ 248 test (30.76923076923077%) started, 558 in queue, 24 running] Running Test farfar_mrna ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/farfar_mrna/command.sh Finished ligand_dock_cholesterol in 71 seconds [~ 249 test (30.893300248138956%) started, 557 in queue, 24 running] Running Test backrub_pilot ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/backrub_pilot/command.sh Finished UBQ_E2_thioester in 107 seconds [~ 250 test (31.017369727047146%) started, 556 in queue, 24 running] Running Test task_selector ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/task_selector/command.sh Finished cycpep_rdkit_metric in 99 seconds [~ 251 test (31.141439205955336%) started, 555 in queue, 24 running] Running Test netcharge_design_symm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/netcharge_design_symm/command.sh Finished cycpep_design_pipeline in 99 seconds [~ 252 test (31.265508684863523%) started, 554 in queue, 24 running] Running Test swa_protein_build_at_Nterminus ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_protein_build_at_Nterminus/command.sh Finished evolution in 132 seconds [~ 253 test (31.389578163771713%) started, 553 in queue, 24 running] Running Test flexpepdock_abinitio ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/flexpepdock_abinitio/command.sh Finished docking_site_constraints in 112 seconds [~ 254 test (31.5136476426799%) started, 552 in queue, 24 running] Running Test favor_native_residue ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/favor_native_residue/command.sh Finished bundlegridsampler in 76 seconds [~ 255 test (31.63771712158809%) started, 551 in queue, 24 running] Running Test constraints_metric ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/constraints_metric/command.sh Finished AnchoredDesign in 102 seconds [~ 256 test (31.76178660049628%) started, 550 in queue, 24 running] Running Test bundlegridsampler_design_nstruct_mode ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/bundlegridsampler_design_nstruct_mode/command.sh Finished UBQ_E2_thioester_extra_bodies in 204 seconds [~ 257 test (31.885856079404466%) started, 549 in queue, 24 running] Finished rna_farfar_block_stack in 87 seconds [~ 257 test (31.885856079404466%) started, 549 in queue, 23 running] Running Test swm_rna_move_inside_helix_by_jump ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_rna_move_inside_helix_by_jump/command.sh Running Test splice_in_4loops_shorter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/splice_in_4loops_shorter/command.sh Finished features_parallel in 67 seconds [~ 259 test (32.13399503722084%) started, 547 in queue, 24 running] Running Test rs_flexbbmoves ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rs_flexbbmoves/command.sh Finished symm_rotamer_boltzmann in 98 seconds [~ 260 test (32.25806451612903%) started, 546 in queue, 24 running] Running Test ppi_v3_suiteG ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ppi_v3_suiteG/command.sh Finished interaction_graph_summary_metric in 61 seconds [~ 261 test (32.38213399503722%) started, 545 in queue, 24 running] Running Test ppi_v3_suiteD ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ppi_v3_suiteD/command.sh Finished dock_glycans in 119 seconds [~ 262 test (32.50620347394541%) started, 544 in queue, 24 running] Running Test pose_sewing ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/pose_sewing/command.sh Finished splice_out_H1_H2_longer in 84 seconds [~ 263 test (32.630272952853595%) started, 543 in queue, 24 running] Running Test ncaa_fixbb ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ncaa_fixbb/command.sh Finished splice_out_L3_longer in 87 seconds [~ 264 test (32.754342431761785%) started, 542 in queue, 24 running] Running Test features ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/features/command.sh Finished farfar_mrna in 74 seconds [~ 265 test (32.878411910669975%) started, 541 in queue, 24 running] Running Test cycpep_symmetry_filter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cycpep_symmetry_filter/command.sh Finished rotamer_probability in 91 seconds [~ 266 test (33.002481389578165%) started, 540 in queue, 24 running] Running Test cleanAlignment ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cleanAlignment/command.sh Finished iphold in 92 seconds [~ 267 test (33.126550868486355%) started, 539 in queue, 24 running] Running Test balancedKIC ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/balancedKIC/command.sh Finished mixed_monte_carlo in 102 seconds [~ 268 test (33.25062034739454%) started, 538 in queue, 24 running] Running Test simple_metrics_b_factor ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_metrics_b_factor/command.sh Finished rna_denovo_new_FT_2in_dens in 115 seconds [~ 269 test (33.37468982630273%) started, 537 in queue, 24 running] Running Test simple_grafting_movers ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_grafting_movers/command.sh Finished simple_cycpep_predict_beta_thioether_lariat in 107 seconds [~ 270 test (33.49875930521092%) started, 536 in queue, 24 running] Running Test hbnet_use_input_rot ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hbnet_use_input_rot/command.sh Finished task_selector in 96 seconds [~ 271 test (33.62282878411911%) started, 535 in queue, 24 running] Running Test Enzrevert_xml ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/Enzrevert_xml/command.sh Finished backrub_pilot in 100 seconds [~ 272 test (33.7468982630273%) started, 534 in queue, 24 running] Running Test swm_rna_singleloop ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_rna_singleloop/command.sh Finished constraints_metric in 65 seconds [~ 273 test (33.87096774193548%) started, 533 in queue, 24 running] Running Test rosie_ligand_docking ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rosie_ligand_docking/command.sh Finished netcharge_design_symm in 91 seconds [~ 274 test (33.99503722084367%) started, 532 in queue, 24 running] Running Test ligand_dock_7cpa ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ligand_dock_7cpa/command.sh Finished swa_protein_build_at_Nterminus in 92 seconds [~ 275 test (34.11910669975186%) started, 531 in queue, 24 running] Running Test kinemage_grid_output ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/kinemage_grid_output/command.sh Finished simple_metrics_b_factor in 37 seconds [~ 276 test (34.24317617866005%) started, 530 in queue, 24 running] Running Test fold_from_loops ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/fold_from_loops/command.sh Finished favor_native_residue in 86 seconds [~ 277 test (34.36724565756824%) started, 529 in queue, 24 running] Running Test doug_dock_design_min_mod2_cal_cal ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/doug_dock_design_min_mod2_cal_cal/command.sh Finished simple_grafting_movers in 36 seconds [~ 278 test (34.49131513647643%) started, 528 in queue, 24 running] No correct command.sh file found for trRosettaConstraintGenerator. Skipping. Running Test HDXEnergy ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/HDXEnergy/command.sh Finished pose_sewing in 59 seconds [~ 280 test (34.7394540942928%) started, 526 in queue, 24 running] Running Test splice_out_L1_L2_longer ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/splice_out_L1_L2_longer/command.sh Finished splice_in_4loops_shorter in 76 seconds [~ 281 test (34.86352357320099%) started, 525 in queue, 24 running] Running Test splice_in_4loops_longer ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/splice_in_4loops_longer/command.sh Finished rs_flexbbmoves in 76 seconds [~ 282 test (34.98759305210918%) started, 524 in queue, 24 running] Running Test simple_cycpep_predict_1_4_bbmb ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_1_4_bbmb/command.sh Finished flexpepdock_abinitio in 98 seconds [~ 283 test (35.11166253101737%) started, 523 in queue, 24 running] Running Test hydrate ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hydrate/command.sh Finished bundlegridsampler_design_nstruct_mode in 85 seconds [~ 284 test (35.235732009925556%) started, 522 in queue, 24 running] Running Test docking_full_protocol ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/docking_full_protocol/command.sh Finished features in 62 seconds [~ 285 test (35.359801488833746%) started, 521 in queue, 24 running] Running Test dock_with_hotspot_place_simultaneously ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/dock_with_hotspot_place_simultaneously/command.sh Finished ppi_v3_suiteG in 83 seconds [~ 286 test (35.483870967741936%) started, 520 in queue, 24 running] Running Test UBQ_Gp_LYX-Cterm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/UBQ_Gp_LYX-Cterm/command.sh Finished genkic_sugars in 132 seconds [~ 287 test (35.607940446650126%) started, 519 in queue, 24 running] Running Test threefold_symm_peptide_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/threefold_symm_peptide_design/command.sh Finished ppi_v3_suiteD in 84 seconds [~ 288 test (35.732009925558316%) started, 518 in queue, 24 running] Running Test splice_out_L3_same ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/splice_out_L3_same/command.sh Finished cycpep_symmetry_filter in 65 seconds [~ 289 test (35.8560794044665%) started, 517 in queue, 24 running] Running Test splice_out_H1_H2_same ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/splice_out_H1_H2_same/command.sh Finished balancedKIC in 65 seconds [~ 290 test (35.98014888337469%) started, 516 in queue, 24 running] Running Test simple_hbondstoatom ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_hbondstoatom/command.sh Finished rna_denovo_new_libs in 221 seconds [~ 291 test (36.10421836228288%) started, 515 in queue, 24 running] Running Test simple_cycpep_predict_thioether_cis_sampling ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_thioether_cis_sampling/command.sh Finished hbnet_use_input_rot in 64 seconds [~ 292 test (36.22828784119107%) started, 514 in queue, 24 running] Running Test simple_cycpep_predict_symm_gly ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_symm_gly/command.sh Finished cleanAlignment in 82 seconds [~ 293 test (36.35235732009926%) started, 513 in queue, 24 running] Running Test simple_cycpep_predict_cispro ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_cispro/command.sh Finished swm_rna_move_inside_helix_by_jump in 116 seconds [~ 294 test (36.47642679900744%) started, 512 in queue, 24 running] Running Test rosetta_scripts_include ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rosetta_scripts_include/command.sh Finished HDXEnergy in 55 seconds [~ 295 test (36.60049627791563%) started, 511 in queue, 24 running] Running Test perturb_helical_bundle ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/perturb_helical_bundle/command.sh Finished kinemage_grid_output in 62 seconds [~ 296 test (36.72456575682382%) started, 510 in queue, 24 running] Running Test match_1n9l ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/match_1n9l/command.sh Finished hydrate in 58 seconds [~ 297 test (36.84863523573201%) started, 509 in queue, 24 running] Running Test genkic_lowmemory_mode ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/genkic_lowmemory_mode/command.sh Finished ncaa_fixbb in 117 seconds [~ 298 test (36.9727047146402%) started, 508 in queue, 24 running] Running Test KIC_refine ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/KIC_refine/command.sh Finished Enzrevert_xml in 85 seconds [~ 299 test (37.096774193548384%) started, 507 in queue, 24 running] Running Test InterfaceAnalyzer ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/InterfaceAnalyzer/command.sh Finished rosie_ligand_docking in 83 seconds [~ 300 test (37.220843672456574%) started, 506 in queue, 24 running] Running Test pocket_relax ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/pocket_relax/command.sh Finished swm_rna_singleloop in 86 seconds [~ 301 test (37.344913151364764%) started, 505 in queue, 24 running] Finished splice_out_L1_L2_longer in 68 seconds [~ 301 test (37.344913151364764%) started, 505 in queue, 23 running] Running Test multistage_rosetta_scripts ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/multistage_rosetta_scripts/command.sh Running Test helical_bundle_nonideal ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/helical_bundle_nonideal/command.sh Finished splice_in_4loops_longer in 69 seconds [~ 303 test (37.593052109181144%) started, 503 in queue, 24 running] Running Test favor_coupling_tensor ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/favor_coupling_tensor/command.sh Finished simple_cycpep_predict_1_4_bbmb in 72 seconds [~ 304 test (37.71712158808933%) started, 502 in queue, 24 running] Running Test KIC_vicinity ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/KIC_vicinity/command.sh Finished fold_from_loops in 78 seconds [~ 305 test (37.84119106699752%) started, 501 in queue, 24 running] Running Test torsion_restricted_sampling ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/torsion_restricted_sampling/command.sh Finished dock_with_hotspot_place_simultaneously in 69 seconds [~ 306 test (37.96526054590571%) started, 500 in queue, 24 running] Finished simple_hbondstoatom in 58 seconds [~ 306 test (37.96526054590571%) started, 500 in queue, 23 running] Running Test sequence_profile_constraints ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/sequence_profile_constraints/command.sh Running Test score12_docking ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/score12_docking/command.sh Finished splice_out_H1_H2_same in 62 seconds [~ 308 test (38.21339950372209%) started, 498 in queue, 24 running] Running Test place_simultaneously ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/place_simultaneously/command.sh Finished doug_dock_design_min_mod2_cal_cal in 87 seconds [~ 309 test (38.33746898263027%) started, 497 in queue, 24 running] Running Test bundlegridsampler_z1_offset ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/bundlegridsampler_z1_offset/command.sh Finished splice_out_L3_same in 73 seconds [~ 310 test (38.46153846153846%) started, 496 in queue, 24 running] Running Test bundlegridsampler_z0_offset ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/bundlegridsampler_z0_offset/command.sh Finished ligand_dock_7cpa in 96 seconds [~ 311 test (38.58560794044665%) started, 495 in queue, 24 running] Running Test auto-drrafter_final_results ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/auto-drrafter_final_results/command.sh Finished threefold_symm_peptide_design in 82 seconds [~ 312 test (38.70967741935484%) started, 494 in queue, 24 running] Running Test symmetry_multicomponent ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/symmetry_multicomponent/command.sh Finished docking_full_protocol in 86 seconds [~ 313 test (38.83374689826303%) started, 493 in queue, 24 running] Running Test swm_protein_loop_sampler ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_protein_loop_sampler/command.sh Finished rosetta_scripts_include in 56 seconds [~ 314 test (38.95781637717121%) started, 492 in queue, 24 running] Running Test swm_beta_peptide_loop ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_beta_peptide_loop/command.sh Finished UBQ_Gp_LYX-Cterm in 88 seconds [~ 315 test (39.0818858560794%) started, 491 in queue, 24 running] Running Test splice_out_L1_L2_same ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/splice_out_L1_L2_same/command.sh Finished simple_cycpep_predict_cispro in 70 seconds [~ 316 test (39.20595533498759%) started, 490 in queue, 24 running] Running Test simple_metric_filter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_metric_filter/command.sh Finished simple_cycpep_predict_symm_gly in 76 seconds [~ 317 test (39.33002481389578%) started, 489 in queue, 24 running] Running Test match_6cpa ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/match_6cpa/command.sh Finished perturb_helical_bundle in 58 seconds [~ 318 test (39.45409429280397%) started, 488 in queue, 24 running] Running Test ligand_motif_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ligand_motif_design/command.sh Finished genkic_lowmemory_mode in 59 seconds [~ 319 test (39.578163771712155%) started, 487 in queue, 24 running] Running Test density_refine ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/density_refine/command.sh Finished helical_bundle_nonideal in 55 seconds [~ 320 test (39.702233250620345%) started, 486 in queue, 24 running] Running Test crosslinkermover_trigonal_pyramidal ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_trigonal_pyramidal/command.sh Finished multistage_rosetta_scripts in 56 seconds [~ 321 test (39.826302729528535%) started, 485 in queue, 24 running] Running Test cart_min_glycans ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cart_min_glycans/command.sh Finished InterfaceAnalyzer in 63 seconds [~ 322 test (39.950372208436725%) started, 484 in queue, 24 running] Running Test backrub_interface_ddG ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/backrub_interface_ddG/command.sh Finished auto-drrafter_final_results in 47 seconds [~ 323 test (40.074441687344915%) started, 483 in queue, 24 running] Running Test loop_modeling ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/loop_modeling/command.sh Finished simple_cycpep_predict_thioether_cis_sampling in 110 seconds [~ 324 test (40.1985111662531%) started, 482 in queue, 24 running] Finished symmetry_multicomponent in 44 seconds [~ 324 test (40.1985111662531%) started, 482 in queue, 23 running] Running Test loop_grower_N_term_symm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/loop_grower_N_term_symm/command.sh Running Test jd2test_PDBin_mmCIFout ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/jd2test_PDBin_mmCIFout/command.sh Finished favor_coupling_tensor in 70 seconds [~ 326 test (40.44665012406948%) started, 480 in queue, 24 running] Running Test jd2test_PDBIO ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/jd2test_PDBIO/command.sh Finished score12_docking in 62 seconds [~ 327 test (40.57071960297767%) started, 479 in queue, 24 running] Running Test inv_kin_lig_loop_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/inv_kin_lig_loop_design/command.sh Finished sequence_profile_constraints in 64 seconds [~ 328 test (40.69478908188586%) started, 478 in queue, 24 running] Running Test hbonds ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hbonds/command.sh Finished KIC_refine in 82 seconds [~ 329 test (40.81885856079405%) started, 477 in queue, 24 running] Running Test design_w_custom_palette-NCAAs ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/design_w_custom_palette-NCAAs/command.sh Finished place_simultaneously in 65 seconds [~ 330 test (40.94292803970223%) started, 476 in queue, 24 running] Running Test crosslinkermover_trigonal_planar ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_trigonal_planar/command.sh Finished pocket_relax in 86 seconds [~ 331 test (41.06699751861042%) started, 475 in queue, 24 running] Running Test bin_initialization ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/bin_initialization/command.sh Finished bundlegridsampler_z1_offset in 68 seconds [~ 332 test (41.19106699751861%) started, 474 in queue, 24 running] Running Test swm_general_polymer_sampler ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_general_polymer_sampler/command.sh Finished bundlegridsampler_z0_offset in 68 seconds [~ 333 test (41.3151364764268%) started, 473 in queue, 24 running] Running Test splice_out_L3_shorter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/splice_out_L3_shorter/command.sh Finished KIC_vicinity in 80 seconds [~ 334 test (41.43920595533499%) started, 472 in queue, 24 running] Running Test simple_metric_features ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_metric_features/command.sh Finished simple_metric_filter in 52 seconds [~ 335 test (41.563275434243174%) started, 471 in queue, 24 running] Running Test simple_glycosylation_alternate_AAs ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_glycosylation_alternate_AAs/command.sh Finished splice_out_L1_L2_same in 60 seconds [~ 336 test (41.687344913151364%) started, 470 in queue, 24 running] Running Test simple_cycpep_predict_tetrahedral_metal_asp ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_tetrahedral_metal_asp/command.sh Finished swm_protein_loop_sampler in 72 seconds [~ 337 test (41.811414392059554%) started, 469 in queue, 24 running] Running Test simple_cycpep_predict_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_design/command.sh Finished swm_beta_peptide_loop in 72 seconds [~ 338 test (41.935483870967744%) started, 468 in queue, 24 running] Running Test score_only_silence ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/score_only_silence/command.sh Finished torsion_restricted_sampling in 101 seconds [~ 339 test (42.059553349875934%) started, 467 in queue, 24 running] Running Test residue_energy_breakdown ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/residue_energy_breakdown/command.sh Finished ligand_motif_design in 69 seconds [~ 340 test (42.18362282878412%) started, 466 in queue, 24 running] Running Test oligourea_predict ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/oligourea_predict/command.sh Finished cart_min_glycans in 63 seconds [~ 341 test (42.30769230769231%) started, 465 in queue, 24 running] Running Test multistage_rosetta_scripts_clustering ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/multistage_rosetta_scripts_clustering/command.sh Finished crosslinkermover_trigonal_pyramidal in 64 seconds [~ 342 test (42.4317617866005%) started, 464 in queue, 24 running] Running Test membrane_abinitio ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/membrane_abinitio/command.sh Finished loop_grower_N_term_symm in 50 seconds [~ 343 test (42.55583126550869%) started, 463 in queue, 24 running] Running Test make_mainchain_potential ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/make_mainchain_potential/command.sh Finished backrub_interface_ddG in 64 seconds [~ 344 test (42.67990074441688%) started, 462 in queue, 24 running] Running Test jd2test_PDBin_mmCIFout_extra_data_separate ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/jd2test_PDBin_mmCIFout_extra_data_separate/command.sh Finished density_refine in 71 seconds [~ 345 test (42.80397022332506%) started, 461 in queue, 24 running] Running Test design_w_custom_palette-CAAs ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/design_w_custom_palette-CAAs/command.sh Finished jd2test_PDBin_mmCIFout in 61 seconds [~ 346 test (42.92803970223325%) started, 460 in queue, 24 running] Running Test carbohydrates ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/carbohydrates/command.sh Finished simple_cycpep_predict_tetrahedral_metal_asp in 40 seconds [~ 347 test (43.05210918114144%) started, 459 in queue, 24 running] Running Test bundlegridsampler_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/bundlegridsampler_design/command.sh Finished jd2test_PDBIO in 60 seconds [~ 348 test (43.17617866004963%) started, 458 in queue, 24 running] Running Test RunSimpleMetric_b_factor_test ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/RunSimpleMetric_b_factor_test/command.sh Finished match_6cpa in 94 seconds [~ 349 test (43.30024813895782%) started, 457 in queue, 24 running] Running Test tcrmodel ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/tcrmodel/command.sh Finished crosslinkermover_trigonal_planar in 60 seconds [~ 350 test (43.424317617866%) started, 456 in queue, 24 running] Running Test splice_out_H1_H2_shorter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/splice_out_H1_H2_shorter/command.sh /home/benchmark/rosetta/tests/integration/new/simple_metric_features/command.sh: line 12: dump.sql: No such file or directory Finished simple_metric_features in 53 seconds [~ 351 test (43.54838709677419%) started, 455 in queue, 24 running] Running Test simple_metrics_in_protocols ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_metrics_in_protocols/command.sh Finished simple_glycosylation_alternate_AAs in 51 seconds [~ 352 test (43.67245657568238%) started, 454 in queue, 24 running] Running Test simple_metric_cache ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_metric_cache/command.sh Finished design_w_custom_palette-NCAAs in 64 seconds [~ 353 test (43.79652605459057%) started, 453 in queue, 24 running] Finished splice_out_L3_shorter in 57 seconds [~ 353 test (43.79652605459057%) started, 453 in queue, 23 running] Running Test rna_farfar_noncanonical_hairpin ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_farfar_noncanonical_hairpin/command.sh Running Test rna_puzzle11_H2H3H4_run3_connectU40 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_puzzle11_H2H3H4_run3_connectU40/command.sh Finished inv_kin_lig_loop_design in 68 seconds [~ 355 test (44.044665012406945%) started, 451 in queue, 24 running] Running Test mm_params ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mm_params/command.sh Finished hbonds in 74 seconds [~ 356 test (44.168734491315135%) started, 450 in queue, 24 running] Running Test minimize_with_elec_dens ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/minimize_with_elec_dens/command.sh Finished bin_initialization in 69 seconds [~ 357 test (44.292803970223325%) started, 449 in queue, 24 running] Running Test enumerative_sampling ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/enumerative_sampling/command.sh Finished score_only_silence in 53 seconds [~ 358 test (44.416873449131515%) started, 448 in queue, 24 running] Running Test centroid_from_fullatom ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/centroid_from_fullatom/command.sh Finished residue_energy_breakdown in 49 seconds [~ 359 test (44.540942928039705%) started, 447 in queue, 24 running] Running Test antibody_designer_camelid ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/antibody_designer_camelid/command.sh Finished oligourea_predict in 46 seconds [~ 360 test (44.66501240694789%) started, 446 in queue, 24 running] Running Test AnchorFinder ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/AnchorFinder/command.sh Finished match_1n9l in 174 seconds [~ 361 test (44.78908188585608%) started, 445 in queue, 24 running] Running Test simple_cycpep_predict_thioether_lariat ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_thioether_lariat/command.sh Finished multistage_rosetta_scripts_clustering in 43 seconds [~ 362 test (44.91315136476427%) started, 444 in queue, 24 running] Running Test sasa_metric_options ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/sasa_metric_options/command.sh Finished tcrmodel in 25 seconds [~ 363 test (45.03722084367246%) started, 443 in queue, 24 running] Running Test motif_score_filter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/motif_score_filter/command.sh Finished loop_modeling in 99 seconds [~ 364 test (45.16129032258065%) started, 442 in queue, 24 running] Running Test mhc_epitope_nmer_preload ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mhc_epitope_nmer_preload/command.sh Finished simple_cycpep_predict_design in 70 seconds [~ 365 test (45.28535980148883%) started, 441 in queue, 24 running] Running Test mf_fixbb_des ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mf_fixbb_des/command.sh Finished RunSimpleMetric_b_factor_test in 43 seconds [~ 366 test (45.40942928039702%) started, 440 in queue, 24 running] Running Test glycan_anomers ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/glycan_anomers/command.sh Finished carbohydrates in 50 seconds [~ 367 test (45.53349875930521%) started, 439 in queue, 24 running] Running Test crosslinkermover_trigonal_pyramidal_c3_symm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_trigonal_pyramidal_c3_symm/command.sh Finished jd2test_PDBin_mmCIFout_extra_data_separate in 59 seconds [~ 368 test (45.6575682382134%) started, 438 in queue, 24 running] Running Test crosslinkermover_trigonal_planar_c3_symm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_trigonal_planar_c3_symm/command.sh Finished simple_metrics_in_protocols in 45 seconds [~ 369 test (45.78163771712159%) started, 437 in queue, 24 running] Running Test bundlegridsampler_multirepeat ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/bundlegridsampler_multirepeat/command.sh Finished design_w_custom_palette-CAAs in 60 seconds [~ 370 test (45.90570719602977%) started, 436 in queue, 24 running] Running Test UBQ_Gp_CYD-CYD ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/UBQ_Gp_CYD-CYD/command.sh Finished membrane_abinitio in 67 seconds [~ 371 test (46.02977667493796%) started, 435 in queue, 24 running] Running Test LayerSelector ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/LayerSelector/command.sh Finished simple_metric_cache in 46 seconds [~ 372 test (46.15384615384615%) started, 434 in queue, 24 running] Running Test splice_out_L1_L2_shorter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/splice_out_L1_L2_shorter/command.sh Finished make_mainchain_potential in 69 seconds [~ 373 test (46.27791563275434%) started, 433 in queue, 24 running] Running Test ncbb_packer_palette ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ncbb_packer_palette/command.sh Finished mm_params in 47 seconds [~ 374 test (46.40198511166253%) started, 432 in queue, 24 running] Running Test match_xml ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/match_xml/command.sh Finished bundlegridsampler_design in 58 seconds [~ 375 test (46.526054590570716%) started, 431 in queue, 24 running] Running Test hbonds_sp2 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hbonds_sp2/command.sh Finished splice_out_H1_H2_shorter in 57 seconds [~ 376 test (46.650124069478906%) started, 430 in queue, 24 running] Running Test crosslinkermover_methyllanthionine ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_methyllanthionine/command.sh Finished centroid_from_fullatom in 44 seconds [~ 377 test (46.774193548387096%) started, 429 in queue, 24 running] Running Test add_constraints_to_current_conformation ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/add_constraints_to_current_conformation/command.sh Finished antibody_designer_camelid in 45 seconds [~ 378 test (46.898263027295286%) started, 428 in queue, 24 running] Running Test InterfaceAnalyzer_metrics ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/InterfaceAnalyzer_metrics/command.sh Finished minimize_with_elec_dens in 52 seconds [~ 379 test (47.022332506203476%) started, 427 in queue, 24 running] Running Test AnchoredPDBCreator ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/AnchoredPDBCreator/command.sh Finished motif_score_filter in 41 seconds [~ 380 test (47.146401985111666%) started, 426 in queue, 24 running] Running Test thermal_sampler ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/thermal_sampler/command.sh Finished enumerative_sampling in 54 seconds [~ 381 test (47.27047146401985%) started, 425 in queue, 24 running] Running Test swa_protein_build_at_Cterminus ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_protein_build_at_Cterminus/command.sh Finished swm_general_polymer_sampler in 125 seconds [~ 382 test (47.39454094292804%) started, 424 in queue, 24 running] Running Test splice_out_H3_same ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/splice_out_H3_same/command.sh Finished sasa_metric_options in 48 seconds [~ 383 test (47.51861042183623%) started, 423 in queue, 24 running] Running Test rollmover ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rollmover/command.sh Finished AnchorFinder in 53 seconds [~ 384 test (47.64267990074442%) started, 422 in queue, 24 running] Running Test recon_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/recon_design/command.sh Finished simple_cycpep_predict_thioether_lariat in 51 seconds [~ 385 test (47.76674937965261%) started, 421 in queue, 24 running] Running Test metropolis_hastings ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/metropolis_hastings/command.sh Finished mhc_epitope_nmer_preload in 51 seconds [~ 386 test (47.89081885856079%) started, 420 in queue, 24 running] Running Test ligand_dock_grid ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ligand_dock_grid/command.sh Finished rna_farfar_noncanonical_hairpin in 77 seconds [~ 387 test (48.01488833746898%) started, 419 in queue, 24 running] Running Test density_denovo ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/density_denovo/command.sh Finished glycan_anomers in 49 seconds [~ 388 test (48.13895781637717%) started, 418 in queue, 24 running] Running Test broker ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/broker/command.sh Finished bundlegridsampler_multirepeat in 49 seconds [~ 389 test (48.26302729528536%) started, 417 in queue, 24 running] Running Test antibody_graft ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/antibody_graft/command.sh Finished crosslinkermover_trigonal_pyramidal_c3_symm in 53 seconds [~ 390 test (48.38709677419355%) started, 416 in queue, 24 running] Running Test UBQ_E2_thioester_two_ubiquitins ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/UBQ_E2_thioester_two_ubiquitins/command.sh Finished mf_fixbb_des in 67 seconds [~ 391 test (48.511166253101734%) started, 415 in queue, 24 running] Finished crosslinkermover_trigonal_planar_c3_symm in 52 seconds [~ 391 test (48.511166253101734%) started, 415 in queue, 23 running] Running Test ThreadingInputter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ThreadingInputter/command.sh Running Test thread_local_tracers_check ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/thread_local_tracers_check/command.sh Finished thread_local_tracers_check in 0 seconds [~ 393 test (48.759305210918114%) started, 413 in queue, 24 running] Running Test simple_cycpep_predict_square_planar_metal ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_square_planar_metal/command.sh Finished splice_out_L1_L2_shorter in 50 seconds [~ 394 test (48.883374689826304%) started, 412 in queue, 24 running] Running Test posttranslationalmod_io ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/posttranslationalmod_io/command.sh Finished LayerSelector in 56 seconds [~ 395 test (49.007444168734494%) started, 411 in queue, 24 running] Running Test perturb_helical_bundle_setting ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/perturb_helical_bundle_setting/command.sh Finished crosslinkermover_methyllanthionine in 46 seconds [~ 396 test (49.13151364764268%) started, 410 in queue, 24 running] Running Test oligourea_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/oligourea_design/command.sh Finished InterfaceAnalyzer_metrics in 47 seconds [~ 397 test (49.25558312655087%) started, 409 in queue, 24 running] Running Test min_pack_min ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/min_pack_min/command.sh Finished ncbb_packer_palette in 60 seconds [~ 398 test (49.37965260545906%) started, 408 in queue, 24 running] Running Test ReadResfile_with_selector ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ReadResfile_with_selector/command.sh Finished UBQ_Gp_CYD-CYD in 66 seconds [~ 399 test (49.50372208436725%) started, 407 in queue, 24 running] Running Test LayerDesign ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/LayerDesign/command.sh Finished add_constraints_to_current_conformation in 54 seconds [~ 400 test (49.62779156327544%) started, 406 in queue, 24 running] Running Test zinc_homodimer_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/zinc_homodimer_design/command.sh Finished match_xml in 63 seconds [~ 401 test (49.75186104218362%) started, 405 in queue, 24 running] Running Test startfrom_file ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/startfrom_file/command.sh Finished rna_puzzle11_H2H3H4_run3_connectU40 in 112 seconds [~ 402 test (49.87593052109181%) started, 404 in queue, 24 running] Finished rollmover in 44 seconds [~ 402 test (49.87593052109181%) started, 404 in queue, 23 running] Running Test splice_out_H3_shorter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/splice_out_H3_shorter/command.sh Running Test simple_cycpep_predict_peptoid ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_peptoid/command.sh Finished splice_out_H3_same in 48 seconds [~ 404 test (50.12406947890819%) started, 402 in queue, 24 running] Running Test repack_with_elec_dens ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/repack_with_elec_dens/command.sh Finished hbonds_sp2 in 68 seconds [~ 405 test (50.24813895781638%) started, 401 in queue, 24 running] Finished metropolis_hastings in 45 seconds [~ 405 test (50.24813895781638%) started, 401 in queue, 23 running] Running Test pna ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/pna/command.sh Running Test glycan_sequon_scanner ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/glycan_sequon_scanner/command.sh Finished recon_design in 46 seconds [~ 407 test (50.49627791563275%) started, 399 in queue, 24 running] Running Test glycan_refinment ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/glycan_refinment/command.sh Finished thermal_sampler in 55 seconds [~ 408 test (50.62034739454094%) started, 398 in queue, 24 running] Running Test enzscore_filter_metal_sym ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/enzscore_filter_metal_sym/command.sh Finished swa_protein_build_at_Cterminus in 54 seconds [~ 409 test (50.74441687344913%) started, 397 in queue, 24 running] Running Test enzscore_filter_dimetal_sym ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/enzscore_filter_dimetal_sym/command.sh Finished density_denovo in 42 seconds [~ 410 test (50.86848635235732%) started, 396 in queue, 24 running] Running Test coarse_rna_scoring ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/coarse_rna_scoring/command.sh Finished ligand_dock_grid in 43 seconds [~ 411 test (50.992555831265506%) started, 395 in queue, 24 running] Running Test classic_relax_1a19 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/classic_relax_1a19/command.sh Finished simple_cycpep_predict_square_planar_metal in 30 seconds [~ 412 test (51.116625310173696%) started, 394 in queue, 24 running] Running Test backbonegridsampler_nstruct_mode ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/backbonegridsampler_nstruct_mode/command.sh Finished AnchoredPDBCreator in 66 seconds [~ 413 test (51.240694789081886%) started, 393 in queue, 24 running] Running Test PeptideCyclizeMover ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/PeptideCyclizeMover/command.sh Finished broker in 53 seconds [~ 414 test (51.364764267990076%) started, 392 in queue, 24 running] Running Test test_computed_saxs_spectrum ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/test_computed_saxs_spectrum/command.sh Finished posttranslationalmod_io in 41 seconds [~ 415 test (51.488833746898266%) started, 391 in queue, 24 running] Running Test swm_rna_checkpoint_partition ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_rna_checkpoint_partition/command.sh Finished oligourea_design in 43 seconds [~ 416 test (51.61290322580645%) started, 390 in queue, 24 running] Running Test swm_protein_move_inside_helix_by_bond ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_protein_move_inside_helix_by_bond/command.sh Finished ThreadingInputter in 51 seconds [~ 417 test (51.73697270471464%) started, 389 in queue, 24 running] Running Test simple_dna_test ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_dna_test/command.sh Finished perturb_helical_bundle_setting in 44 seconds [~ 418 test (51.86104218362283%) started, 388 in queue, 24 running] Running Test rosetta_scripts_hbond_options ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rosetta_scripts_hbond_options/command.sh Finished antibody_graft in 56 seconds [~ 419 test (51.98511166253102%) started, 387 in queue, 24 running] Running Test ppk ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ppk/command.sh Finished startfrom_file in 40 seconds [~ 420 test (52.10918114143921%) started, 386 in queue, 24 running] Running Test mp_ligand_interface ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_ligand_interface/command.sh Finished glycan_sequon_scanner in 37 seconds [~ 421 test (52.23325062034739%) started, 385 in queue, 24 running] Running Test genkic_rama_filter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/genkic_rama_filter/command.sh Finished splice_out_H3_shorter in 42 seconds [~ 422 test (52.35732009925558%) started, 384 in queue, 24 running] Running Test fuzzy ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/fuzzy/command.sh Finished ReadResfile_with_selector in 48 seconds [~ 423 test (52.48138957816377%) started, 383 in queue, 24 running] Running Test enzscore_filter_metal ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/enzscore_filter_metal/command.sh Finished repack_with_elec_dens in 41 seconds [~ 424 test (52.60545905707196%) started, 382 in queue, 24 running] Running Test enzscore_filter_dimetal ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/enzscore_filter_dimetal/command.sh Finished glycan_refinment in 40 seconds [~ 425 test (52.72952853598015%) started, 381 in queue, 24 running] Running Test ddG_scan ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ddG_scan/command.sh Finished LayerDesign in 49 seconds [~ 426 test (52.853598014888334%) started, 380 in queue, 24 running] Running Test crosslinkermover_tetrahedral_metal_asp ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_tetrahedral_metal_asp/command.sh Finished UBQ_E2_thioester_two_ubiquitins in 68 seconds [~ 427 test (52.977667493796524%) started, 379 in queue, 24 running] Running Test crosslinkermover_lanthionine ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_lanthionine/command.sh Finished coarse_rna_scoring in 42 seconds [~ 428 test (53.101736972704714%) started, 378 in queue, 24 running] Running Test backbonegridsampler_multiresidue ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/backbonegridsampler_multiresidue/command.sh Finished enzscore_filter_metal_sym in 44 seconds [~ 429 test (53.225806451612904%) started, 377 in queue, 24 running] Running Test symmetric_docking ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/symmetric_docking/command.sh Finished enzscore_filter_dimetal_sym in 44 seconds [~ 430 test (53.349875930521094%) started, 376 in queue, 24 running] Running Test sim_cryo ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/sim_cryo/command.sh Finished PeptideCyclizeMover in 36 seconds [~ 431 test (53.473945409429284%) started, 375 in queue, 24 running] Running Test rosetta_scripts_setup ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rosetta_scripts_setup/command.sh Finished zinc_homodimer_design in 54 seconds [~ 432 test (53.59801488833747%) started, 374 in queue, 24 running] Running Test rna_denovo_base_pair_setup ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_base_pair_setup/command.sh Finished backbonegridsampler_nstruct_mode in 46 seconds [~ 433 test (53.72208436724566%) started, 373 in queue, 24 running] Running Test repeat_propagate_v3 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/repeat_propagate_v3/command.sh Finished classic_relax_1a19 in 55 seconds [~ 434 test (53.84615384615385%) started, 372 in queue, 24 running] Running Test repeat_propagate ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/repeat_propagate/command.sh Finished min_pack_min in 70 seconds [~ 435 test (53.97022332506204%) started, 371 in queue, 24 running] Running Test protocol_metric ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/protocol_metric/command.sh Finished test_computed_saxs_spectrum in 40 seconds [~ 436 test (54.09429280397023%) started, 370 in queue, 24 running] Running Test perturb_helical_bundle_z_offset ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/perturb_helical_bundle_z_offset/command.sh Finished rosetta_scripts_hbond_options in 36 seconds [~ 437 test (54.21836228287841%) started, 369 in queue, 24 running] Running Test perturb_helical_bundle_epsilon ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/perturb_helical_bundle_epsilon/command.sh Finished simple_cycpep_predict_peptoid in 70 seconds [~ 438 test (54.3424317617866%) started, 368 in queue, 24 running] Running Test metalloprotein_abrelax ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/metalloprotein_abrelax/command.sh Finished ppk in 37 seconds [~ 439 test (54.46650124069479%) started, 367 in queue, 24 running] Running Test grid_scores_features ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/grid_scores_features/command.sh Finished pna in 69 seconds [~ 440 test (54.59057071960298%) started, 366 in queue, 24 running] Running Test exclusively_shared_jumps ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/exclusively_shared_jumps/command.sh Finished mp_ligand_interface in 39 seconds [~ 441 test (54.71464019851117%) started, 365 in queue, 24 running] Running Test custom_basetype_packer_palette ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/custom_basetype_packer_palette/command.sh Finished genkic_rama_filter in 40 seconds [~ 442 test (54.83870967741935%) started, 364 in queue, 24 running] Running Test crosslinkermover_thioether ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_thioether/command.sh Finished crosslinkermover_tetrahedral_metal_asp in 39 seconds [~ 443 test (54.96277915632754%) started, 363 in queue, 24 running] Running Test create_sequence_motif ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/create_sequence_motif/command.sh Finished ddG_scan in 40 seconds [~ 444 test (55.08684863523573%) started, 362 in queue, 24 running] Running Test UnsatSelector ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/UnsatSelector/command.sh Finished enzscore_filter_metal in 42 seconds [~ 445 test (55.21091811414392%) started, 361 in queue, 24 running] Finished fuzzy in 43 seconds [~ 446 test (55.33498759305211%) started, 360 in queue, 24 running] Running Test LayerDesign_symm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/LayerDesign_symm/command.sh Running Test FloppyTail ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/FloppyTail/command.sh Finished crosslinkermover_lanthionine in 38 seconds [~ 447 test (55.459057071960295%) started, 359 in queue, 24 running] Running Test FlipChirality ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/FlipChirality/command.sh Finished rosetta_scripts_setup in 35 seconds [~ 448 test (55.583126550868485%) started, 358 in queue, 24 running] Running Test ContactMolecularSurface ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ContactMolecularSurface/command.sh Finished backbonegridsampler_multiresidue in 38 seconds [~ 449 test (55.707196029776675%) started, 357 in queue, 24 running] Running Test write_mol_file ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/write_mol_file/command.sh Finished enzscore_filter_dimetal in 44 seconds [~ 450 test (55.831265508684865%) started, 356 in queue, 24 running] Running Test vancomycin ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/vancomycin/command.sh Finished swm_protein_move_inside_helix_by_bond in 57 seconds [~ 451 test (55.955334987593055%) started, 355 in queue, 24 running] Running Test threefoldlinkermover_tbmb_symmetric ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/threefoldlinkermover_tbmb_symmetric/command.sh Finished rna_denovo_base_pair_setup in 38 seconds [~ 452 test (56.07940446650124%) started, 354 in queue, 24 running] Running Test threefoldlinkermover_tbmb ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/threefoldlinkermover_tbmb/command.sh Finished simple_dna_test in 60 seconds [~ 453 test (56.20347394540943%) started, 353 in queue, 24 running] Running Test symmetry_data_resource ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/symmetry_data_resource/command.sh Finished repeat_propagate_v3 in 35 seconds [~ 454 test (56.32754342431762%) started, 352 in queue, 24 running] Running Test symmetric_cycpep_align_and_symmetrize ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/symmetric_cycpep_align_and_symmetrize/command.sh Finished swm_rna_checkpoint_partition in 69 seconds [~ 455 test (56.45161290322581%) started, 351 in queue, 24 running] Finished symmetric_docking in 45 seconds [~ 455 test (56.45161290322581%) started, 351 in queue, 23 running] Running Test sample_seq_from_probs ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/sample_seq_from_probs/command.sh Running Test rotamer_recovery ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rotamer_recovery/command.sh Finished repeat_propagate in 37 seconds [~ 457 test (56.69975186104218%) started, 349 in queue, 24 running] Running Test rna_farfar_syn_chi_res ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_farfar_syn_chi_res/command.sh Finished protocol_metric in 37 seconds [~ 458 test (56.82382133995037%) started, 348 in queue, 24 running] Running Test resource_database_locator ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/resource_database_locator/command.sh Finished perturb_helical_bundle_z_offset in 37 seconds [~ 459 test (56.94789081885856%) started, 347 in queue, 24 running] Running Test res_lipo_ref2015_memb ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/res_lipo_ref2015_memb/command.sh Finished perturb_helical_bundle_epsilon in 38 seconds [~ 460 test (57.07196029776675%) started, 346 in queue, 24 running] Running Test repeat_propagate_v2 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/repeat_propagate_v2/command.sh Finished grid_scores_features in 36 seconds [~ 461 test (57.19602977667494%) started, 345 in queue, 24 running] Running Test real_virt_mover ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/real_virt_mover/command.sh Finished exclusively_shared_jumps in 36 seconds [~ 462 test (57.32009925558312%) started, 344 in queue, 24 running] Running Test readin_dna_rna_protein ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/readin_dna_rna_protein/command.sh Finished sim_cryo in 59 seconds [~ 463 test (57.44416873449131%) started, 343 in queue, 24 running] Running Test rdkit_metrics ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rdkit_metrics/command.sh Finished metalloprotein_abrelax in 45 seconds [~ 464 test (57.5682382133995%) started, 342 in queue, 24 running] Running Test rama_mutation_selector ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rama_mutation_selector/command.sh Finished custom_basetype_packer_palette in 37 seconds [~ 465 test (57.69230769230769%) started, 341 in queue, 24 running] Running Test pna_base_pairs ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/pna_base_pairs/command.sh Finished UnsatSelector in 33 seconds [~ 466 test (57.81637717121588%) started, 340 in queue, 24 running] Running Test mp_span_ang_ref2015_memb ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_span_ang_ref2015_memb/command.sh Finished FlipChirality in 33 seconds [~ 467 test (57.940446650124066%) started, 339 in queue, 24 running] Running Test mp_quick_relax_ref2015_memb ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_quick_relax_ref2015_memb/command.sh Finished crosslinkermover_thioether in 40 seconds [~ 468 test (58.064516129032256%) started, 338 in queue, 24 running] Running Test mf_flexbb_sc ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mf_flexbb_sc/command.sh Finished create_sequence_motif in 37 seconds [~ 469 test (58.188585607940446%) started, 337 in queue, 24 running] Running Test make_rot_lib ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/make_rot_lib/command.sh Finished ContactMolecularSurface in 36 seconds [~ 470 test (58.312655086848636%) started, 336 in queue, 24 running] Finished write_mol_file in 35 seconds [~ 470 test (58.312655086848636%) started, 336 in queue, 23 running] Running Test loop_creation ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/loop_creation/command.sh Running Test genkic_ramaprepro_sampling ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/genkic_ramaprepro_sampling/command.sh Finished threefoldlinkermover_tbmb_symmetric in 35 seconds [~ 472 test (58.56079404466501%) started, 334 in queue, 24 running] Running Test features_pdb ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/features_pdb/command.sh Finished LayerDesign_symm in 39 seconds [~ 473 test (58.6848635235732%) started, 333 in queue, 24 running] Running Test database_session_resource ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/database_session_resource/command.sh Finished threefoldlinkermover_tbmb in 35 seconds [~ 474 test (58.80893300248139%) started, 332 in queue, 24 running] Running Test cst_info ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cst_info/command.sh Finished symmetry_data_resource in 33 seconds [~ 475 test (58.93300248138958%) started, 331 in queue, 24 running] Running Test crosslinkermover_tetrahedral_metal ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crosslinkermover_tetrahedral_metal/command.sh Finished symmetric_cycpep_align_and_symmetrize in 33 seconds [~ 476 test (59.05707196029777%) started, 330 in queue, 24 running] Running Test bin_perturbation ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/bin_perturbation/command.sh Finished sample_seq_from_probs in 34 seconds [~ 477 test (59.18114143920595%) started, 329 in queue, 24 running] Running Test autosetup_metals_centroid ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/autosetup_metals_centroid/command.sh Finished vancomycin in 44 seconds [~ 478 test (59.30521091811414%) started, 328 in queue, 24 running] Running Test RBOut ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/RBOut/command.sh Finished FloppyTail in 48 seconds [~ 479 test (59.42928039702233%) started, 327 in queue, 24 running] Running Test PDB_diagnostic ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/PDB_diagnostic/command.sh Finished rotamer_recovery in 40 seconds [~ 480 test (59.55334987593052%) started, 326 in queue, 24 running] Running Test InterfaceDdG ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/InterfaceDdG/command.sh Finished resource_database_locator in 34 seconds [~ 481 test (59.67741935483871%) started, 325 in queue, 24 running] Running Test DumpTrajectoryEnergy_packing ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/DumpTrajectoryEnergy_packing/command.sh Finished res_lipo_ref2015_memb in 34 seconds [~ 482 test (59.8014888337469%) started, 324 in queue, 24 running] Running Test ConsensusLoopDesign ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ConsensusLoopDesign/command.sh Finished repeat_propagate_v2 in 33 seconds [~ 483 test (59.925558312655085%) started, 323 in queue, 24 running] Running Test BFactorSelector ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/BFactorSelector/command.sh Finished real_virt_mover in 35 seconds [~ 484 test (60.049627791563275%) started, 322 in queue, 24 running] Running Test swm_rna_fourwayjunction ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_rna_fourwayjunction/command.sh Finished rdkit_metrics in 35 seconds [~ 485 test (60.173697270471465%) started, 321 in queue, 24 running] Running Test swm_protein_move_inside_coiledcoil_by_bond ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_protein_move_inside_coiledcoil_by_bond/command.sh Finished rna_farfar_syn_chi_res in 46 seconds [~ 486 test (60.297766749379655%) started, 320 in queue, 24 running] Running Test swm_protein_CCDmove ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_protein_CCDmove/command.sh Finished rama_mutation_selector in 34 seconds [~ 487 test (60.421836228287845%) started, 319 in queue, 24 running] Running Test swa_rna_gagu_15_combine_long_loop_sampling ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_15_combine_long_loop_sampling/command.sh Finished pna_base_pairs in 35 seconds [~ 488 test (60.54590570719603%) started, 318 in queue, 24 running] Running Test smallmover_resselector ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/smallmover_resselector/command.sh Finished mp_span_ang_ref2015_memb in 34 seconds [~ 489 test (60.66997518610422%) started, 317 in queue, 24 running] Running Test sequence_recovery ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/sequence_recovery/command.sh Finished mp_quick_relax_ref2015_memb in 33 seconds [~ 490 test (60.79404466501241%) started, 316 in queue, 24 running] Running Test selected_residue_count_metric ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/selected_residue_count_metric/command.sh Finished loop_creation in 34 seconds [~ 491 test (60.9181141439206%) started, 315 in queue, 24 running] Running Test rna_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_design/command.sh Finished mf_flexbb_sc in 36 seconds [~ 492 test (61.04218362282879%) started, 314 in queue, 24 running] Running Test rna_assemble ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_assemble/command.sh Finished genkic_ramaprepro_sampling in 35 seconds [~ 493 test (61.16625310173697%) started, 313 in queue, 24 running] Running Test genkic_bin_perturbing ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/genkic_bin_perturbing/command.sh Finished database_session_resource in 33 seconds [~ 494 test (61.29032258064516%) started, 312 in queue, 24 running] Running Test fold_cst_new ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/fold_cst_new/command.sh Finished cst_info in 33 seconds [~ 495 test (61.41439205955335%) started, 311 in queue, 24 running] Running Test enzscore_filter_ligand ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/enzscore_filter_ligand/command.sh Finished features_pdb in 35 seconds [~ 496 test (61.53846153846154%) started, 310 in queue, 24 running] Running Test dihedral_constraint_generator ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/dihedral_constraint_generator/command.sh Finished readin_dna_rna_protein in 50 seconds [~ 497 test (61.66253101736973%) started, 309 in queue, 24 running] Running Test cluster_alns ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cluster_alns/command.sh Finished crosslinkermover_tetrahedral_metal in 35 seconds [~ 498 test (61.78660049627791%) started, 308 in queue, 24 running] Running Test add_job_pair_data ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/add_job_pair_data/command.sh Finished bin_perturbation in 35 seconds [~ 499 test (61.9106699751861%) started, 307 in queue, 24 running] Running Test StrandHelixGeometryFilter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/StrandHelixGeometryFilter/command.sh Finished autosetup_metals_centroid in 35 seconds [~ 500 test (62.03473945409429%) started, 306 in queue, 24 running] Running Test StrandCurvatureByLevels ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/StrandCurvatureByLevels/command.sh Finished RBOut in 34 seconds [~ 501 test (62.15880893300248%) started, 305 in queue, 24 running] Running Test SecondaryStructureFilter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/SecondaryStructureFilter/command.sh Finished InterfaceDdG in 34 seconds [~ 502 test (62.28287841191067%) started, 304 in queue, 24 running] Running Test PeptideStubMover_prependRepeat ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/PeptideStubMover_prependRepeat/command.sh Finished make_rot_lib in 48 seconds [~ 503 test (62.406947890818856%) started, 303 in queue, 24 running] Running Test OversaturatedHbondAcceptorFilter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/OversaturatedHbondAcceptorFilter/command.sh Finished PDB_diagnostic in 37 seconds [~ 504 test (62.531017369727046%) started, 302 in queue, 24 running] Running Test MutateResidue_selector ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/MutateResidue_selector/command.sh Finished DumpTrajectoryEnergy_packing in 37 seconds [~ 505 test (62.655086848635236%) started, 301 in queue, 24 running] Running Test LoopLengthChange ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/LoopLengthChange/command.sh Finished ConsensusLoopDesign in 37 seconds [~ 506 test (62.779156327543426%) started, 300 in queue, 24 running] Running Test HelixBendFilter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/HelixBendFilter/command.sh Finished BFactorSelector in 37 seconds [~ 507 test (62.903225806451616%) started, 299 in queue, 24 running] Running Test FilterReportAsPoseExtraScoresMover ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/FilterReportAsPoseExtraScoresMover/command.sh Finished smallmover_resselector in 32 seconds [~ 508 test (63.0272952853598%) started, 298 in queue, 24 running] Running Test FavorSequenceProfileMover ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/FavorSequenceProfileMover/command.sh Finished selected_residue_count_metric in 33 seconds [~ 509 test (63.15136476426799%) started, 297 in queue, 24 running] Running Test DumpTrajectoryEnergy ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/DumpTrajectoryEnergy/command.sh Finished swm_protein_CCDmove in 40 seconds [~ 510 test (63.27543424317618%) started, 296 in queue, 24 running] Running Test AddConstraintsToCurrentConformationMover ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/AddConstraintsToCurrentConformationMover/command.sh Finished sequence_recovery in 35 seconds [~ 511 test (63.39950372208437%) started, 295 in queue, 24 running] Running Test swm_rna_protonated_adenosine ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_rna_protonated_adenosine/command.sh Finished enzscore_filter_ligand in 32 seconds [~ 512 test (63.52357320099256%) started, 294 in queue, 24 running] Running Test swa_rna_gagu_23_append_and_kic_close ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_23_append_and_kic_close/command.sh Finished swm_protein_move_inside_coiledcoil_by_bond in 47 seconds [~ 513 test (63.64764267990074%) started, 293 in queue, 24 running] Running Test swa_rna_gagu_22_prepend_and_kic_close ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_22_prepend_and_kic_close/command.sh Finished add_job_pair_data in 32 seconds [~ 514 test (63.77171215880893%) started, 292 in queue, 24 running] Running Test swa_rna_gagu_16_prepend_dinucleotide_on_dinucleotide ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_16_prepend_dinucleotide_on_dinucleotide/command.sh Finished dihedral_constraint_generator in 34 seconds [~ 515 test (63.89578163771712%) started, 291 in queue, 24 running] Running Test swa_rna_gagu_13_chunk_combination_and_closure ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_13_chunk_combination_and_closure/command.sh Finished rna_assemble in 36 seconds [~ 516 test (64.0198511166253%) started, 290 in queue, 24 running] Running Test swa_rna_gagu_10_prepend_and_ccd_close ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_10_prepend_and_ccd_close/command.sh Finished StrandHelixGeometryFilter in 33 seconds [~ 517 test (64.1439205955335%) started, 289 in queue, 24 running] Running Test stored_residue_subset ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/stored_residue_subset/command.sh Finished StrandCurvatureByLevels in 33 seconds [~ 518 test (64.26799007444168%) started, 288 in queue, 24 running] Running Test simple_cycpep_predict_terminal_disulfide_internal_permutations ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_terminal_disulfide_internal_permutations/command.sh Finished swm_rna_fourwayjunction in 54 seconds [~ 519 test (64.39205955334988%) started, 287 in queue, 24 running] Running Test simple_cycpep_predict_sidechain_isopeptide ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_sidechain_isopeptide/command.sh Finished swa_rna_gagu_15_combine_long_loop_sampling in 48 seconds [~ 520 test (64.51612903225806%) started, 286 in queue, 24 running] Running Test oop_dock_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/oop_dock_design/command.sh Finished SecondaryStructureFilter in 33 seconds [~ 521 test (64.64019851116625%) started, 285 in queue, 24 running] Running Test mp_symmetry_load ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_symmetry_load/command.sh Finished cluster_alns in 42 seconds [~ 522 test (64.76426799007444%) started, 284 in queue, 24 running] Running Test mf_fixbb_sc ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mf_fixbb_sc/command.sh Finished PeptideStubMover_prependRepeat in 32 seconds [~ 523 test (64.88833746898263%) started, 283 in queue, 24 running] Running Test genkic_dihedral_copying ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/genkic_dihedral_copying/command.sh Finished OversaturatedHbondAcceptorFilter in 32 seconds [~ 524 test (65.01240694789082%) started, 282 in queue, 24 running] Running Test design_w_custom_palette-RNA ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/design_w_custom_palette-RNA/command.sh Finished MutateResidue_selector in 32 seconds [~ 525 test (65.136476426799%) started, 281 in queue, 24 running] Running Test density_refine_symm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/density_refine_symm/command.sh Finished genkic_bin_perturbing in 45 seconds [~ 526 test (65.26054590570719%) started, 280 in queue, 24 running] Running Test dehydro_aa_patch ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/dehydro_aa_patch/command.sh Finished fold_cst_new in 45 seconds [~ 527 test (65.38461538461539%) started, 279 in queue, 24 running] Running Test buried_area_filter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/buried_area_filter/command.sh Finished LoopLengthChange in 32 seconds [~ 528 test (65.50868486352357%) started, 278 in queue, 24 running] Running Test ambiguous_nmr_distance_constraint ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ambiguous_nmr_distance_constraint/command.sh Finished HelixBendFilter in 33 seconds [~ 529 test (65.63275434243177%) started, 277 in queue, 24 running] Running Test SSElementSelector ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/SSElementSelector/command.sh Finished FilterReportAsPoseExtraScoresMover in 33 seconds [~ 530 test (65.75682382133995%) started, 276 in queue, 24 running] Running Test symmetrical_residue_selector ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/symmetrical_residue_selector/command.sh Finished FavorSequenceProfileMover in 34 seconds [~ 531 test (65.88089330024813%) started, 275 in queue, 24 running] Running Test swm_build_full_model ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_build_full_model/command.sh Finished AddConstraintsToCurrentConformationMover in 32 seconds [~ 532 test (66.00496277915633%) started, 274 in queue, 24 running] Running Test swm_add_rosettascripts ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_add_rosettascripts/command.sh Finished DumpTrajectoryEnergy in 33 seconds [~ 533 test (66.12903225806451%) started, 273 in queue, 24 running] Running Test swa_rna_gagu_18_rebuild_bulge ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_18_rebuild_bulge/command.sh Finished stored_residue_subset in 30 seconds [~ 534 test (66.25310173697271%) started, 272 in queue, 24 running] Running Test swa_rna_gagu_11_append_and_ccd_close ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_11_append_and_ccd_close/command.sh Finished swa_rna_gagu_23_append_and_kic_close in 38 seconds [~ 535 test (66.37717121588089%) started, 271 in queue, 24 running] Running Test set_torsion ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/set_torsion/command.sh Finished swa_rna_gagu_22_prepend_and_kic_close in 39 seconds [~ 536 test (66.50124069478908%) started, 270 in queue, 24 running] Running Test referencepose_mutateresidue ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/referencepose_mutateresidue/command.sh Finished swa_rna_gagu_10_prepend_and_ccd_close in 37 seconds [~ 537 test (66.62531017369727%) started, 269 in queue, 24 running] Finished mp_symmetry_load in 31 seconds [~ 537 test (66.62531017369727%) started, 269 in queue, 23 running] Running Test phiselector ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/phiselector/command.sh Running Test pocket_measure ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/pocket_measure/command.sh Finished swa_rna_gagu_16_prepend_dinucleotide_on_dinucleotide in 39 seconds [~ 539 test (66.87344913151365%) started, 267 in queue, 24 running] Running Test mp_dock ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_dock/command.sh Finished rna_design in 75 seconds [~ 540 test (66.99751861042184%) started, 266 in queue, 24 running] Finished simple_cycpep_predict_sidechain_isopeptide in 34 seconds [~ 540 test (66.99751861042184%) started, 266 in queue, 23 running] Running Test metal_setup ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/metal_setup/command.sh Running Test make_and_perturb_bundle_multirepeat ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/make_and_perturb_bundle_multirepeat/command.sh Finished buried_area_filter in 29 seconds [~ 542 test (67.24565756823822%) started, 264 in queue, 24 running] Running Test longest_continuous_polar_segment_filter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/longest_continuous_polar_segment_filter/command.sh Finished swa_rna_gagu_13_chunk_combination_and_closure in 39 seconds [~ 543 test (67.3697270471464%) started, 263 in queue, 24 running] Running Test hbondstoresidue_selector ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hbondstoresidue_selector/command.sh Finished mf_fixbb_sc in 31 seconds [~ 544 test (67.4937965260546%) started, 262 in queue, 24 running] Running Test genkic_bin_setting ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/genkic_bin_setting/command.sh Finished design_w_custom_palette-RNA in 32 seconds [~ 545 test (67.61786600496278%) started, 261 in queue, 24 running] Running Test create_clash-based_repack_shell ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/create_clash-based_repack_shell/command.sh Finished simple_cycpep_predict_terminal_disulfide_internal_permutations in 38 seconds [~ 546 test (67.74193548387096%) started, 260 in queue, 24 running] Running Test copy_rotamer_mover ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/copy_rotamer_mover/command.sh Finished genkic_dihedral_copying in 33 seconds [~ 547 test (67.86600496277916%) started, 259 in queue, 24 running] Running Test binselector_probins ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/binselector_probins/command.sh Finished dehydro_aa_patch in 32 seconds [~ 548 test (67.99007444168734%) started, 258 in queue, 24 running] Running Test binselector ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/binselector/command.sh Finished symmetrical_residue_selector in 28 seconds [~ 549 test (68.11414392059554%) started, 257 in queue, 24 running] Running Test backbonegridsampler ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/backbonegridsampler/command.sh Finished ambiguous_nmr_distance_constraint in 33 seconds [~ 550 test (68.23821339950372%) started, 256 in queue, 24 running] Running Test ModifyVariantTypeMover ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ModifyVariantTypeMover/command.sh Finished swm_rna_protonated_adenosine in 52 seconds [~ 551 test (68.3622828784119%) started, 255 in queue, 24 running] Finished density_refine_symm in 36 seconds [~ 551 test (68.3622828784119%) started, 255 in queue, 23 running] Finished SSElementSelector in 33 seconds [~ 551 test (68.3622828784119%) started, 255 in queue, 22 running] Running Test tna_base_pairs ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/tna_base_pairs/command.sh Running Test swm_rna_move_inside_helix_by_bond ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_rna_move_inside_helix_by_bond/command.sh Running Test surface_docking ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/surface_docking/command.sh Finished oop_dock_design in 45 seconds [~ 554 test (68.73449131513648%) started, 252 in queue, 24 running] Running Test rnp_ddg_relax_command_1 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rnp_ddg_relax_command_1/command.sh Finished swm_build_full_model in 34 seconds [~ 555 test (68.85856079404466%) started, 251 in queue, 24 running] Running Test rna_puzzle6_j67_into_p6p7rigidbody_thread1 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_puzzle6_j67_into_p6p7rigidbody_thread1/command.sh Finished pocket_measure in 22 seconds [~ 556 test (68.98263027295286%) started, 250 in queue, 24 running] Running Test rna_denovo ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo/command.sh Finished swa_rna_gagu_18_rebuild_bulge in 37 seconds [~ 557 test (69.10669975186104%) started, 249 in queue, 24 running] Running Test helix_from_sequence ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/helix_from_sequence/command.sh Finished set_torsion in 27 seconds [~ 558 test (69.23076923076923%) started, 248 in queue, 24 running] Running Test helical_bundle ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/helical_bundle/command.sh Finished swm_add_rosettascripts in 39 seconds [~ 559 test (69.35483870967742%) started, 247 in queue, 24 running] Running Test genkic_bin_sampling ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/genkic_bin_sampling/command.sh Finished phiselector in 28 seconds [~ 560 test (69.4789081885856%) started, 246 in queue, 24 running] Running Test zinc_homodimer_setup ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/zinc_homodimer_setup/command.sh Finished swa_rna_gagu_11_append_and_ccd_close in 35 seconds [~ 561 test (69.6029776674938%) started, 245 in queue, 24 running] Finished referencepose_mutateresidue in 29 seconds [~ 561 test (69.6029776674938%) started, 245 in queue, 23 running] Running Test target_clash ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/target_clash/command.sh Running Test swa_rna_gagu_12_helix_addition ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_12_helix_addition/command.sh Finished longest_continuous_polar_segment_filter in 28 seconds [~ 563 test (69.85111662531017%) started, 243 in queue, 24 running] Running Test simple_cycpep_predict_terminal_disulfide_tails ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_terminal_disulfide_tails/command.sh Finished make_and_perturb_bundle_multirepeat in 30 seconds [~ 564 test (69.97518610421837%) started, 242 in queue, 24 running] Finished hbondstoresidue_selector in 29 seconds [~ 564 test (69.97518610421837%) started, 242 in queue, 23 running] Running Test simple_cycpep_predict_symmetric_sampling ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_symmetric_sampling/command.sh Running Test simple_cycpep_predict_nterm_isopeptide_lariat_tailless ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_nterm_isopeptide_lariat_tailless/command.sh Finished genkic_bin_setting in 29 seconds [~ 566 test (70.22332506203475%) started, 240 in queue, 24 running] Running Test simple_cycpep_predict_nterm_isopeptide_lariat ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_nterm_isopeptide_lariat/command.sh Finished metal_setup in 32 seconds [~ 567 test (70.34739454094293%) started, 239 in queue, 24 running] Finished binselector in 29 seconds [~ 567 test (70.34739454094293%) started, 239 in queue, 23 running] Running Test rna_denovo_new_FT_5P_j12_leadzyme ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_new_FT_5P_j12_leadzyme/command.sh Running Test recces_turner ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/recces_turner/command.sh Finished copy_rotamer_mover in 29 seconds [~ 569 test (70.59553349875931%) started, 237 in queue, 24 running] Running Test mp_mutate_relax ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_mutate_relax/command.sh Finished binselector_probins in 29 seconds [~ 570 test (70.71960297766749%) started, 236 in queue, 24 running] Running Test mmtfIO_score_test ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mmtfIO_score_test/command.sh Finished backbonegridsampler in 29 seconds [~ 571 test (70.84367245657569%) started, 235 in queue, 24 running] Running Test database_jd2_io ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/database_jd2_io/command.sh Finished ModifyVariantTypeMover in 29 seconds [~ 572 test (70.96774193548387%) started, 234 in queue, 24 running] Running Test database_jd2_compact_io ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/database_jd2_compact_io/command.sh Finished mp_dock in 39 seconds [~ 573 test (71.09181141439205%) started, 233 in queue, 24 running] Running Test abinitio ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/abinitio/command.sh Finished tna_base_pairs in 33 seconds [~ 574 test (71.21588089330025%) started, 232 in queue, 24 running] Running Test swm_rna_nickedhelix ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_rna_nickedhelix/command.sh Finished create_clash-based_repack_shell in 38 seconds [~ 575 test (71.33995037220843%) started, 231 in queue, 24 running] Running Test simple_cycpep_predict_sidechain_isopeptide_reverse ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_sidechain_isopeptide_reverse/command.sh Finished rnp_ddg_relax_command_1 in 30 seconds [~ 576 test (71.46401985111663%) started, 230 in queue, 24 running] Running Test score_jd2 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/score_jd2/command.sh Finished surface_docking in 36 seconds [~ 577 test (71.58808933002481%) started, 229 in queue, 24 running] Running Test mp_range_relax ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_range_relax/command.sh Finished swm_rna_move_inside_helix_by_bond in 41 seconds [~ 578 test (71.712158808933%) started, 228 in queue, 24 running] Running Test molfile_to_params ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/molfile_to_params/command.sh Finished zinc_homodimer_setup in 24 seconds [~ 579 test (71.8362282878412%) started, 227 in queue, 24 running] Running Test hshash_utils ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hshash_utils/command.sh Finished helical_bundle in 27 seconds [~ 580 test (71.96029776674938%) started, 226 in queue, 24 running] Running Test glycosylation ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/glycosylation/command.sh Finished simple_cycpep_predict_terminal_disulfide_tails in 23 seconds [~ 581 test (72.08436724565757%) started, 225 in queue, 24 running] Running Test InterfaceAnalyzer_resfile ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/InterfaceAnalyzer_resfile/command.sh Finished genkic_bin_sampling in 28 seconds [~ 582 test (72.20843672456576%) started, 224 in queue, 24 running] Running Test InterfaceAnalyzer_bothpack ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/InterfaceAnalyzer_bothpack/command.sh Finished helix_from_sequence in 32 seconds [~ 583 test (72.33250620347394%) started, 223 in queue, 24 running] Finished simple_cycpep_predict_symmetric_sampling in 27 seconds [~ 583 test (72.33250620347394%) started, 223 in queue, 23 running] Running Test unfolded_state_energy_calc ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/unfolded_state_energy_calc/command.sh Running Test stepwise_lores ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/stepwise_lores/command.sh Finished target_clash in 32 seconds [~ 585 test (72.58064516129032%) started, 221 in queue, 24 running] Running Test simple_cycpep_predict_cterm_isopeptide_lariat_tailless ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_cterm_isopeptide_lariat_tailless/command.sh Finished swa_rna_gagu_12_helix_addition in 32 seconds [~ 586 test (72.70471464019852%) started, 220 in queue, 24 running] Running Test rna_predict_chem_map ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_predict_chem_map/command.sh Finished simple_cycpep_predict_nterm_isopeptide_lariat in 30 seconds [~ 587 test (72.8287841191067%) started, 219 in queue, 24 running] Running Test rb_recces ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rb_recces/command.sh Finished database_jd2_io in 27 seconds [~ 588 test (72.95285359801488%) started, 218 in queue, 24 running] Running Test mpi_multistate_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mpi_multistate_design/command.sh Finished mmtfIO_score_test in 28 seconds [~ 589 test (73.07692307692308%) started, 217 in queue, 24 running] Running Test mp_mutate_repack ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_mutate_repack/command.sh Finished rna_puzzle6_j67_into_p6p7rigidbody_thread1 in 41 seconds [~ 590 test (73.20099255583126%) started, 216 in queue, 24 running] Running Test gen_apo_grids ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/gen_apo_grids/command.sh Finished simple_cycpep_predict_nterm_isopeptide_lariat_tailless in 32 seconds [~ 591 test (73.32506203473946%) started, 215 in queue, 24 running] Running Test fold_and_dock ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/fold_and_dock/command.sh Finished database_jd2_compact_io in 27 seconds [~ 592 test (73.44913151364764%) started, 214 in queue, 24 running] Running Test energy_based_clustering_alpha_aa_scorefile ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/energy_based_clustering_alpha_aa_scorefile/command.sh Finished mp_mutate_relax in 32 seconds [~ 593 test (73.57320099255583%) started, 213 in queue, 24 running] Running Test docking_prepack ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/docking_prepack/command.sh Finished molfile_to_params in 17 seconds [~ 594 test (73.69727047146402%) started, 212 in queue, 24 running] Running Test broker_membrane ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/broker_membrane/command.sh Finished glycosylation in 14 seconds [~ 595 test (73.8213399503722%) started, 211 in queue, 24 running] Running Test blob_finder ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/blob_finder/command.sh Finished recces_turner in 34 seconds [~ 596 test (73.9454094292804%) started, 210 in queue, 24 running] Running Test trRosetta_test_predict_ubiquitin_cst_file_write_only ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/trRosetta_test_predict_ubiquitin_cst_file_write_only/command.sh Finished score_jd2 in 26 seconds [~ 597 test (74.06947890818859%) started, 209 in queue, 24 running] Running Test trRosetta_test_predict_ubiquitin_cst_file_write ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/trRosetta_test_predict_ubiquitin_cst_file_write/command.sh Finished rna_denovo_new_FT_5P_j12_leadzyme in 37 seconds [~ 598 test (74.19354838709677%) started, 208 in queue, 24 running] No correct command.sh file found for tensorflow_manager. Skipping. Running Test trRosetta_test_predict_ubiquitin ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/trRosetta_test_predict_ubiquitin/command.sh Finished mp_range_relax in 29 seconds [~ 600 test (74.44168734491315%) started, 206 in queue, 24 running] Running Test swm_rna_loop_design ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_rna_loop_design/command.sh Finished hshash_utils in 22 seconds [~ 601 test (74.56575682382135%) started, 205 in queue, 24 running] Running Test swm_protein_from_scratch ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_protein_from_scratch/command.sh Finished abinitio in 36 seconds [~ 602 test (74.68982630272953%) started, 204 in queue, 24 running] Running Test simple_cycpep_predict_cterm_isopeptide_lariat ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_cterm_isopeptide_lariat/command.sh Finished rna_predict_chem_map in 14 seconds [~ 603 test (74.81389578163771%) started, 203 in queue, 24 running] Running Test rna_puzzle6_U75G76A77_on_thread1 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_puzzle6_U75G76A77_on_thread1/command.sh Finished simple_cycpep_predict_sidechain_isopeptide_reverse in 34 seconds [~ 604 test (74.93796526054591%) started, 202 in queue, 24 running] Running Test mp_transform_optimize ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_transform_optimize/command.sh Finished fold_and_dock in 13 seconds [~ 605 test (75.06203473945409%) started, 201 in queue, 24 running] Running Test assemble_domains_jd2 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/assemble_domains_jd2/command.sh Finished trRosetta_test_predict_ubiquitin_cst_file_write_only in 10 seconds [~ 606 test (75.18610421836229%) started, 200 in queue, 24 running] No correct command.sh file found for tensorflow_simple_model_load_and_evaluate. Skipping. No correct command.sh file found for tensorflow_connection_test. Skipping. Running Test InterfaceAnalyzer_prepack ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/InterfaceAnalyzer_prepack/command.sh Finished stepwise_lores in 21 seconds [~ 609 test (75.55831265508685%) started, 197 in queue, 24 running] Running Test swa_rna_gagu_17_append_floating_base ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_17_append_floating_base/command.sh Finished trRosetta_test_predict_ubiquitin_cst_file_write in 10 seconds [~ 610 test (75.68238213399503%) started, 196 in queue, 24 running] Running Test swa_rna_gagu_03_append_to_silent ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_03_append_to_silent/command.sh Finished unfolded_state_energy_calc in 22 seconds [~ 611 test (75.80645161290323%) started, 195 in queue, 24 running] Finished swm_rna_nickedhelix in 38 seconds [~ 612 test (75.93052109181141%) started, 194 in queue, 24 running] Running Test rna_motif ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_motif/command.sh Running Test simple_cycpep_predict_nmethyl ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_nmethyl/command.sh Finished InterfaceAnalyzer_resfile in 26 seconds [~ 613 test (76.0545905707196%) started, 193 in queue, 24 running] Running Test restype_converter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/restype_converter/command.sh Finished trRosetta_test_predict_ubiquitin in 10 seconds [~ 614 test (76.1786600496278%) started, 192 in queue, 24 running] Running Test phosphorylation ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/phosphorylation/command.sh Finished InterfaceAnalyzer_bothpack in 26 seconds [~ 615 test (76.30272952853598%) started, 191 in queue, 24 running] Running Test pepspec_anchor_dock ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/pepspec_anchor_dock/command.sh Finished mp_mutate_repack in 22 seconds [~ 616 test (76.42679900744417%) started, 190 in queue, 24 running] Running Test mp_dock_setup ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_dock_setup/command.sh Finished energy_based_clustering_alpha_aa_scorefile in 21 seconds [~ 617 test (76.55086848635236%) started, 189 in queue, 24 running] Running Test ligand_motif_discovery ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ligand_motif_discovery/command.sh Finished blob_finder in 18 seconds [~ 618 test (76.67493796526054%) started, 188 in queue, 24 running] Running Test docking_low_res ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/docking_low_res/command.sh Finished broker_membrane in 21 seconds [~ 619 test (76.79900744416874%) started, 187 in queue, 24 running] Running Test InterfaceAnalyzer_tracer ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/InterfaceAnalyzer_tracer/command.sh Finished restype_converter in 8 seconds [~ 620 test (76.92307692307692%) started, 186 in queue, 24 running] Running Test InterfaceAnalyzer_allscores ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/InterfaceAnalyzer_allscores/command.sh Finished gen_apo_grids in 27 seconds [~ 621 test (77.04714640198512%) started, 185 in queue, 24 running] Running Test swa_rna_gagu_21_prepend_dinucleotide_on_dinucleotide_by_jump ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_21_prepend_dinucleotide_on_dinucleotide_by_jump/command.sh Finished rb_recces in 29 seconds [~ 622 test (77.1712158808933%) started, 184 in queue, 24 running] Running Test swa_rna_gagu_20_append_floating_base_by_jump ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_20_append_floating_base_by_jump/command.sh Finished mpi_multistate_design in 30 seconds [~ 623 test (77.29528535980148%) started, 183 in queue, 24 running] Running Test swa_rna_gagu_08_append_dinucleotide ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_08_append_dinucleotide/command.sh Finished simple_cycpep_predict_cterm_isopeptide_lariat_tailless in 31 seconds [~ 624 test (77.41935483870968%) started, 182 in queue, 24 running] Running Test swa_rna_gagu_07_prepend_dinucleotide ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_07_prepend_dinucleotide/command.sh Finished docking_prepack in 29 seconds [~ 625 test (77.54342431761786%) started, 181 in queue, 24 running] Running Test swa_rna_gagu_06_append_to_3primeterminus ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_06_append_to_3primeterminus/command.sh Finished swm_rna_loop_design in 23 seconds [~ 626 test (77.66749379652606%) started, 180 in queue, 24 running] Running Test swa_rna_gagu_05_prepend_to_5primeterminus ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_05_prepend_to_5primeterminus/command.sh Finished swm_protein_from_scratch in 25 seconds [~ 627 test (77.79156327543424%) started, 179 in queue, 24 running] Finished phosphorylation in 18 seconds [~ 627 test (77.79156327543424%) started, 179 in queue, 23 running] Running Test swa_rna_gagu_02_prepend ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_02_prepend/command.sh Running Test swa_rna_gagu_01_append ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_01_append/command.sh Finished simple_cycpep_predict_nmethyl in 19 seconds [~ 629 test (78.03970223325062%) started, 177 in queue, 24 running] Running Test simple_cycpep_predict_terminal_disulfide ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_terminal_disulfide/command.sh Finished swa_rna_gagu_17_append_floating_base in 21 seconds [~ 630 test (78.1637717121588%) started, 176 in queue, 24 running] Running Test simple_cycpep_predict_lanthionine ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/simple_cycpep_predict_lanthionine/command.sh Finished rna_motif in 20 seconds [~ 631 test (78.287841191067%) started, 175 in queue, 24 running] Running Test rna_puzzle5_p2_GAAA_mini ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_puzzle5_p2_GAAA_mini/command.sh Finished InterfaceAnalyzer_prepack in 23 seconds [~ 632 test (78.41191066997519%) started, 174 in queue, 24 running] Running Test rna_denovo_grid_vdw ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_grid_vdw/command.sh Finished assemble_domains_jd2 in 25 seconds [~ 633 test (78.53598014888337%) started, 173 in queue, 24 running] Running Test orbitals ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/orbitals/command.sh Finished swa_rna_gagu_03_append_to_silent in 23 seconds [~ 634 test (78.66004962779157%) started, 172 in queue, 24 running] Running Test metalloprotein_broker ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/metalloprotein_broker/command.sh Finished simple_cycpep_predict_cterm_isopeptide_lariat in 28 seconds [~ 635 test (78.78411910669975%) started, 171 in queue, 24 running] Finished mp_transform_optimize in 27 seconds [~ 635 test (78.78411910669975%) started, 171 in queue, 23 running] Running Test jscore ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/jscore/command.sh Running Test hotspot_stub_constraints ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hotspot_stub_constraints/command.sh Finished rna_puzzle6_U75G76A77_on_thread1 in 28 seconds [~ 637 test (79.03225806451613%) started, 169 in queue, 24 running] Finished pepspec_anchor_dock in 21 seconds [~ 637 test (79.03225806451613%) started, 169 in queue, 23 running] Running Test SID_rescore ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/SID_rescore/command.sh Running Test cmaes_minimizer ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cmaes_minimizer/command.sh Finished docking_low_res in 21 seconds [~ 639 test (79.28039702233251%) started, 167 in queue, 24 running] Running Test InterfaceAnalyzer_ligand ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/InterfaceAnalyzer_ligand/command.sh Finished InterfaceAnalyzer_tracer in 19 seconds [~ 640 test (79.40446650124069%) started, 166 in queue, 24 running] Finished swa_rna_gagu_21_prepend_dinucleotide_on_dinucleotide_by_jump in 18 seconds [~ 640 test (79.40446650124069%) started, 166 in queue, 23 running] Running Test swa_rna_gagu_19_prepend_floating_base_by_jump ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_19_prepend_floating_base_by_jump/command.sh Running Test swm_rna_move_align_dock ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_rna_move_align_dock/command.sh Finished InterfaceAnalyzer_allscores in 19 seconds [~ 642 test (79.65260545905707%) started, 164 in queue, 24 running] Running Test struc_set_fragment_picker ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/struc_set_fragment_picker/command.sh Finished swa_rna_gagu_20_append_floating_base_by_jump in 18 seconds [~ 643 test (79.77667493796525%) started, 163 in queue, 24 running] Running Test sequence_tolerance ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/sequence_tolerance/command.sh Finished mp_dock_setup in 25 seconds [~ 644 test (79.90074441687345%) started, 162 in queue, 24 running] Running Test rna_minimize ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_minimize/command.sh Finished swa_rna_gagu_08_append_dinucleotide in 18 seconds [~ 645 test (80.02481389578163%) started, 161 in queue, 24 running] Finished swa_rna_gagu_07_prepend_dinucleotide in 18 seconds [~ 645 test (80.02481389578163%) started, 161 in queue, 23 running] Running Test rna_helix ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_helix/command.sh Running Test phosphonate ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/phosphonate/command.sh Finished ligand_motif_discovery in 26 seconds [~ 647 test (80.27295285359801%) started, 159 in queue, 24 running] Running Test output_schema ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/output_schema/command.sh Finished swa_rna_gagu_06_append_to_3primeterminus in 19 seconds [~ 648 test (80.3970223325062%) started, 158 in queue, 24 running] Running Test ligand_motif_identification ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ligand_motif_identification/command.sh Finished metalloprotein_broker in 12 seconds [~ 649 test (80.5210918114144%) started, 157 in queue, 24 running] Running Test identify_cdr_clusters ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/identify_cdr_clusters/command.sh Finished swa_rna_gagu_05_prepend_to_5primeterminus in 18 seconds [~ 650 test (80.64516129032258%) started, 156 in queue, 24 running] Running Test energy_based_clustering_alpha_aa_dihedral ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/energy_based_clustering_alpha_aa_dihedral/command.sh Finished swa_rna_gagu_02_prepend in 18 seconds [~ 651 test (80.76923076923077%) started, 155 in queue, 24 running] Running Test duplicate_header_guards ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/duplicate_header_guards/command.sh Finished simple_cycpep_predict_terminal_disulfide in 18 seconds [~ 652 test (80.89330024813896%) started, 154 in queue, 24 running] Running Test cartesianddg ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cartesianddg/command.sh Finished rna_denovo_grid_vdw in 17 seconds [~ 653 test (81.01736972704714%) started, 153 in queue, 24 running] Running Test antibody_numbering_converter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/antibody_numbering_converter/command.sh Finished swa_rna_gagu_01_append in 19 seconds [~ 654 test (81.14143920595534%) started, 152 in queue, 24 running] Running Test ProQ ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ProQ/command.sh Finished duplicate_header_guards in 1 seconds [~ 655 test (81.26550868486352%) started, 151 in queue, 24 running] Running Test swm_protein_preminimize ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_protein_preminimize/command.sh Finished simple_cycpep_predict_lanthionine in 19 seconds [~ 656 test (81.38957816377172%) started, 150 in queue, 24 running] Running Test swa_protein_cluster ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_protein_cluster/command.sh Finished orbitals in 20 seconds [~ 657 test (81.5136476426799%) started, 149 in queue, 24 running] Finished hotspot_stub_constraints in 19 seconds [~ 657 test (81.5136476426799%) started, 149 in queue, 23 running] Finished SID_rescore in 18 seconds [~ 657 test (81.5136476426799%) started, 149 in queue, 22 running] Running Test rna_ribosome_tether ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_ribosome_tether/command.sh Running Test rna_denovo_bps ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_bps/command.sh Running Test pymol_cif ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/pymol_cif/command.sh Finished jscore in 20 seconds [~ 660 test (81.88585607940446%) started, 146 in queue, 24 running] Running Test pwsho ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/pwsho/command.sh Finished struc_set_fragment_picker in 16 seconds [~ 661 test (82.00992555831266%) started, 145 in queue, 24 running] Running Test per_residue_energies ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/per_residue_energies/command.sh Finished rna_puzzle5_p2_GAAA_mini in 24 seconds [~ 662 test (82.13399503722084%) started, 144 in queue, 24 running] Running Test mutate ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mutate/command.sh Finished InterfaceAnalyzer_ligand in 18 seconds [~ 663 test (82.25806451612904%) started, 143 in queue, 24 running] Running Test mp_vis_emb ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_vis_emb/command.sh Finished cmaes_minimizer in 21 seconds [~ 664 test (82.38213399503722%) started, 142 in queue, 24 running] Running Test mp_interface_statistics ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_interface_statistics/command.sh Finished swa_rna_gagu_19_prepend_floating_base_by_jump in 17 seconds [~ 665 test (82.5062034739454%) started, 141 in queue, 24 running] Running Test mg_modeler ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mg_modeler/command.sh Finished sequence_tolerance in 19 seconds [~ 666 test (82.6302729528536%) started, 140 in queue, 24 running] Finished phosphonate in 17 seconds [~ 666 test (82.6302729528536%) started, 140 in queue, 23 running] Running Test jrelax ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/jrelax/command.sh Running Test interface_energy ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/interface_energy/command.sh Finished output_schema in 18 seconds [~ 668 test (82.87841191066998%) started, 138 in queue, 24 running] Running Test ig_dump ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ig_dump/command.sh Finished swm_rna_move_align_dock in 22 seconds [~ 669 test (83.00248138957816%) started, 137 in queue, 24 running] Running Test glycan_clash_check ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/glycan_clash_check/command.sh Finished ligand_motif_identification in 16 seconds [~ 670 test (83.12655086848635%) started, 136 in queue, 24 running] Running Test geometric_solvation ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/geometric_solvation/command.sh Finished rna_helix in 20 seconds [~ 671 test (83.25062034739454%) started, 135 in queue, 24 running] Running Test gen_lig_grids ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/gen_lig_grids/command.sh Finished energy_based_clustering_alpha_aa_dihedral in 15 seconds [~ 672 test (83.37468982630273%) started, 134 in queue, 24 running] Running Test fragmentpicker_integration_demo ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/fragmentpicker_integration_demo/command.sh Finished rna_minimize in 22 seconds [~ 673 test (83.49875930521092%) started, 133 in queue, 24 running] Running Test extract_atomtree_diffs ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/extract_atomtree_diffs/command.sh Finished swm_protein_preminimize in 15 seconds [~ 674 test (83.62282878411911%) started, 132 in queue, 24 running] Running Test erraser_minimize ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/erraser_minimize/command.sh Finished identify_cdr_clusters in 19 seconds [~ 675 test (83.74689826302729%) started, 131 in queue, 24 running] Finished swa_protein_cluster in 15 seconds [~ 675 test (83.74689826302729%) started, 131 in queue, 23 running] Running Test energy_based_clustering_alpha_aa_bin_analysis ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/energy_based_clustering_alpha_aa_bin_analysis/command.sh Running Test energy_based_clustering_alpha_aa ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/energy_based_clustering_alpha_aa/command.sh Finished ProQ in 17 seconds [~ 677 test (83.99503722084367%) started, 129 in queue, 24 running] Running Test docking_local_refine_min ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/docking_local_refine_min/command.sh Finished rna_ribosome_tether in 14 seconds [~ 678 test (84.11910669975187%) started, 128 in queue, 24 running] Running Test distances ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/distances/command.sh Finished pymol_cif in 14 seconds [~ 679 test (84.24317617866005%) started, 127 in queue, 24 running] Running Test density_tools ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/density_tools/command.sh Finished rna_denovo_bps in 14 seconds [~ 680 test (84.36724565756823%) started, 126 in queue, 24 running] Running Test constel ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/constel/command.sh Finished cartesianddg in 19 seconds [~ 681 test (84.49131513647643%) started, 125 in queue, 24 running] Running Test coenzymes ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/coenzymes/command.sh Finished antibody_numbering_converter in 19 seconds [~ 682 test (84.61538461538461%) started, 124 in queue, 24 running] Running Test cl_complex_rescore ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cl_complex_rescore/command.sh Finished mutate in 14 seconds [~ 683 test (84.73945409429281%) started, 123 in queue, 24 running] Running Test c-term_conjugation ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/c-term_conjugation/command.sh Finished per_residue_energies in 15 seconds [~ 684 test (84.863523573201%) started, 122 in queue, 24 running] Running Test DARC_sampling_on_the_fly ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/DARC_sampling_on_the_fly/command.sh Finished mp_interface_statistics in 15 seconds [~ 685 test (84.98759305210918%) started, 121 in queue, 24 running] Running Test DARC_make_ray_files ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/DARC_make_ray_files/command.sh Finished mp_vis_emb in 15 seconds [~ 686 test (85.11166253101737%) started, 120 in queue, 24 running] Running Test swm_rna_move_two_strands ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swm_rna_move_two_strands/command.sh Finished mg_modeler in 16 seconds [~ 687 test (85.23573200992556%) started, 119 in queue, 24 running] Finished jrelax in 14 seconds [~ 687 test (85.23573200992556%) started, 119 in queue, 23 running] Running Test sweep_respair_energies ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/sweep_respair_energies/command.sh Running Test swa_rna_loop_sampler ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_loop_sampler/command.sh Finished glycan_clash_check in 12 seconds [~ 689 test (85.48387096774194%) started, 117 in queue, 24 running] Running Test site_constraint ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/site_constraint/command.sh Finished interface_energy in 14 seconds [~ 690 test (85.60794044665012%) started, 116 in queue, 24 running] Running Test shobuns ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/shobuns/command.sh Finished fragmentpicker_integration_demo in 12 seconds [~ 691 test (85.73200992555832%) started, 115 in queue, 24 running] Running Test rotamer_recovery_compare_two_structures ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rotamer_recovery_compare_two_structures/command.sh Finished ig_dump in 15 seconds [~ 692 test (85.8560794044665%) started, 114 in queue, 24 running] Running Test rna_score ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_score/command.sh Finished pwsho in 21 seconds [~ 693 test (85.9801488833747%) started, 113 in queue, 24 running] Running Test rna_denovo_bps_helix_ends ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_bps_helix_ends/command.sh Finished geometric_solvation in 15 seconds [~ 694 test (86.10421836228288%) started, 112 in queue, 24 running] Running Test rna_denovo_bps_fixed_ends ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_bps_fixed_ends/command.sh Finished gen_lig_grids in 15 seconds [~ 695 test (86.22828784119106%) started, 111 in queue, 24 running] Running Test read_polymeric_components ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/read_polymeric_components/command.sh Finished extract_atomtree_diffs in 16 seconds [~ 696 test (86.35235732009926%) started, 110 in queue, 24 running] Running Test pocket_suggest_targets ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/pocket_suggest_targets/command.sh grep: full_minimize_temp_1.out: No such file or directory Finished erraser_minimize in 15 seconds [~ 697 test (86.47642679900744%) started, 109 in queue, 24 running] Running Test noe_assignment ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/noe_assignment/command.sh Finished energy_based_clustering_alpha_aa_bin_analysis in 15 seconds [~ 698 test (86.60049627791564%) started, 108 in queue, 24 running] Running Test mp_transform ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_transform/command.sh Finished energy_based_clustering_alpha_aa in 15 seconds [~ 699 test (86.72456575682382%) started, 107 in queue, 24 running] Running Test mp_score_jd2 ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_score_jd2/command.sh Finished c-term_conjugation in 11 seconds [~ 700 test (86.848635235732%) started, 106 in queue, 24 running] Running Test mp_dock_prepack ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_dock_prepack/command.sh Finished rna_denovo in 129 seconds [~ 701 test (86.9727047146402%) started, 105 in queue, 24 running] Running Test measure_lcaa_radii ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/measure_lcaa_radii/command.sh Finished distances in 14 seconds [~ 702 test (87.09677419354838%) started, 104 in queue, 24 running] Running Test fragment_picker ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/fragment_picker/command.sh Finished docking_local_refine_min in 16 seconds [~ 703 test (87.22084367245658%) started, 103 in queue, 24 running] Running Test fix_alignment_to_match_pdb ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/fix_alignment_to_match_pdb/command.sh Finished sweep_respair_energies in 9 seconds [~ 704 test (87.34491315136476%) started, 102 in queue, 24 running] Running Test cs_rosetta_rna ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cs_rosetta_rna/command.sh Finished constel in 14 seconds [~ 705 test (87.46898263027295%) started, 101 in queue, 24 running] Running Test cluster ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cluster/command.sh Finished coenzymes in 15 seconds [~ 706 test (87.59305210918114%) started, 100 in queue, 24 running] Running Test buried_unsat_kinemage ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/buried_unsat_kinemage/command.sh Finished density_tools in 16 seconds [~ 707 test (87.71712158808933%) started, 99 in queue, 24 running] Finished site_constraint in 10 seconds [~ 707 test (87.71712158808933%) started, 99 in queue, 23 running] Running Test trRosettaProtocolMover_rosettascripts_diskwrite_only ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/trRosettaProtocolMover_rosettascripts_diskwrite_only/command.sh Running Test trRosettaProtocolMover_rosettascripts_diskwrite ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/trRosettaProtocolMover_rosettascripts_diskwrite/command.sh Finished cl_complex_rescore in 15 seconds [~ 709 test (87.9652605459057%) started, 97 in queue, 24 running] Finished DARC_make_ray_files in 13 seconds [~ 709 test (87.9652605459057%) started, 97 in queue, 23 running] Running Test rna_denovo_new_FT_rna_two_chains ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_denovo_new_FT_rna_two_chains/command.sh Running Test trRosettaProtocolMover_rosettascripts ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/trRosettaProtocolMover_rosettascripts/command.sh Finished swm_rna_move_two_strands in 13 seconds [~ 711 test (88.21339950372209%) started, 95 in queue, 24 running] Running Test pH_mode ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/pH_mode/command.sh Finished read_polymeric_components in 9 seconds [~ 712 test (88.33746898263027%) started, 94 in queue, 24 running] Running Test mpil_find_pore_bbarrel ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mpil_find_pore_bbarrel/command.sh Finished rotamer_recovery_compare_two_structures in 13 seconds [~ 713 test (88.46153846153847%) started, 93 in queue, 24 running] Running Test mp_loadtime ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_loadtime/command.sh Finished swa_rna_loop_sampler in 15 seconds [~ 714 test (88.58560794044665%) started, 92 in queue, 24 running] Finished shobuns in 14 seconds [~ 714 test (88.58560794044665%) started, 92 in queue, 23 running] Finished rna_denovo_bps_helix_ends in 12 seconds [~ 714 test (88.58560794044665%) started, 92 in queue, 22 running] Running Test mg_modeler_lores ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mg_modeler_lores/command.sh Running Test match_1c2t ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/match_1c2t/command.sh Running Test make_mainchain_potential_symm_preproline ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/make_mainchain_potential_symm_preproline/command.sh Finished rna_score in 13 seconds [~ 717 test (88.95781637717121%) started, 89 in queue, 24 running] Running Test make_mainchain_potential_symm ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/make_mainchain_potential_symm/command.sh Finished DARC_sampling_on_the_fly in 18 seconds [~ 718 test (89.08188585607941%) started, 88 in queue, 24 running] Running Test make_exemplar ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/make_exemplar/command.sh Finished rna_denovo_bps_fixed_ends in 13 seconds [~ 719 test (89.20595533498759%) started, 87 in queue, 24 running] Running Test features_database_schema ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/features_database_schema/command.sh Finished noe_assignment in 10 seconds [~ 720 test (89.33002481389578%) started, 86 in queue, 24 running] Running Test drrafter_setup_ribosome_test ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/drrafter_setup_ribosome_test/command.sh Finished pocket_suggest_targets in 14 seconds [~ 721 test (89.45409429280397%) started, 85 in queue, 24 running] Running Test drrafter_setup_real_test_H_no_init ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/drrafter_setup_real_test_H_no_init/command.sh Finished mp_transform in 13 seconds [~ 722 test (89.57816377171216%) started, 84 in queue, 24 running] Running Test drrafter_setup_real_test_H ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/drrafter_setup_real_test_H/command.sh Finished mpil_find_pore_bbarrel in 8 seconds [~ 723 test (89.70223325062035%) started, 83 in queue, 24 running] Running Test contactMap ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/contactMap/command.sh Finished mp_dock_prepack in 15 seconds [~ 724 test (89.82630272952854%) started, 82 in queue, 24 running] Finished measure_lcaa_radii in 15 seconds [~ 724 test (89.82630272952854%) started, 82 in queue, 23 running] Finished fix_alignment_to_match_pdb in 14 seconds [~ 724 test (89.82630272952854%) started, 82 in queue, 22 running] Finished cs_rosetta_rna in 14 seconds [~ 724 test (89.82630272952854%) started, 82 in queue, 21 running] Finished mp_loadtime in 8 seconds [~ 724 test (89.82630272952854%) started, 82 in queue, 20 running] Running Test ResidueDisorder ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ResidueDisorder/command.sh Running Test template_features ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/template_features/command.sh Finished trRosettaProtocolMover_rosettascripts_diskwrite_only in 12 seconds [~ 729 test (90.44665012406948%) started, 77 in queue, 24 running] Running Test RescorePDDF ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/RescorePDDF/command.sh Running Test cluster_filter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cluster_filter/command.sh Running Test super_aln ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/super_aln/command.sh Running Test silent2frag ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/silent2frag/command.sh Finished mp_score_jd2 in 15 seconds [~ 730 test (90.57071960297766%) started, 76 in queue, 24 running] Finished trRosettaProtocolMover_rosettascripts_diskwrite in 13 seconds [~ 730 test (90.57071960297766%) started, 76 in queue, 23 running] Running Test rna_screen_phosphates ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_screen_phosphates/command.sh Running Test rings ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rings/command.sh Finished rna_denovo_new_FT_rna_two_chains in 12 seconds [~ 732 test (90.81885856079404%) started, 74 in queue, 24 running] Finished pH_mode in 11 seconds [~ 732 test (90.81885856079404%) started, 74 in queue, 23 running] Finished drrafter_setup_ribosome_test in 6 seconds [~ 732 test (90.81885856079404%) started, 74 in queue, 22 running] Running Test non-canonical_connectivities ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/non-canonical_connectivities/command.sh Running Test nucleobase_sample_around ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/nucleobase_sample_around/command.sh Running Test motif_extraction ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/motif_extraction/command.sh Finished cluster in 14 seconds [~ 735 test (91.1910669975186%) started, 71 in queue, 24 running] Finished buried_unsat_kinemage in 14 seconds [~ 735 test (91.1910669975186%) started, 71 in queue, 23 running] Finished trRosettaProtocolMover_rosettascripts in 13 seconds [~ 735 test (91.1910669975186%) started, 71 in queue, 22 running] Running Test ld_converter ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ld_converter/command.sh Running Test code_template_tests_citations ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/code_template_tests_citations/command.sh Running Test centroid_disulfide_scores ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/centroid_disulfide_scores/command.sh Finished fragment_picker in 16 seconds [~ 738 test (91.56327543424318%) started, 68 in queue, 24 running] Running Test test_idealize ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/test_idealize/command.sh Finished make_mainchain_potential_symm_preproline in 10 seconds [~ 739 test (91.68734491315136%) started, 67 in queue, 24 running] Finished make_mainchain_potential_symm in 10 seconds [~ 739 test (91.68734491315136%) started, 67 in queue, 23 running] Running Test test_d_l_readin ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/test_d_l_readin/command.sh Running Test select_best_unique_ligand_poses ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/select_best_unique_ligand_poses/command.sh Finished make_exemplar in 10 seconds [~ 741 test (91.93548387096774%) started, 65 in queue, 24 running] Running Test rosetta_scripts_info ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rosetta_scripts_info/command.sh Finished drrafter_setup_real_test_H_no_init in 6 seconds [~ 742 test (92.05955334987593%) started, 64 in queue, 24 running] Running Test rna_minimize_6D_loop_close ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_minimize_6D_loop_close/command.sh Finished drrafter_setup_real_test_H in 7 seconds [~ 743 test (92.18362282878412%) started, 63 in queue, 24 running] Finished contactMap in 6 seconds [~ 743 test (92.18362282878412%) started, 63 in queue, 23 running] Running Test r_pdb2top ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/r_pdb2top/command.sh Running Test per_residue_sc_sasa ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/per_residue_sc_sasa/command.sh Finished mg_modeler_lores in 14 seconds [~ 745 test (92.43176178660049%) started, 61 in queue, 24 running] Finished test_d_l_readin in 3 seconds [~ 745 test (92.43176178660049%) started, 61 in queue, 23 running] Running Test oop_create ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/oop_create/command.sh Running Test mpil_load_implicit_lipids ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mpil_load_implicit_lipids/command.sh Finished template_features in 6 seconds [~ 747 test (92.67990074441687%) started, 59 in queue, 24 running] Running Test mpil_find_pore_ahelical ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mpil_find_pore_ahelical/command.sh Finished super_aln in 6 seconds [~ 748 test (92.80397022332507%) started, 58 in queue, 24 running] Finished centroid_disulfide_scores in 5 seconds [~ 748 test (92.80397022332507%) started, 58 in queue, 23 running] ‘database/citations/rosetta_citations.txt’ -> ‘database/citations/rosetta_citations.original.txt’ First script ran successfully. Second script ran successfully. Output matches expectation. Running Test minimize_6Dloopclose ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/minimize_6Dloopclose/command.sh Running Test fit_helixparams_rms ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/fit_helixparams_rms/command.sh Finished silent2frag in 7 seconds [~ 750 test (93.05210918114143%) started, 56 in queue, 24 running] Finished code_template_tests_citations in 6 seconds [~ 750 test (93.05210918114143%) started, 56 in queue, 23 running] Running Test drrafter_error_estimation ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/drrafter_error_estimation/command.sh Running Test cstfile_to_theozyme_pdb ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cstfile_to_theozyme_pdb/command.sh Finished match_1c2t in 15 seconds [~ 752 test (93.30024813895781%) started, 54 in queue, 24 running] Finished rings in 7 seconds [~ 752 test (93.30024813895781%) started, 54 in queue, 23 running] Running Test angle_recovery_stats ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/angle_recovery_stats/command.sh Running Test code_template_tests_src ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/code_template_tests_src/command.sh Finished features_database_schema in 14 seconds [~ 754 test (93.54838709677419%) started, 52 in queue, 24 running] Running Test N-terminal_acetylation ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/N-terminal_acetylation/command.sh Finished test_idealize in 7 seconds [~ 755 test (93.67245657568238%) started, 51 in queue, 24 running] Finished select_best_unique_ligand_poses in 6 seconds [~ 755 test (93.67245657568238%) started, 51 in queue, 23 running] Running Test DARC_shapeonly ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/DARC_shapeonly/command.sh Running Test DNA_methylation ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/DNA_methylation/command.sh test_general test_abstract test_mover test_ws_energy_method test_1b_energy_method test_2b_energy_method test_task_operation test_features_reporter test_residue_selector test_residue_selector_in_core test_crosslinker_mover_helper test_util Finished code_template_tests_src in 1 seconds [~ 757 test (93.92059553349876%) started, 49 in queue, 24 running] Running Test DARC_electrostatics ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/DARC_electrostatics/command.sh Finished rna_minimize_6D_loop_close in 5 seconds [~ 758 test (94.04466501240695%) started, 48 in queue, 24 running] Running Test CCS_PARCS ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/CCS_PARCS/command.sh Finished rna_screen_phosphates in 9 seconds [~ 759 test (94.16873449131513%) started, 47 in queue, 24 running] Finished motif_extraction in 9 seconds [~ 759 test (94.16873449131513%) started, 47 in queue, 23 running] Running Test CCD_loop_closure Running Test swa_rna_loop_clusterer ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/CCD_loop_closure/command.sh ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_loop_clusterer/command.sh Finished ResidueDisorder in 10 seconds [~ 761 test (94.41687344913151%) started, 45 in queue, 24 running] Finished ld_converter in 9 seconds [~ 761 test (94.41687344913151%) started, 45 in queue, 23 running] Running Test swa_rna_gagu_14_combine_long_loop_filtering ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_14_combine_long_loop_filtering/command.sh Running Test swa_rna_gagu_04_clustering ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/swa_rna_gagu_04_clustering/command.sh Finished nucleobase_sample_around in 9 seconds [~ 763 test (94.6650124069479%) started, 43 in queue, 24 running] Running Test rna_suitename ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_suitename/command.sh Finished per_residue_sc_sasa in 5 seconds [~ 764 test (94.78908188585608%) started, 42 in queue, 24 running] Running Test rna_cluster ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_cluster/command.sh Finished RescorePDDF in 10 seconds [~ 765 test (94.91315136476427%) started, 41 in queue, 24 running] Running Test rna_add_WC_stats ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rna_add_WC_stats/command.sh Finished r_pdb2top in 6 seconds [~ 766 test (95.03722084367246%) started, 40 in queue, 24 running] Running Test report_hbonds_for_plugin ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/report_hbonds_for_plugin/command.sh Finished mpil_load_implicit_lipids in 6 seconds [~ 767 test (95.16129032258064%) started, 39 in queue, 24 running] Running Test ralford_dump_rotamers ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/ralford_dump_rotamers/command.sh Finished minimize_6Dloopclose in 5 seconds [~ 768 test (95.28535980148884%) started, 38 in queue, 24 running] Finished N-terminal_acetylation in 4 seconds [~ 768 test (95.28535980148884%) started, 38 in queue, 23 running] Running Test number_of_residuetypes ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/number_of_residuetypes/command.sh Running Test r_rmsf ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/r_rmsf/command.sh Finished cluster_filter in 13 seconds [~ 770 test (95.53349875930522%) started, 36 in queue, 24 running] Finished mpil_find_pore_ahelical in 6 seconds [~ 770 test (95.53349875930522%) started, 36 in queue, 23 running] Finished drrafter_error_estimation in 6 seconds [~ 770 test (95.53349875930522%) started, 36 in queue, 22 running] Running Test loop_hash ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/loop_hash/command.sh Running Test include_cc_check ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/include_cc_check/command.sh Running Test fit_helixparams_a3b ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/fit_helixparams_a3b/command.sh >>> Illegal use of .cc file in an include statement detected! Encounter error while executing: ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/include_cc_check/command.sh *** Test include_cc_check did not run! Check your --mode flag and paths. [2025-03-25 15:36:46.900477] Finished angle_recovery_stats in 6 seconds [~ 773 test (95.90570719602978%) started, 33 in queue, 24 running] Finished include_cc_check in 0 seconds [~ 773 test (95.90570719602978%) started, 33 in queue, 23 running] Running Test calculate_sasa ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/calculate_sasa/command.sh Running Test test_energy_method_options ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/test_energy_method_options/command.sh Finished cstfile_to_theozyme_pdb in 7 seconds [~ 775 test (96.15384615384616%) started, 31 in queue, 24 running] Finished CCS_PARCS in 5 seconds [~ 775 test (96.15384615384616%) started, 31 in queue, 23 running] Finished test_energy_method_options in 0 seconds [~ 775 test (96.15384615384616%) started, 31 in queue, 22 running] Running Test mp_span_from_pdb ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_span_from_pdb/command.sh Running Test per_residue_solvent_exposure ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/per_residue_solvent_exposure/command.sh Running Test hierarchical_clustering ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/hierarchical_clustering/command.sh Finished oop_create in 8 seconds [~ 778 test (96.52605459057072%) started, 28 in queue, 24 running] Running Test fit_helixparams ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/fit_helixparams/command.sh Finished DNA_methylation in 6 seconds [~ 779 test (96.6501240694789%) started, 27 in queue, 24 running] Finished DARC_shapeonly in 6 seconds [~ 779 test (96.6501240694789%) started, 27 in queue, 23 running] Finished DARC_electrostatics in 6 seconds [~ 779 test (96.6501240694789%) started, 27 in queue, 22 running] Finished swa_rna_loop_clusterer in 5 seconds [~ 779 test (96.6501240694789%) started, 27 in queue, 21 running] Finished per_residue_solvent_exposure in 0 seconds [~ 779 test (96.6501240694789%) started, 27 in queue, 20 running] Finished hierarchical_clustering in 0 seconds [~ 779 test (96.6501240694789%) started, 27 in queue, 19 running] No correct command.sh file found for basic_gcn_tensorflow_test. Skipping. Running Test burial_measure_centroid ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/burial_measure_centroid/command.sh Running Test combine_silent ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/combine_silent/command.sh Running Test BuildPeptide ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/BuildPeptide/command.sh Running Test trRosettaConstraintGenerator_rosettascripts ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/trRosettaConstraintGenerator_rosettascripts/command.sh Running Test score_aln ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/score_aln/command.sh Running Test header_using_check ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/header_using_check/command.sh Finished swa_rna_gagu_04_clustering in 5 seconds [~ 786 test (97.51861042183623%) started, 20 in queue, 24 running] Finished rna_cluster in 4 seconds [~ 786 test (97.51861042183623%) started, 20 in queue, 23 running] Finished header_using_check in 0 seconds [~ 786 test (97.51861042183623%) started, 20 in queue, 22 running] Running Test extract_pdbs ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/extract_pdbs/command.sh Running Test crossaln ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/crossaln/command.sh Running Test rnp_ddg_relax_setup ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rnp_ddg_relax_setup/command.sh PYTHON IS /home/benchmark/prefix/hojo-2/linux/python_virtual_environments/python-3.9/df3055f6f81b525b8050290cef45e968/bin/python Finished rna_suitename in 5 seconds [~ 789 test (97.89081885856079%) started, 17 in queue, 24 running] Finished rna_add_WC_stats in 4 seconds [~ 789 test (97.89081885856079%) started, 17 in queue, 23 running] Finished burial_measure_centroid in 0 seconds [~ 789 test (97.89081885856079%) started, 17 in queue, 22 running] Finished trRosettaConstraintGenerator_rosettascripts in 0 seconds [~ 789 test (97.89081885856079%) started, 17 in queue, 21 running] Finished score_aln in 0 seconds [~ 789 test (97.89081885856079%) started, 17 in queue, 20 running] Finished rnp_ddg_relax_setup in 0 seconds [~ 789 test (97.89081885856079%) started, 17 in queue, 19 running] Running Test rnp_ddg_finalize ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rnp_ddg_finalize/command.sh Running Test rnp_ddg_relax_finalize ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rnp_ddg_relax_finalize/command.sh Running Test rnp_ddg_calc_setup ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/rnp_ddg_calc_setup/command.sh Running Test mp_quick_relax ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/mp_quick_relax/command.sh Running Test features_scientific_benchmark ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/features_scientific_benchmark/command.sh Running Test features_postgres ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/features_postgres/command.sh PYTHON IS /home/benchmark/prefix/hojo-2/linux/python_virtual_environments/python-3.9/df3055f6f81b525b8050290cef45e968/bin/python PYTHON IS /home/benchmark/prefix/hojo-2/linux/python_virtual_environments/python-3.9/df3055f6f81b525b8050290cef45e968/bin/python PYTHON is /home/benchmark/prefix/hojo-2/linux/python_virtual_environments/python-3.9/df3055f6f81b525b8050290cef45e968/bin/python Finished non-canonical_connectivities in 15 seconds [~ 795 test (98.63523573200993%) started, 11 in queue, 24 running] Finished rosetta_scripts_info in 13 seconds [~ 795 test (98.63523573200993%) started, 11 in queue, 23 running] Finished swa_rna_gagu_14_combine_long_loop_filtering in 5 seconds [~ 795 test (98.63523573200993%) started, 11 in queue, 22 running] Finished loop_hash in 2 seconds [~ 795 test (98.63523573200993%) started, 11 in queue, 21 running] Finished rnp_ddg_relax_finalize in 0 seconds [~ 795 test (98.63523573200993%) started, 11 in queue, 20 running] Finished rnp_ddg_finalize in 0 seconds [~ 795 test (98.63523573200993%) started, 11 in queue, 19 running] Finished rnp_ddg_calc_setup in 0 seconds [~ 795 test (98.63523573200993%) started, 11 in queue, 18 running] Finished mp_quick_relax in 0 seconds [~ 795 test (98.63523573200993%) started, 11 in queue, 17 running] Finished features_scientific_benchmark in 0 seconds [~ 795 test (98.63523573200993%) started, 11 in queue, 16 running] Finished features_postgres in 0 seconds [~ 795 test (98.63523573200993%) started, 11 in queue, 15 running] Running Test drrafter_setup_simple ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/drrafter_setup_simple/command.sh Running Test drrafter_setup_protein_dock ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/drrafter_setup_protein_dock/command.sh Running Test drrafter_setup_build_missing ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/drrafter_setup_build_missing/command.sh Running Test drrafter_setup ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/drrafter_setup/command.sh Running Test code_template_tests_unit ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/code_template_tests_unit/command.sh Running Test code_template_tests_app ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/code_template_tests_app/command.sh Running Test cluster_calibur ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/cluster_calibur/command.sh Running Test central_class_modification ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/central_class_modification/command.sh Running Test case_sensitive_filenames ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/case_sensitive_filenames/command.sh Running Test Werror_check ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/Werror_check/command.sh Calibur clustering has been broken since its inception. The external version was never successfully integration tested because of typos in the integration test. The version ported to Rosetta has never worked either. Since now it causes hard-failures on release_debug, it needs to be deactivated for now. Checking the status of the -Werror option in the Scons build settings: PASS Checking the status of the -Werror option in the CMake build settings: PASS Finished fit_helixparams_rms in 9 seconds [~ 805 test (99.87593052109182%) started, 1 in queue, 24 running] Finished extract_pdbs in 0 seconds [~ 805 test (99.87593052109182%) started, 1 in queue, 23 running] Finished crossaln in 0 seconds [~ 805 test (99.87593052109182%) started, 1 in queue, 22 running] Finished code_template_tests_unit in 0 seconds [~ 805 test (99.87593052109182%) started, 1 in queue, 21 running] Finished cluster_calibur in 0 seconds [~ 805 test (99.87593052109182%) started, 1 in queue, 20 running] Finished central_class_modification in 0 seconds [~ 805 test (99.87593052109182%) started, 1 in queue, 19 running] Finished Werror_check in 0 seconds [~ 805 test (99.87593052109182%) started, 1 in queue, 18 running] Running Test RescoreSAXS ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/RescoreSAXS/command.sh Running Test HOW_TO_MAKE_TESTS ulimit -t 3600 && bash /home/benchmark/rosetta/tests/integration/new/HOW_TO_MAKE_TESTS/command.sh Finished drrafter_setup_simple in 0 seconds [~ 806 test (100.0%) started, 0 in queue, 18 running] Finished drrafter_setup in 0 seconds [~ 806 test (100.0%) started, 0 in queue, 17 running] Finished code_template_tests_app in 0 seconds [~ 806 test (100.0%) started, 0 in queue, 16 running] Finished RescoreSAXS in 0 seconds [~ 806 test (100.0%) started, 0 in queue, 15 running] Finished HOW_TO_MAKE_TESTS in 0 seconds [~ 806 test (100.0%) started, 0 in queue, 14 running] Finished drrafter_setup_protein_dock in 0 seconds [~ 806 test (100.0%) started, 0 in queue, 13 running] Finished mp_span_from_pdb in 2 seconds [~ 806 test (100.0%) started, 0 in queue, 12 running] Finished drrafter_setup_build_missing in 0 seconds [~ 806 test (100.0%) started, 0 in queue, 11 running] Finished report_hbonds_for_plugin in 5 seconds [~ 806 test (100.0%) started, 0 in queue, 10 running] Finished ralford_dump_rotamers in 5 seconds [~ 806 test (100.0%) started, 0 in queue, 9 running] Finished number_of_residuetypes in 4 seconds [~ 806 test (100.0%) started, 0 in queue, 8 running] Finished fit_helixparams in 2 seconds [~ 806 test (100.0%) started, 0 in queue, 7 running] Finished combine_silent in 1 seconds [~ 806 test (100.0%) started, 0 in queue, 6 running] Finished CCD_loop_closure in 7 seconds [~ 806 test (100.0%) started, 0 in queue, 5 running] Finished r_rmsf in 4 seconds [~ 806 test (100.0%) started, 0 in queue, 4 running] Finished fit_helixparams_a3b in 4 seconds [~ 806 test (100.0%) started, 0 in queue, 3 running] Finished calculate_sasa in 3 seconds [~ 806 test (100.0%) started, 0 in queue, 2 running] Finished BuildPeptide in 3 seconds [~ 806 test (100.0%) started, 0 in queue, 1 running] /usr/local/bin/git 7ff170db059b0ec642ec65933626395bfc321c4e Finished case_sensitive_filenames in 2 seconds [~ 806 test (100.0%) started, 0 in queue, 0 running] Skipping comparison/analysis phase because command line option "--skip-comparison" was specified... Missing new/runtimes.yaml ──────────────── 'hojo-2' comparing commits:20668 linux.clang.integration.release_debug_no_symbols test_id=852756 vs. main:62149 previous_test_id=852263 ────────────────
Brief Diff: Files /home/benchmark/working_dir/main:62149/features/log_db_output and /home/benchmark/working_dir/commits:20668/features/log_db_output differ Full Diff: diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62149/features/log_db_output /home/benchmark/working_dir/commits:20668/features/log_db_output 708,710d707 < basic.io.database: Database file opened: scoring/score_functions/custom_pair_distance/pos_charge_repulsion < basic.io.database: Database file opened: scoring/score_functions/custom_pair_distance/neg_charge_repulsion < core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy: Added 8 AtomPairFuncList lists
Brief Diff: Files /home/benchmark/working_dir/main:62149/include_cc_check/cc_includes.txt and /home/benchmark/working_dir/commits:20668/include_cc_check/cc_includes.txt differ Only in /home/benchmark/working_dir/commits:20668/include_cc_check: .test_did_not_run.log Full Diff: diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62149/include_cc_check/cc_includes.txt /home/benchmark/working_dir/commits:20668/include_cc_check/cc_includes.txt 0a1 > [Tue Mar 25 15:36:46 EDT 2025] src/apps/public/motif_ligand_discovery/remove_duplicate_motifs.cc://#include <protocols/motifs/FindMotifPositionsOnLigandHelper.cc> Only in /home/benchmark/working_dir/commits:20668/include_cc_check: .test_did_not_run.log Compare(...): Marking as "Script failed" due to presense of .test_did_not_run.log or .test_got_timeout_kill.log file!
Brief Diff: Only in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 4s0v_motifs.motifs Only in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 4s0v.pdb Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio16_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120970_SubRatio_0.803259.pdb Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio22_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120911_SubRatio_0.793778.pdb Only in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000_rep_5.200045_atr_-19.001764_delta_-21.724721_constr_6.287128.pdb Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000_WholeRatio_0.120947_SubRatio_0.802667.pdb Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio46_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120951_SubRatio_0.776593.pdb Only in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000_rep_5.346809_atr_-18.851113_delta_-21.657672_constr_0.245685.pdb Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000_WholeRatio_0.120987_SubRatio_0.801185.pdb Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio97_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120951_SubRatio_0.802667.pdb Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_suv_0.pdb Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_suv_1.pdb Only in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 6h4q_motifs.motifs Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: empty_WholeRatio_0.119936_SubRatio_0.645037.pdb Files /home/benchmark/working_dir/main:62149/ligand_motif_discovery/flags and /home/benchmark/working_dir/commits:20668/ligand_motif_discovery/flags differ Files /home/benchmark/working_dir/main:62149/ligand_motif_discovery/log and /home/benchmark/working_dir/commits:20668/ligand_motif_discovery/log differ Full Diff: Only in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 4s0v_motifs.motifs Only in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 4s0v.pdb Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio16_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120970_SubRatio_0.803259.pdb Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio22_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120911_SubRatio_0.793778.pdb Only in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000_rep_5.200045_atr_-19.001764_delta_-21.724721_constr_6.287128.pdb Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000_WholeRatio_0.120947_SubRatio_0.802667.pdb Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio46_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120951_SubRatio_0.776593.pdb Only in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000_rep_5.346809_atr_-18.851113_delta_-21.657672_constr_0.245685.pdb Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000_WholeRatio_0.120987_SubRatio_0.801185.pdb Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio97_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120951_SubRatio_0.802667.pdb Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_suv_0.pdb Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_suv_1.pdb Only in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 6h4q_motifs.motifs Only in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: empty_WholeRatio_0.119936_SubRatio_0.645037.pdb diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62149/ligand_motif_discovery/flags /home/benchmark/working_dir/commits:20668/ligand_motif_discovery/flags 0a1 > #input empty receptor protein 1a3,4 > > #directory of ligand(s) to attempt to dock 2a6,7 > > #ligand motifs library 3a9,10 > > #index of residue(s) to dock ligands against 4a12,13 > > #minimum cutoffs for fa_atr, fa_rep, and combined fa_atr_rep to be under 6a16,17 > > #constrain coordinates 7a19,53 > > #optional flags for demonstrative purposes of extra features of app: > > #space fill method > #define cube-shaped binding pocket about coordinate (coordinate corresponds to within 4s0v.pdb, shifts with script) > -binding_pocket_center_sf 54,6,53 > -binding_pocket_radius_sf 7 > #define cutoff of how much of binding pocket volume must be filled compared to empty pocket (>15% more filled than empty when ligand is placed) > -space_fill_cutoff_differential_score_sub 0.15 > > #optional export of space fill matrices to PDB (only recommended for debugging and tuning cutoffs for binding pocket) > #Including in this test, since it can help show off the feature and troubleshoot if this test breaks > -output_space_fill_matrix_pdbs true > > #placement motifs collection > -collect_motifs_from_placed_ligand true > > #motifs against residues of interest > -significant_residues_for_motifs 447,450,419,134,86,423,451,85,62 > -minimum_motifs_formed_cutoff 6 > -minimum_significant_motifs_formed_cutoff 1 > > #mandatory at least 1 real motif > -minimum_ratio_of_real_motifs_from_ligand 0.01 > > #must form a motif with ASN423 > -mandatory_residues_for_motifs 423 > > #check real motifs > -check_if_ligand_motifs_match_real true > -duplicate_dist_cutoff 1.2 > -duplicate_angle_cutoff 0.45 > > #do not output generated ligand motifs as pdbs > -output_motifs_as_pdb false diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62149/ligand_motif_discovery/log /home/benchmark/working_dir/commits:20668/ligand_motif_discovery/log 19,21d18 < LigandDiscoverySearch_get_motif_sublibrary_by_aa: Created motif sub-library for residue ASN with 24 motifs in it. < LDS_app: Running discovery for 4s0v_receptor_only < LigandDiscoverySearch_get_motif_sublibrary_by_aa: Created motif sub-library for residue ASN with 24 motifs in it. 41,341c38 < core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. < basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb < LigandDiscoverySearch_create_protein_matrix: Creating protein clash coordinate matrix. Dimensions of matrix are 88,53,113 < LigandDiscoverySearch_out: Using user-inputted fa_rep cutoff of: 500 < LigandDiscoverySearch_out: Using user-inputted fa_atr cutoff of: 500 < LigandDiscoverySearch_out: Starting to iterate through all ligands < LigandDiscoverySearch_out: On ligand suv < LigandDiscoverySearch_out: NBR_RADIUS of ligand is: 9.77457 < LigandDiscoverySearch_out: Finding all atom trios < LigandDiscoverySearch_out: Looking through all atom trios < LigandDiscoverySearch_out: #trios = 104 < LigandDiscoverySearch_out: On trio # 1 < LigandDiscoverySearch_out: Trio is C9 N3 C13 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 2 < LigandDiscoverySearch_out: Trio is C9 N3 C10 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 3 < LigandDiscoverySearch_out: Trio is C9 C8 N1 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 4 < LigandDiscoverySearch_out: Trio is N3 C9 C8 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 5 < LigandDiscoverySearch_out: Trio is N3 C13 C14 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 6 < LigandDiscoverySearch_out: Trio is N3 C13 O2 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 7 < LigandDiscoverySearch_out: Trio is N3 C10 C23 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 8 < LigandDiscoverySearch_out: Trio is N3 C10 C11 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 9 < LigandDiscoverySearch_out: Trio is C13 N3 C9 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 10 < LigandDiscoverySearch_out: Trio is C13 N3 C10 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 11 < LigandDiscoverySearch_out: Trio is C13 C14 C15 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 12 < LigandDiscoverySearch_out: Trio is C13 C14 C19 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 13 < LigandDiscoverySearch_out: Trio is C14 C13 N3 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 14 < LigandDiscoverySearch_out: Trio is C14 C13 O2 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 15 < LigandDiscoverySearch_out: Trio is C14 C15 N4 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 16 < LigandDiscoverySearch_out: Trio is C14 C15 C16 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: 62, 65, 66, 71, 79, 81, 82, 83, 85, 86, 89, 134, 137, 138, 139, 151, 153, 154, 155, 156, 161, 162, 163, 165, 166, 169, 170, 173, 174, 416, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 436, 439, 440, 442, 443, 444, 446, 447, 450, 451, Made minipose of size 56 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 1 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 1 < LigandDiscoverySearch_out: On trio # 17 < LigandDiscoverySearch_out: Trio is C14 C19 C18 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 18 < LigandDiscoverySearch_out: Trio is C15 C14 C13 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 19 < LigandDiscoverySearch_out: Trio is C15 C14 C19 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 20 < LigandDiscoverySearch_out: Trio is C15 N4 N5 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 21 < LigandDiscoverySearch_out: Trio is C15 N4 N6 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 22 < LigandDiscoverySearch_out: Trio is C15 C16 C17 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 1 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 1 < LigandDiscoverySearch_out: On trio # 23 < LigandDiscoverySearch_out: Trio is N4 C15 C14 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 24 < LigandDiscoverySearch_out: Trio is N4 C15 C16 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 25 < LigandDiscoverySearch_out: Trio is N4 N5 C20 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 26 < LigandDiscoverySearch_out: Trio is N4 N6 C21 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 27 < LigandDiscoverySearch_out: Trio is N5 N4 C15 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 28 < LigandDiscoverySearch_out: Trio is N5 N4 N6 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 29 < LigandDiscoverySearch_out: Trio is N5 C20 C21 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 30 < LigandDiscoverySearch_out: Trio is C20 N5 N4 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 31 < LigandDiscoverySearch_out: Trio is C20 C21 N6 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 32 < LigandDiscoverySearch_out: Trio is C21 C20 N5 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 33 < LigandDiscoverySearch_out: Trio is C21 N6 N4 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 34 < LigandDiscoverySearch_out: Trio is N6 N4 C15 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 35 < LigandDiscoverySearch_out: Trio is N6 N4 N5 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 36 < LigandDiscoverySearch_out: Trio is N6 C21 C20 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat < core.scoring.elec.util: Read 40 countpair representative atoms < basic.io.database: Database file opened: scoring/score_functions/disulfides/fa_SS_distance_score < core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. < LigandDiscoverySearch_out: Pre-move delta score = 109.803, fa_atr = -16.397, fa_rep = 163.157, coordinate_constraint = 0 --- > LDS_app: Running discovery for 4s0v_receptor_only 345a43,48 > protocols.motifs.LigandDiscoverySearch.discover: Current anchor residue position: 423 > protocols.motifs.LigandDiscoverySearch.create_protein_matrix_space_fill: binding_pocket_dimensions: 7,7,7 > protocols.motifs.LigandDiscoverySearch.create_protein_matrix_space_fill: binding_pocket_dimensions: 7,7,7 > protocols.motifs.LigandDiscoverySearch.create_protein_matrix_space_fill: Sub-region stats without placed region, bound by adjusted coordinates: x(47->61) y(19->33) z(74->88) > protocols.motifs.LigandDiscoverySearch.discover: Starting to iterate through all ligands > protocols.motifs.LigandDiscoverySearch.discover: On ligand suv 352,917c55,154 < protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -815.271 -815.271 < LigandDiscoverySearch_out: Post-dock delta score = -21.7247, fa_atr = -19.0018, fa_rep = 5.20004, coordinate_constraint = 6.28713 < LigandDiscoverySearch_out: Making pdb file for: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000_rep_5.200045_atr_-19.001764_delta_-21.724721_constr_6.287128.pdb < LigandDiscoverySearch_out: # passing cases for this trio = 1 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 1 < LigandDiscoverySearch_out: On trio # 37 < LigandDiscoverySearch_out: Trio is C16 C15 C14 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 38 < LigandDiscoverySearch_out: Trio is C16 C15 N4 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 39 < LigandDiscoverySearch_out: Trio is C16 C17 C18 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 40 < LigandDiscoverySearch_out: Trio is C17 C16 C15 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 41 < LigandDiscoverySearch_out: Trio is C17 C18 C19 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 42 < LigandDiscoverySearch_out: Trio is C17 C18 C22 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 43 < LigandDiscoverySearch_out: Trio is C18 C17 C16 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 44 < LigandDiscoverySearch_out: Trio is C18 C19 C14 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 45 < LigandDiscoverySearch_out: Trio is C19 C14 C13 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 46 < LigandDiscoverySearch_out: Trio is C19 C14 C15 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 1 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 1 < LigandDiscoverySearch_out: On trio # 47 < LigandDiscoverySearch_out: Trio is C19 C18 C17 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 48 < LigandDiscoverySearch_out: Trio is C19 C18 C22 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 49 < LigandDiscoverySearch_out: Trio is C22 C18 C17 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 50 < LigandDiscoverySearch_out: Trio is C22 C18 C19 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 51 < LigandDiscoverySearch_out: Trio is O2 C13 N3 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 52 < LigandDiscoverySearch_out: Trio is O2 C13 C14 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: Pre-move delta score = -19.2048, fa_atr = -18.8845, fa_rep = 8.53383, coordinate_constraint = 0 < protocols.ligand_docking.ligand_options.Protocol: Initializing options: < protocols.ligand_docking.ligand_options.Protocol: allow_minimization_: 1 < protocols.ligand_docking.ligand_options.Protocol: allow_repacking_: 1 < protocols.ligand_docking.ligand_options.Protocol: all_residues_: 0 < core.pack.task: Packer task: initialize from command line() < core.pack.task: Packer task: initialize from command line() < core.pack.task: Packer task: initialize from command line() < protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -815.681 -815.681 < LigandDiscoverySearch_out: Post-dock delta score = -21.6577, fa_atr = -18.8511, fa_rep = 5.34681, coordinate_constraint = 0.245685 < LigandDiscoverySearch_out: Making pdb file for: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000_rep_5.346809_atr_-18.851113_delta_-21.657672_constr_0.245685.pdb < LigandDiscoverySearch_out: # passing cases for this trio = 1 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 1 < LigandDiscoverySearch_out: On trio # 53 < LigandDiscoverySearch_out: Trio is C10 N3 C9 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 54 < LigandDiscoverySearch_out: Trio is C10 N3 C13 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 55 < LigandDiscoverySearch_out: Trio is C10 C11 C12 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 56 < LigandDiscoverySearch_out: Trio is C23 C10 N3 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 57 < LigandDiscoverySearch_out: Trio is C23 C10 C11 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 58 < LigandDiscoverySearch_out: Trio is C11 C10 N3 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 59 < LigandDiscoverySearch_out: Trio is C11 C10 C23 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 60 < LigandDiscoverySearch_out: Trio is C11 C12 N1 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 61 < LigandDiscoverySearch_out: Trio is C12 C11 C10 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 62 < LigandDiscoverySearch_out: Trio is C12 N1 C8 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 63 < LigandDiscoverySearch_out: Trio is C12 N1 C1 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 64 < LigandDiscoverySearch_out: Trio is N1 C12 C11 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 65 < LigandDiscoverySearch_out: Trio is N1 C8 C9 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 66 < LigandDiscoverySearch_out: Trio is N1 C1 O1 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 67 < LigandDiscoverySearch_out: Trio is N1 C1 N2 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 68 < LigandDiscoverySearch_out: Trio is C8 C9 N3 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 69 < LigandDiscoverySearch_out: Trio is C8 N1 C12 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 70 < LigandDiscoverySearch_out: Trio is C8 N1 C1 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 71 < LigandDiscoverySearch_out: Trio is C1 N1 C12 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 72 < LigandDiscoverySearch_out: Trio is C1 N1 C8 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 73 < LigandDiscoverySearch_out: Trio is C1 O1 C7 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 74 < LigandDiscoverySearch_out: Trio is C1 N2 C2 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 75 < LigandDiscoverySearch_out: Trio is O1 C1 N1 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 76 < LigandDiscoverySearch_out: Trio is O1 C1 N2 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 77 < LigandDiscoverySearch_out: Trio is O1 C7 C6 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 78 < LigandDiscoverySearch_out: Trio is O1 C7 C2 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 79 < LigandDiscoverySearch_out: Trio is C7 O1 C1 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 80 < LigandDiscoverySearch_out: Trio is C7 C6 C5 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 81 < LigandDiscoverySearch_out: Trio is C7 C2 C3 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 82 < LigandDiscoverySearch_out: Trio is C7 C2 N2 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 83 < LigandDiscoverySearch_out: Trio is C6 C7 O1 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 84 < LigandDiscoverySearch_out: Trio is C6 C7 C2 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 85 < LigandDiscoverySearch_out: Trio is C6 C5 C4 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 86 < LigandDiscoverySearch_out: Trio is C5 C6 C7 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 87 < LigandDiscoverySearch_out: Trio is C5 C4 C3 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 88 < LigandDiscoverySearch_out: Trio is C5 C4 CL1 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 89 < LigandDiscoverySearch_out: Trio is C4 C5 C6 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 90 < LigandDiscoverySearch_out: Trio is C4 C3 C2 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 91 < LigandDiscoverySearch_out: Trio is C3 C4 C5 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 92 < LigandDiscoverySearch_out: Trio is C3 C4 CL1 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 93 < LigandDiscoverySearch_out: Trio is C3 C2 C7 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 94 < LigandDiscoverySearch_out: Trio is C3 C2 N2 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 95 < LigandDiscoverySearch_out: Trio is C2 C7 O1 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 96 < LigandDiscoverySearch_out: Trio is C2 C7 C6 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 97 < LigandDiscoverySearch_out: Trio is C2 C3 C4 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 1 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 1 < LigandDiscoverySearch_out: On trio # 98 < LigandDiscoverySearch_out: Trio is C2 N2 C1 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 99 < LigandDiscoverySearch_out: Trio is N2 C1 N1 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 100 < LigandDiscoverySearch_out: Trio is N2 C1 O1 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 101 < LigandDiscoverySearch_out: Trio is N2 C2 C7 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 102 < LigandDiscoverySearch_out: Trio is N2 C2 C3 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 1 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 103 < LigandDiscoverySearch_out: Trio is CL1 C4 C5 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: On trio # 104 < LigandDiscoverySearch_out: Trio is CL1 C4 C3 < LigandDiscoverySearch_out: Looking through all motifs < LigandDiscoverySearch_out: #motifs = 24 < LigandDiscoverySearch_out: # passing cases for this trio = 0 < LigandDiscoverySearch_out: # clashing cases for this trio = 0 < LigandDiscoverySearch_out: # post motif filter cases for this trio = 0 < LigandDiscoverySearch_out: Total cases for trio: 0 < LigandDiscoverySearch_out: Done iterating all trios, moving to next ligand < LigandDiscoverySearch_out: Total passing attempts for ligand is 2 < LigandDiscoverySearch_out: Total clashing attempts for ligand is 4 < LigandDiscoverySearch_out: Number of placements that passed all filters: 2 --- > protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -1945.71 -1945.71 > basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat > core.scoring.elec.util: Read 40 countpair representative atoms > basic.io.database: Database file opened: scoring/score_functions/disulfides/fa_SS_distance_score > core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. > protocols.motifs.Motif: Res1 name is THR > protocols.motifs.Motif: atom1 name is CH2 > protocols.motifs.Motif: atom2 name is aroC > protocols.motifs.Motif: atom3 name is Cl > protocols.motifs.Motif: Res1 name is PRO > protocols.motifs.Motif: atom1 name is Oaro > protocols.motifs.Motif: atom2 name is aroC > protocols.motifs.Motif: atom3 name is aroC > protocols.motifs.Motif: Res1 name is GLN > protocols.motifs.Motif: atom1 name is Oaro > protocols.motifs.Motif: atom2 name is aroC > protocols.motifs.Motif: atom3 name is aroC > protocols.motifs.Motif: Res1 name is THR > protocols.motifs.Motif: atom1 name is CH2 > protocols.motifs.Motif: atom2 name is Nhis > protocols.motifs.Motif: atom3 name is aroC > protocols.motifs.Motif: Res1 name is GLN > protocols.motifs.Motif: atom1 name is CH2 > protocols.motifs.Motif: atom2 name is CH2 > protocols.motifs.Motif: atom3 name is Nhis > protocols.motifs.Motif: Res1 name is PHE > protocols.motifs.Motif: atom1 name is CH3 > protocols.motifs.Motif: atom2 name is CH1 > protocols.motifs.Motif: atom3 name is CH2 > protocols.motifs.Motif: Res1 name is ILE > protocols.motifs.Motif: atom1 name is aroC > protocols.motifs.Motif: atom2 name is aroC > protocols.motifs.Motif: atom3 name is Nhis > protocols.motifs.Motif: Res1 name is ASN > protocols.motifs.Motif: atom1 name is aroC > protocols.motifs.Motif: atom2 name is COO > protocols.motifs.Motif: atom3 name is ONH2 > protocols.motifs.Motif: Res1 name is HIS > protocols.motifs.Motif: atom1 name is aroC > protocols.motifs.Motif: atom2 name is aroC > protocols.motifs.Motif: atom3 name is CH3 > protocols.motifs.Motif: Res1 name is VAL > protocols.motifs.Motif: atom1 name is aroC > protocols.motifs.Motif: atom2 name is aroC > protocols.motifs.Motif: atom3 name is aroC > protocols.motifs.Motif: Res1 name is TYR > protocols.motifs.Motif: atom1 name is aroC > protocols.motifs.Motif: atom2 name is aroC > protocols.motifs.Motif: atom3 name is CH3 > core.pack.task: Packer task: initialize from command line() > core.pack.task: Packer task: initialize from command line() > core.pack.task: Packer task: initialize from command line() > protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -1945.34 -1945.34 > protocols.motifs.Motif: Res1 name is THR > protocols.motifs.Motif: atom1 name is CH2 > protocols.motifs.Motif: atom2 name is aroC > protocols.motifs.Motif: atom3 name is Cl > protocols.motifs.Motif: Res1 name is PRO > protocols.motifs.Motif: atom1 name is Oaro > protocols.motifs.Motif: atom2 name is aroC > protocols.motifs.Motif: atom3 name is aroC > protocols.motifs.Motif: Res1 name is GLN > protocols.motifs.Motif: atom1 name is Oaro > protocols.motifs.Motif: atom2 name is aroC > protocols.motifs.Motif: atom3 name is aroC > protocols.motifs.Motif: Res1 name is THR > protocols.motifs.Motif: atom1 name is CH2 > protocols.motifs.Motif: atom2 name is Nhis > protocols.motifs.Motif: atom3 name is aroC > protocols.motifs.Motif: Res1 name is GLN > protocols.motifs.Motif: atom1 name is CH2 > protocols.motifs.Motif: atom2 name is CH2 > protocols.motifs.Motif: atom3 name is Nhis > protocols.motifs.Motif: Res1 name is PHE > protocols.motifs.Motif: atom1 name is aroC > protocols.motifs.Motif: atom2 name is aroC > protocols.motifs.Motif: atom3 name is Nhis > protocols.motifs.Motif: Res1 name is ILE > protocols.motifs.Motif: atom1 name is aroC > protocols.motifs.Motif: atom2 name is aroC > protocols.motifs.Motif: atom3 name is Nhis > protocols.motifs.Motif: Res1 name is ASN > protocols.motifs.Motif: atom1 name is aroC > protocols.motifs.Motif: atom2 name is COO > protocols.motifs.Motif: atom3 name is ONH2 > protocols.motifs.Motif: Res1 name is HIS > protocols.motifs.Motif: atom1 name is aroC > protocols.motifs.Motif: atom2 name is aroC > protocols.motifs.Motif: atom3 name is CH3 > protocols.motifs.Motif: Res1 name is VAL > protocols.motifs.Motif: atom1 name is aroC > protocols.motifs.Motif: atom2 name is aroC > protocols.motifs.Motif: atom3 name is aroC > protocols.motifs.Motif: Res1 name is TYR > protocols.motifs.Motif: atom1 name is CH2 > protocols.motifs.Motif: atom2 name is aroC > protocols.motifs.Motif: atom3 name is Cl > protocols.motifs.LigandDiscoverySearch.discover: Done iterating all trios, moving to next ligand > protocols.motifs.LigandDiscoverySearch.discover: Total passing attempts for ligand is 2 > protocols.motifs.LigandDiscoverySearch.discover: Total clashing attempts for ligand is 2
Brief Diff: Files /home/benchmark/working_dir/main:62149/ligand_motif_identification/log and /home/benchmark/working_dir/commits:20668/ligand_motif_identification/log differ Full Diff: diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62149/ligand_motif_identification/log /home/benchmark/working_dir/commits:20668/ligand_motif_identification/log 8,26d7 < apps.pilot.ligand_motifs: motif_pdb_output_path_: < apps.pilot.ligand_motifs: motif_file_output_: AllMattMotifs.motifs < apps.pilot.ligand_motifs: output_motifs_: 1 < apps.pilot.ligand_motifs: output_motifs_as_pdb_: 1 < core.scoring.etable: Starting energy table calculation < core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well < core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) < core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) < core.scoring.etable: Finished calculating energy tables. < basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine < basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA < basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n < core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. < basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop < basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv < basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv < basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv < basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv < basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv 57a39,48 > core.scoring.etable: Starting energy table calculation > core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well > core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) > core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) > core.scoring.etable: Finished calculating energy tables. > basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv > basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv > basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv > basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv > basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv 63a55,58 > basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA > basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n > core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. > basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop 71a67 > basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine 73,923d68 < apps.pilot.ligand_motifs: in ligand splitter block, found my ligand, lig_pos is 479 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 1 < apps.pilot.ligand_motifs: atom name is C1 < apps.pilot.ligand_motifs: ATOM j: 2 Name: N1 < apps.pilot.ligand_motifs: ATOM k: 1 Name: C1 < apps.pilot.ligand_motifs: Connected triplet is: 1, type is aroC; 2, type is Nhis; 1, type is aroC < apps.pilot.ligand_motifs: ATOM k: 17 Name: C11 < apps.pilot.ligand_motifs: Connected triplet is: 1, type is aroC; 2, type is Nhis; 17, type is CH2 < apps.pilot.ligand_motifs: atom_i: 1 < apps.pilot.ligand_motifs: atom_i to atom_j: 2 < apps.pilot.ligand_motifs: atom_j to atom_k: 17 < apps.pilot.ligand_motifs: ATOM k: 21 Name: C16 < apps.pilot.ligand_motifs: Connected triplet is: 1, type is aroC; 2, type is Nhis; 21, type is CH2 < apps.pilot.ligand_motifs: atom_i: 1 < apps.pilot.ligand_motifs: atom_i to atom_j: 2 < apps.pilot.ligand_motifs: atom_j to atom_k: 21 < apps.pilot.ligand_motifs: ATOM j: 3 Name: O1 < apps.pilot.ligand_motifs: ATOM k: 1 Name: C1 < apps.pilot.ligand_motifs: Connected triplet is: 1, type is aroC; 3, type is Oaro; 1, type is aroC < apps.pilot.ligand_motifs: ATOM k: 16 Name: C8 < apps.pilot.ligand_motifs: Connected triplet is: 1, type is aroC; 3, type is Oaro; 16, type is aroC < apps.pilot.ligand_motifs: atom_i: 1 < apps.pilot.ligand_motifs: atom_i to atom_j: 3 < apps.pilot.ligand_motifs: atom_j to atom_k: 16 < apps.pilot.ligand_motifs: ATOM j: 5 Name: N2 < apps.pilot.ligand_motifs: ATOM k: 1 Name: C1 < apps.pilot.ligand_motifs: Connected triplet is: 1, type is aroC; 5, type is Nhis; 1, type is aroC < apps.pilot.ligand_motifs: ATOM k: 7 Name: C3 < apps.pilot.ligand_motifs: Connected triplet is: 1, type is aroC; 5, type is Nhis; 7, type is aroC < apps.pilot.ligand_motifs: atom_i: 1 < apps.pilot.ligand_motifs: atom_i to atom_j: 5 < apps.pilot.ligand_motifs: atom_j to atom_k: 7 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 2 < apps.pilot.ligand_motifs: atom name is N1 < apps.pilot.ligand_motifs: ATOM j: 1 Name: C1 < apps.pilot.ligand_motifs: ATOM k: 2 Name: N1 < apps.pilot.ligand_motifs: Connected triplet is: 2, type is Nhis; 1, type is aroC; 2, type is Nhis < apps.pilot.ligand_motifs: ATOM k: 3 Name: O1 < apps.pilot.ligand_motifs: Connected triplet is: 2, type is Nhis; 1, type is aroC; 3, type is Oaro < apps.pilot.ligand_motifs: atom_i: 2 < apps.pilot.ligand_motifs: atom_i to atom_j: 1 < apps.pilot.ligand_motifs: atom_j to atom_k: 3 < apps.pilot.ligand_motifs: ATOM k: 5 Name: N2 < apps.pilot.ligand_motifs: Connected triplet is: 2, type is Nhis; 1, type is aroC; 5, type is Nhis < apps.pilot.ligand_motifs: atom_i: 2 < apps.pilot.ligand_motifs: atom_i to atom_j: 1 < apps.pilot.ligand_motifs: atom_j to atom_k: 5 < apps.pilot.ligand_motifs: ATOM j: 17 Name: C11 < apps.pilot.ligand_motifs: ATOM k: 2 Name: N1 < apps.pilot.ligand_motifs: Connected triplet is: 2, type is Nhis; 17, type is CH2; 2, type is Nhis < apps.pilot.ligand_motifs: ATOM k: 18 Name: C12 < apps.pilot.ligand_motifs: Connected triplet is: 2, type is Nhis; 17, type is CH2; 18, type is CH2 < apps.pilot.ligand_motifs: atom_i: 2 < apps.pilot.ligand_motifs: atom_i to atom_j: 17 < apps.pilot.ligand_motifs: atom_j to atom_k: 18 < apps.pilot.ligand_motifs: ATOM j: 21 Name: C16 < apps.pilot.ligand_motifs: ATOM k: 2 Name: N1 < apps.pilot.ligand_motifs: Connected triplet is: 2, type is Nhis; 21, type is CH2; 2, type is Nhis < apps.pilot.ligand_motifs: ATOM k: 20 Name: C15 < apps.pilot.ligand_motifs: Connected triplet is: 2, type is Nhis; 21, type is CH2; 20, type is CH2 < apps.pilot.ligand_motifs: atom_i: 2 < apps.pilot.ligand_motifs: atom_i to atom_j: 21 < apps.pilot.ligand_motifs: atom_j to atom_k: 20 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 3 < apps.pilot.ligand_motifs: atom name is O1 < apps.pilot.ligand_motifs: ATOM j: 1 Name: C1 < apps.pilot.ligand_motifs: ATOM k: 2 Name: N1 < apps.pilot.ligand_motifs: Connected triplet is: 3, type is Oaro; 1, type is aroC; 2, type is Nhis < apps.pilot.ligand_motifs: atom_i: 3 < apps.pilot.ligand_motifs: atom_i to atom_j: 1 < apps.pilot.ligand_motifs: atom_j to atom_k: 2 < apps.pilot.ligand_motifs: ATOM k: 3 Name: O1 < apps.pilot.ligand_motifs: Connected triplet is: 3, type is Oaro; 1, type is aroC; 3, type is Oaro < apps.pilot.ligand_motifs: ATOM k: 5 Name: N2 < apps.pilot.ligand_motifs: Connected triplet is: 3, type is Oaro; 1, type is aroC; 5, type is Nhis < apps.pilot.ligand_motifs: atom_i: 3 < apps.pilot.ligand_motifs: atom_i to atom_j: 1 < apps.pilot.ligand_motifs: atom_j to atom_k: 5 < apps.pilot.ligand_motifs: ATOM j: 16 Name: C8 < apps.pilot.ligand_motifs: ATOM k: 3 Name: O1 < apps.pilot.ligand_motifs: Connected triplet is: 3, type is Oaro; 16, type is aroC; 3, type is Oaro < apps.pilot.ligand_motifs: ATOM k: 7 Name: C3 < apps.pilot.ligand_motifs: Connected triplet is: 3, type is Oaro; 16, type is aroC; 7, type is aroC < apps.pilot.ligand_motifs: atom_i: 3 < apps.pilot.ligand_motifs: atom_i to atom_j: 16 < apps.pilot.ligand_motifs: atom_j to atom_k: 7 < apps.pilot.ligand_motifs: ATOM k: 15 Name: C7 < apps.pilot.ligand_motifs: Connected triplet is: 3, type is Oaro; 16, type is aroC; 15, type is aroC < apps.pilot.ligand_motifs: atom_i: 3 < apps.pilot.ligand_motifs: atom_i to atom_j: 16 < apps.pilot.ligand_motifs: atom_j to atom_k: 15 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 4 < apps.pilot.ligand_motifs: atom name is CL1 < apps.pilot.ligand_motifs: ATOM j: 11 Name: C5 < apps.pilot.ligand_motifs: ATOM k: 4 Name: CL1 < apps.pilot.ligand_motifs: Connected triplet is: 4, type is Cl; 11, type is aroC; 4, type is Cl < apps.pilot.ligand_motifs: ATOM k: 9 Name: C4 < apps.pilot.ligand_motifs: Connected triplet is: 4, type is Cl; 11, type is aroC; 9, type is aroC < apps.pilot.ligand_motifs: atom_i: 4 < apps.pilot.ligand_motifs: atom_i to atom_j: 11 < apps.pilot.ligand_motifs: atom_j to atom_k: 9 < apps.pilot.ligand_motifs: ATOM k: 13 Name: C6 < apps.pilot.ligand_motifs: Connected triplet is: 4, type is Cl; 11, type is aroC; 13, type is aroC < apps.pilot.ligand_motifs: atom_i: 4 < apps.pilot.ligand_motifs: atom_i to atom_j: 11 < apps.pilot.ligand_motifs: atom_j to atom_k: 13 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 5 < apps.pilot.ligand_motifs: atom name is N2 < apps.pilot.ligand_motifs: ATOM j: 1 Name: C1 < apps.pilot.ligand_motifs: ATOM k: 2 Name: N1 < apps.pilot.ligand_motifs: Connected triplet is: 5, type is Nhis; 1, type is aroC; 2, type is Nhis < apps.pilot.ligand_motifs: atom_i: 5 < apps.pilot.ligand_motifs: atom_i to atom_j: 1 < apps.pilot.ligand_motifs: atom_j to atom_k: 2 < apps.pilot.ligand_motifs: ATOM k: 3 Name: O1 < apps.pilot.ligand_motifs: Connected triplet is: 5, type is Nhis; 1, type is aroC; 3, type is Oaro < apps.pilot.ligand_motifs: atom_i: 5 < apps.pilot.ligand_motifs: atom_i to atom_j: 1 < apps.pilot.ligand_motifs: atom_j to atom_k: 3 < apps.pilot.ligand_motifs: ATOM k: 5 Name: N2 < apps.pilot.ligand_motifs: Connected triplet is: 5, type is Nhis; 1, type is aroC; 5, type is Nhis < apps.pilot.ligand_motifs: ATOM j: 7 Name: C3 < apps.pilot.ligand_motifs: ATOM k: 5 Name: N2 < apps.pilot.ligand_motifs: Connected triplet is: 5, type is Nhis; 7, type is aroC; 5, type is Nhis < apps.pilot.ligand_motifs: ATOM k: 9 Name: C4 < apps.pilot.ligand_motifs: Connected triplet is: 5, type is Nhis; 7, type is aroC; 9, type is aroC < apps.pilot.ligand_motifs: atom_i: 5 < apps.pilot.ligand_motifs: atom_i to atom_j: 7 < apps.pilot.ligand_motifs: atom_j to atom_k: 9 < apps.pilot.ligand_motifs: ATOM k: 16 Name: C8 < apps.pilot.ligand_motifs: Connected triplet is: 5, type is Nhis; 7, type is aroC; 16, type is aroC < apps.pilot.ligand_motifs: atom_i: 5 < apps.pilot.ligand_motifs: atom_i to atom_j: 7 < apps.pilot.ligand_motifs: atom_j to atom_k: 16 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 6 < apps.pilot.ligand_motifs: atom name is O2 < apps.pilot.ligand_motifs: ATOM j: 22 Name: C17 < apps.pilot.ligand_motifs: ATOM k: 6 Name: O2 < apps.pilot.ligand_motifs: Connected triplet is: 6, type is ONH2; 22, type is COO; 6, type is ONH2 < apps.pilot.ligand_motifs: ATOM k: 8 Name: N3 < apps.pilot.ligand_motifs: Connected triplet is: 6, type is ONH2; 22, type is COO; 8, type is Nhis < apps.pilot.ligand_motifs: atom_i: 6 < apps.pilot.ligand_motifs: atom_i to atom_j: 22 < apps.pilot.ligand_motifs: atom_j to atom_k: 8 < apps.pilot.ligand_motifs: ATOM k: 23 Name: C19 < apps.pilot.ligand_motifs: Connected triplet is: 6, type is ONH2; 22, type is COO; 23, type is aroC < apps.pilot.ligand_motifs: atom_i: 6 < apps.pilot.ligand_motifs: atom_i to atom_j: 22 < apps.pilot.ligand_motifs: atom_j to atom_k: 23 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 7 < apps.pilot.ligand_motifs: atom name is C3 < apps.pilot.ligand_motifs: ATOM j: 5 Name: N2 < apps.pilot.ligand_motifs: ATOM k: 1 Name: C1 < apps.pilot.ligand_motifs: Connected triplet is: 7, type is aroC; 5, type is Nhis; 1, type is aroC < apps.pilot.ligand_motifs: atom_i: 7 < apps.pilot.ligand_motifs: atom_i to atom_j: 5 < apps.pilot.ligand_motifs: atom_j to atom_k: 1 < apps.pilot.ligand_motifs: ATOM k: 7 Name: C3 < apps.pilot.ligand_motifs: Connected triplet is: 7, type is aroC; 5, type is Nhis; 7, type is aroC < apps.pilot.ligand_motifs: ATOM j: 9 Name: C4 < apps.pilot.ligand_motifs: ATOM k: 7 Name: C3 < apps.pilot.ligand_motifs: Connected triplet is: 7, type is aroC; 9, type is aroC; 7, type is aroC < apps.pilot.ligand_motifs: ATOM k: 11 Name: C5 < apps.pilot.ligand_motifs: Connected triplet is: 7, type is aroC; 9, type is aroC; 11, type is aroC < apps.pilot.ligand_motifs: atom_i: 7 < apps.pilot.ligand_motifs: atom_i to atom_j: 9 < apps.pilot.ligand_motifs: atom_j to atom_k: 11 < apps.pilot.ligand_motifs: ATOM j: 16 Name: C8 < apps.pilot.ligand_motifs: ATOM k: 3 Name: O1 < apps.pilot.ligand_motifs: Connected triplet is: 7, type is aroC; 16, type is aroC; 3, type is Oaro < apps.pilot.ligand_motifs: atom_i: 7 < apps.pilot.ligand_motifs: atom_i to atom_j: 16 < apps.pilot.ligand_motifs: atom_j to atom_k: 3 < apps.pilot.ligand_motifs: ATOM k: 7 Name: C3 < apps.pilot.ligand_motifs: Connected triplet is: 7, type is aroC; 16, type is aroC; 7, type is aroC < apps.pilot.ligand_motifs: ATOM k: 15 Name: C7 < apps.pilot.ligand_motifs: Connected triplet is: 7, type is aroC; 16, type is aroC; 15, type is aroC < apps.pilot.ligand_motifs: atom_i: 7 < apps.pilot.ligand_motifs: atom_i to atom_j: 16 < apps.pilot.ligand_motifs: atom_j to atom_k: 15 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 8 < apps.pilot.ligand_motifs: atom name is N3 < apps.pilot.ligand_motifs: ATOM j: 18 Name: C12 < apps.pilot.ligand_motifs: ATOM k: 8 Name: N3 < apps.pilot.ligand_motifs: Connected triplet is: 8, type is Nhis; 18, type is CH2; 8, type is Nhis < apps.pilot.ligand_motifs: ATOM k: 17 Name: C11 < apps.pilot.ligand_motifs: Connected triplet is: 8, type is Nhis; 18, type is CH2; 17, type is CH2 < apps.pilot.ligand_motifs: atom_i: 8 < apps.pilot.ligand_motifs: atom_i to atom_j: 18 < apps.pilot.ligand_motifs: atom_j to atom_k: 17 < apps.pilot.ligand_motifs: ATOM j: 19 Name: C14 < apps.pilot.ligand_motifs: ATOM k: 8 Name: N3 < apps.pilot.ligand_motifs: Connected triplet is: 8, type is Nhis; 19, type is CH1; 8, type is Nhis < apps.pilot.ligand_motifs: ATOM k: 20 Name: C15 < apps.pilot.ligand_motifs: Connected triplet is: 8, type is Nhis; 19, type is CH1; 20, type is CH2 < apps.pilot.ligand_motifs: atom_i: 8 < apps.pilot.ligand_motifs: atom_i to atom_j: 19 < apps.pilot.ligand_motifs: atom_j to atom_k: 20 < apps.pilot.ligand_motifs: ATOM k: 32 Name: C30 < apps.pilot.ligand_motifs: Connected triplet is: 8, type is Nhis; 19, type is CH1; 32, type is CH3 < apps.pilot.ligand_motifs: atom_i: 8 < apps.pilot.ligand_motifs: atom_i to atom_j: 19 < apps.pilot.ligand_motifs: atom_j to atom_k: 32 < apps.pilot.ligand_motifs: ATOM j: 22 Name: C17 < apps.pilot.ligand_motifs: ATOM k: 6 Name: O2 < apps.pilot.ligand_motifs: Connected triplet is: 8, type is Nhis; 22, type is COO; 6, type is ONH2 < apps.pilot.ligand_motifs: atom_i: 8 < apps.pilot.ligand_motifs: atom_i to atom_j: 22 < apps.pilot.ligand_motifs: atom_j to atom_k: 6 < apps.pilot.ligand_motifs: ATOM k: 8 Name: N3 < apps.pilot.ligand_motifs: Connected triplet is: 8, type is Nhis; 22, type is COO; 8, type is Nhis < apps.pilot.ligand_motifs: ATOM k: 23 Name: C19 < apps.pilot.ligand_motifs: Connected triplet is: 8, type is Nhis; 22, type is COO; 23, type is aroC < apps.pilot.ligand_motifs: atom_i: 8 < apps.pilot.ligand_motifs: atom_i to atom_j: 22 < apps.pilot.ligand_motifs: atom_j to atom_k: 23 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 9 < apps.pilot.ligand_motifs: atom name is C4 < apps.pilot.ligand_motifs: ATOM j: 7 Name: C3 < apps.pilot.ligand_motifs: ATOM k: 5 Name: N2 < apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 7, type is aroC; 5, type is Nhis < apps.pilot.ligand_motifs: atom_i: 9 < apps.pilot.ligand_motifs: atom_i to atom_j: 7 < apps.pilot.ligand_motifs: atom_j to atom_k: 5 < apps.pilot.ligand_motifs: ATOM k: 9 Name: C4 < apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 7, type is aroC; 9, type is aroC < apps.pilot.ligand_motifs: ATOM k: 16 Name: C8 < apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 7, type is aroC; 16, type is aroC < apps.pilot.ligand_motifs: atom_i: 9 < apps.pilot.ligand_motifs: atom_i to atom_j: 7 < apps.pilot.ligand_motifs: atom_j to atom_k: 16 < apps.pilot.ligand_motifs: ATOM j: 11 Name: C5 < apps.pilot.ligand_motifs: ATOM k: 4 Name: CL1 < apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 11, type is aroC; 4, type is Cl < apps.pilot.ligand_motifs: atom_i: 9 < apps.pilot.ligand_motifs: atom_i to atom_j: 11 < apps.pilot.ligand_motifs: atom_j to atom_k: 4 < apps.pilot.ligand_motifs: ATOM k: 9 Name: C4 < apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 11, type is aroC; 9, type is aroC < apps.pilot.ligand_motifs: ATOM k: 13 Name: C6 < apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 11, type is aroC; 13, type is aroC < apps.pilot.ligand_motifs: atom_i: 9 < apps.pilot.ligand_motifs: atom_i to atom_j: 11 < apps.pilot.ligand_motifs: atom_j to atom_k: 13 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 10 < apps.pilot.ligand_motifs: atom name is N4 < apps.pilot.ligand_motifs: ATOM j: 12 Name: N5 < apps.pilot.ligand_motifs: ATOM k: 10 Name: N4 < apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 12, type is Nhis; 10, type is Nhis < apps.pilot.ligand_motifs: ATOM k: 29 Name: C27 < apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 12, type is Nhis; 29, type is aroC < apps.pilot.ligand_motifs: atom_i: 10 < apps.pilot.ligand_motifs: atom_i to atom_j: 12 < apps.pilot.ligand_motifs: atom_j to atom_k: 29 < apps.pilot.ligand_motifs: ATOM j: 14 Name: N6 < apps.pilot.ligand_motifs: ATOM k: 10 Name: N4 < apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 14, type is Nhis; 10, type is Nhis < apps.pilot.ligand_motifs: ATOM k: 30 Name: C28 < apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 14, type is Nhis; 30, type is aroC < apps.pilot.ligand_motifs: atom_i: 10 < apps.pilot.ligand_motifs: atom_i to atom_j: 14 < apps.pilot.ligand_motifs: atom_j to atom_k: 30 < apps.pilot.ligand_motifs: ATOM j: 24 Name: C20 < apps.pilot.ligand_motifs: ATOM k: 10 Name: N4 < apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 24, type is aroC; 10, type is Nhis < apps.pilot.ligand_motifs: ATOM k: 23 Name: C19 < apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 24, type is aroC; 23, type is aroC < apps.pilot.ligand_motifs: atom_i: 10 < apps.pilot.ligand_motifs: atom_i to atom_j: 24 < apps.pilot.ligand_motifs: atom_j to atom_k: 23 < apps.pilot.ligand_motifs: ATOM k: 25 Name: C21 < apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 24, type is aroC; 25, type is aroC < apps.pilot.ligand_motifs: atom_i: 10 < apps.pilot.ligand_motifs: atom_i to atom_j: 24 < apps.pilot.ligand_motifs: atom_j to atom_k: 25 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 11 < apps.pilot.ligand_motifs: atom name is C5 < apps.pilot.ligand_motifs: ATOM j: 4 Name: CL1 < apps.pilot.ligand_motifs: ATOM k: 11 Name: C5 < apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 4, type is Cl; 11, type is aroC < apps.pilot.ligand_motifs: ATOM j: 9 Name: C4 < apps.pilot.ligand_motifs: ATOM k: 7 Name: C3 < apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 9, type is aroC; 7, type is aroC < apps.pilot.ligand_motifs: atom_i: 11 < apps.pilot.ligand_motifs: atom_i to atom_j: 9 < apps.pilot.ligand_motifs: atom_j to atom_k: 7 < apps.pilot.ligand_motifs: ATOM k: 11 Name: C5 < apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 9, type is aroC; 11, type is aroC < apps.pilot.ligand_motifs: ATOM j: 13 Name: C6 < apps.pilot.ligand_motifs: ATOM k: 11 Name: C5 < apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 13, type is aroC; 11, type is aroC < apps.pilot.ligand_motifs: ATOM k: 15 Name: C7 < apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 13, type is aroC; 15, type is aroC < apps.pilot.ligand_motifs: atom_i: 11 < apps.pilot.ligand_motifs: atom_i to atom_j: 13 < apps.pilot.ligand_motifs: atom_j to atom_k: 15 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 12 < apps.pilot.ligand_motifs: atom name is N5 < apps.pilot.ligand_motifs: ATOM j: 10 Name: N4 < apps.pilot.ligand_motifs: ATOM k: 12 Name: N5 < apps.pilot.ligand_motifs: Connected triplet is: 12, type is Nhis; 10, type is Nhis; 12, type is Nhis < apps.pilot.ligand_motifs: ATOM k: 14 Name: N6 < apps.pilot.ligand_motifs: Connected triplet is: 12, type is Nhis; 10, type is Nhis; 14, type is Nhis < apps.pilot.ligand_motifs: atom_i: 12 < apps.pilot.ligand_motifs: atom_i to atom_j: 10 < apps.pilot.ligand_motifs: atom_j to atom_k: 14 < apps.pilot.ligand_motifs: ATOM k: 24 Name: C20 < apps.pilot.ligand_motifs: Connected triplet is: 12, type is Nhis; 10, type is Nhis; 24, type is aroC < apps.pilot.ligand_motifs: atom_i: 12 < apps.pilot.ligand_motifs: atom_i to atom_j: 10 < apps.pilot.ligand_motifs: atom_j to atom_k: 24 < apps.pilot.ligand_motifs: ATOM j: 29 Name: C27 < apps.pilot.ligand_motifs: ATOM k: 12 Name: N5 < apps.pilot.ligand_motifs: Connected triplet is: 12, type is Nhis; 29, type is aroC; 12, type is Nhis < apps.pilot.ligand_motifs: ATOM k: 30 Name: C28 < apps.pilot.ligand_motifs: Connected triplet is: 12, type is Nhis; 29, type is aroC; 30, type is aroC < apps.pilot.ligand_motifs: atom_i: 12 < apps.pilot.ligand_motifs: atom_i to atom_j: 29 < apps.pilot.ligand_motifs: atom_j to atom_k: 30 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 13 < apps.pilot.ligand_motifs: atom name is C6 < apps.pilot.ligand_motifs: ATOM j: 11 Name: C5 < apps.pilot.ligand_motifs: ATOM k: 4 Name: CL1 < apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 11, type is aroC; 4, type is Cl < apps.pilot.ligand_motifs: atom_i: 13 < apps.pilot.ligand_motifs: atom_i to atom_j: 11 < apps.pilot.ligand_motifs: atom_j to atom_k: 4 < apps.pilot.ligand_motifs: ATOM k: 9 Name: C4 < apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 11, type is aroC; 9, type is aroC < apps.pilot.ligand_motifs: atom_i: 13 < apps.pilot.ligand_motifs: atom_i to atom_j: 11 < apps.pilot.ligand_motifs: atom_j to atom_k: 9 < apps.pilot.ligand_motifs: ATOM k: 13 Name: C6 < apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 11, type is aroC; 13, type is aroC < apps.pilot.ligand_motifs: ATOM j: 15 Name: C7 < apps.pilot.ligand_motifs: ATOM k: 13 Name: C6 < apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 15, type is aroC; 13, type is aroC < apps.pilot.ligand_motifs: ATOM k: 16 Name: C8 < apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 15, type is aroC; 16, type is aroC < apps.pilot.ligand_motifs: atom_i: 13 < apps.pilot.ligand_motifs: atom_i to atom_j: 15 < apps.pilot.ligand_motifs: atom_j to atom_k: 16 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 14 < apps.pilot.ligand_motifs: atom name is N6 < apps.pilot.ligand_motifs: ATOM j: 10 Name: N4 < apps.pilot.ligand_motifs: ATOM k: 12 Name: N5 < apps.pilot.ligand_motifs: Connected triplet is: 14, type is Nhis; 10, type is Nhis; 12, type is Nhis < apps.pilot.ligand_motifs: atom_i: 14 < apps.pilot.ligand_motifs: atom_i to atom_j: 10 < apps.pilot.ligand_motifs: atom_j to atom_k: 12 < apps.pilot.ligand_motifs: ATOM k: 14 Name: N6 < apps.pilot.ligand_motifs: Connected triplet is: 14, type is Nhis; 10, type is Nhis; 14, type is Nhis < apps.pilot.ligand_motifs: ATOM k: 24 Name: C20 < apps.pilot.ligand_motifs: Connected triplet is: 14, type is Nhis; 10, type is Nhis; 24, type is aroC < apps.pilot.ligand_motifs: atom_i: 14 < apps.pilot.ligand_motifs: atom_i to atom_j: 10 < apps.pilot.ligand_motifs: atom_j to atom_k: 24 < apps.pilot.ligand_motifs: ATOM j: 30 Name: C28 < apps.pilot.ligand_motifs: ATOM k: 14 Name: N6 < apps.pilot.ligand_motifs: Connected triplet is: 14, type is Nhis; 30, type is aroC; 14, type is Nhis < apps.pilot.ligand_motifs: ATOM k: 29 Name: C27 < apps.pilot.ligand_motifs: Connected triplet is: 14, type is Nhis; 30, type is aroC; 29, type is aroC < apps.pilot.ligand_motifs: atom_i: 14 < apps.pilot.ligand_motifs: atom_i to atom_j: 30 < apps.pilot.ligand_motifs: atom_j to atom_k: 29 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 15 < apps.pilot.ligand_motifs: atom name is C7 < apps.pilot.ligand_motifs: ATOM j: 13 Name: C6 < apps.pilot.ligand_motifs: ATOM k: 11 Name: C5 < apps.pilot.ligand_motifs: Connected triplet is: 15, type is aroC; 13, type is aroC; 11, type is aroC < apps.pilot.ligand_motifs: atom_i: 15 < apps.pilot.ligand_motifs: atom_i to atom_j: 13 < apps.pilot.ligand_motifs: atom_j to atom_k: 11 < apps.pilot.ligand_motifs: ATOM k: 15 Name: C7 < apps.pilot.ligand_motifs: Connected triplet is: 15, type is aroC; 13, type is aroC; 15, type is aroC < apps.pilot.ligand_motifs: ATOM j: 16 Name: C8 < apps.pilot.ligand_motifs: ATOM k: 3 Name: O1 < apps.pilot.ligand_motifs: Connected triplet is: 15, type is aroC; 16, type is aroC; 3, type is Oaro < apps.pilot.ligand_motifs: atom_i: 15 < apps.pilot.ligand_motifs: atom_i to atom_j: 16 < apps.pilot.ligand_motifs: atom_j to atom_k: 3 < apps.pilot.ligand_motifs: ATOM k: 7 Name: C3 < apps.pilot.ligand_motifs: Connected triplet is: 15, type is aroC; 16, type is aroC; 7, type is aroC < apps.pilot.ligand_motifs: atom_i: 15 < apps.pilot.ligand_motifs: atom_i to atom_j: 16 < apps.pilot.ligand_motifs: atom_j to atom_k: 7 < apps.pilot.ligand_motifs: ATOM k: 15 Name: C7 < apps.pilot.ligand_motifs: Connected triplet is: 15, type is aroC; 16, type is aroC; 15, type is aroC < apps.pilot.ligand_motifs: in atom iterate block, atom num is 16 < apps.pilot.ligand_motifs: atom name is C8 < apps.pilot.ligand_motifs: ATOM j: 3 Name: O1 < apps.pilot.ligand_motifs: ATOM k: 1 Name: C1 < apps.pilot.ligand_motifs: Connected triplet is: 16, type is aroC; 3, type is Oaro; 1, type is aroC < apps.pilot.ligand_motifs: atom_i: 16 < apps.pilot.ligand_motifs: atom_i to atom_j: 3 < apps.pilot.ligand_motifs: atom_j to atom_k: 1 < apps.pilot.ligand_motifs: ATOM k: 16 Name: C8 < apps.pilot.ligand_motifs: Connected triplet is: 16, type is aroC; 3, type is Oaro; 16, type is aroC < apps.pilot.ligand_motifs: ATOM j: 7 Name: C3 < apps.pilot.ligand_motifs: ATOM k: 5 Name: N2 < apps.pilot.ligand_motifs: Connected triplet is: 16, type is aroC; 7, type is aroC; 5, type is Nhis < apps.pilot.ligand_motifs: atom_i: 16 < apps.pilot.ligand_motifs: atom_i to atom_j: 7 < apps.pilot.ligand_motifs: atom_j to atom_k: 5 < apps.pilot.ligand_motifs: ATOM k: 9 Name: C4 < apps.pilot.ligand_motifs: Connected triplet is: 16, type is aroC; 7, type is aroC; 9, type is aroC < apps.pilot.ligand_motifs: atom_i: 16 < apps.pilot.ligand_motifs: atom_i to atom_j: 7 < apps.pilot.ligand_motifs: atom_j to atom_k: 9 < apps.pilot.ligand_motifs: ATOM k: 16 Name: C8 < apps.pilot.ligand_motifs: Connected triplet is: 16, type is aroC; 7, type is aroC; 16, type is aroC < apps.pilot.ligand_motifs: ATOM j: 15 Name: C7 < apps.pilot.ligand_motifs: ATOM k: 13 Name: C6 < apps.pilot.ligand_motifs: Connected triplet is: 16, type is aroC; 15, type is aroC; 13, type is aroC < apps.pilot.ligand_motifs: atom_i: 16 < apps.pilot.ligand_motifs: atom_i to atom_j: 15 < apps.pilot.ligand_motifs: atom_j to atom_k: 13 < apps.pilot.ligand_motifs: ATOM k: 16 Name: C8 < apps.pilot.ligand_motifs: Connected triplet is: 16, type is aroC; 15, type is aroC; 16, type is aroC < apps.pilot.ligand_motifs: in atom iterate block, atom num is 17 < apps.pilot.ligand_motifs: atom name is C11 < apps.pilot.ligand_motifs: ATOM j: 2 Name: N1 < apps.pilot.ligand_motifs: ATOM k: 1 Name: C1 < apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 2, type is Nhis; 1, type is aroC < apps.pilot.ligand_motifs: atom_i: 17 < apps.pilot.ligand_motifs: atom_i to atom_j: 2 < apps.pilot.ligand_motifs: atom_j to atom_k: 1 < apps.pilot.ligand_motifs: ATOM k: 17 Name: C11 < apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 2, type is Nhis; 17, type is CH2 < apps.pilot.ligand_motifs: ATOM k: 21 Name: C16 < apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 2, type is Nhis; 21, type is CH2 < apps.pilot.ligand_motifs: atom_i: 17 < apps.pilot.ligand_motifs: atom_i to atom_j: 2 < apps.pilot.ligand_motifs: atom_j to atom_k: 21 < apps.pilot.ligand_motifs: ATOM j: 18 Name: C12 < apps.pilot.ligand_motifs: ATOM k: 8 Name: N3 < apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 18, type is CH2; 8, type is Nhis < apps.pilot.ligand_motifs: atom_i: 17 < apps.pilot.ligand_motifs: atom_i to atom_j: 18 < apps.pilot.ligand_motifs: atom_j to atom_k: 8 < apps.pilot.ligand_motifs: ATOM k: 17 Name: C11 < apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 18, type is CH2; 17, type is CH2 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 18 < apps.pilot.ligand_motifs: atom name is C12 < apps.pilot.ligand_motifs: ATOM j: 8 Name: N3 < apps.pilot.ligand_motifs: ATOM k: 18 Name: C12 < apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 8, type is Nhis; 18, type is CH2 < apps.pilot.ligand_motifs: ATOM k: 19 Name: C14 < apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 8, type is Nhis; 19, type is CH1 < apps.pilot.ligand_motifs: atom_i: 18 < apps.pilot.ligand_motifs: atom_i to atom_j: 8 < apps.pilot.ligand_motifs: atom_j to atom_k: 19 < apps.pilot.ligand_motifs: ATOM k: 22 Name: C17 < apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 8, type is Nhis; 22, type is COO < apps.pilot.ligand_motifs: atom_i: 18 < apps.pilot.ligand_motifs: atom_i to atom_j: 8 < apps.pilot.ligand_motifs: atom_j to atom_k: 22 < apps.pilot.ligand_motifs: ATOM j: 17 Name: C11 < apps.pilot.ligand_motifs: ATOM k: 2 Name: N1 < apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 17, type is CH2; 2, type is Nhis < apps.pilot.ligand_motifs: atom_i: 18 < apps.pilot.ligand_motifs: atom_i to atom_j: 17 < apps.pilot.ligand_motifs: atom_j to atom_k: 2 < apps.pilot.ligand_motifs: ATOM k: 18 Name: C12 < apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 17, type is CH2; 18, type is CH2 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 19 < apps.pilot.ligand_motifs: atom name is C14 < apps.pilot.ligand_motifs: ATOM j: 8 Name: N3 < apps.pilot.ligand_motifs: ATOM k: 18 Name: C12 < apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH1; 8, type is Nhis; 18, type is CH2 < apps.pilot.ligand_motifs: atom_i: 19 < apps.pilot.ligand_motifs: atom_i to atom_j: 8 < apps.pilot.ligand_motifs: atom_j to atom_k: 18 < apps.pilot.ligand_motifs: ATOM k: 19 Name: C14 < apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH1; 8, type is Nhis; 19, type is CH1 < apps.pilot.ligand_motifs: ATOM k: 22 Name: C17 < apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH1; 8, type is Nhis; 22, type is COO < apps.pilot.ligand_motifs: atom_i: 19 < apps.pilot.ligand_motifs: atom_i to atom_j: 8 < apps.pilot.ligand_motifs: atom_j to atom_k: 22 < apps.pilot.ligand_motifs: ATOM j: 20 Name: C15 < apps.pilot.ligand_motifs: ATOM k: 19 Name: C14 < apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH1; 20, type is CH2; 19, type is CH1 < apps.pilot.ligand_motifs: ATOM k: 21 Name: C16 < apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH1; 20, type is CH2; 21, type is CH2 < apps.pilot.ligand_motifs: atom_i: 19 < apps.pilot.ligand_motifs: atom_i to atom_j: 20 < apps.pilot.ligand_motifs: atom_j to atom_k: 21 < apps.pilot.ligand_motifs: ATOM j: 32 Name: C30 < apps.pilot.ligand_motifs: ATOM k: 19 Name: C14 < apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH1; 32, type is CH3; 19, type is CH1 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 20 < apps.pilot.ligand_motifs: atom name is C15 < apps.pilot.ligand_motifs: ATOM j: 19 Name: C14 < apps.pilot.ligand_motifs: ATOM k: 8 Name: N3 < apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 19, type is CH1; 8, type is Nhis < apps.pilot.ligand_motifs: atom_i: 20 < apps.pilot.ligand_motifs: atom_i to atom_j: 19 < apps.pilot.ligand_motifs: atom_j to atom_k: 8 < apps.pilot.ligand_motifs: ATOM k: 20 Name: C15 < apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 19, type is CH1; 20, type is CH2 < apps.pilot.ligand_motifs: ATOM k: 32 Name: C30 < apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 19, type is CH1; 32, type is CH3 < apps.pilot.ligand_motifs: atom_i: 20 < apps.pilot.ligand_motifs: atom_i to atom_j: 19 < apps.pilot.ligand_motifs: atom_j to atom_k: 32 < apps.pilot.ligand_motifs: ATOM j: 21 Name: C16 < apps.pilot.ligand_motifs: ATOM k: 2 Name: N1 < apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 21, type is CH2; 2, type is Nhis < apps.pilot.ligand_motifs: atom_i: 20 < apps.pilot.ligand_motifs: atom_i to atom_j: 21 < apps.pilot.ligand_motifs: atom_j to atom_k: 2 < apps.pilot.ligand_motifs: ATOM k: 20 Name: C15 < apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 21, type is CH2; 20, type is CH2 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 21 < apps.pilot.ligand_motifs: atom name is C16 < apps.pilot.ligand_motifs: ATOM j: 2 Name: N1 < apps.pilot.ligand_motifs: ATOM k: 1 Name: C1 < apps.pilot.ligand_motifs: Connected triplet is: 21, type is CH2; 2, type is Nhis; 1, type is aroC < apps.pilot.ligand_motifs: atom_i: 21 < apps.pilot.ligand_motifs: atom_i to atom_j: 2 < apps.pilot.ligand_motifs: atom_j to atom_k: 1 < apps.pilot.ligand_motifs: ATOM k: 17 Name: C11 < apps.pilot.ligand_motifs: Connected triplet is: 21, type is CH2; 2, type is Nhis; 17, type is CH2 < apps.pilot.ligand_motifs: atom_i: 21 < apps.pilot.ligand_motifs: atom_i to atom_j: 2 < apps.pilot.ligand_motifs: atom_j to atom_k: 17 < apps.pilot.ligand_motifs: ATOM k: 21 Name: C16 < apps.pilot.ligand_motifs: Connected triplet is: 21, type is CH2; 2, type is Nhis; 21, type is CH2 < apps.pilot.ligand_motifs: ATOM j: 20 Name: C15 < apps.pilot.ligand_motifs: ATOM k: 19 Name: C14 < apps.pilot.ligand_motifs: Connected triplet is: 21, type is CH2; 20, type is CH2; 19, type is CH1 < apps.pilot.ligand_motifs: atom_i: 21 < apps.pilot.ligand_motifs: atom_i to atom_j: 20 < apps.pilot.ligand_motifs: atom_j to atom_k: 19 < apps.pilot.ligand_motifs: ATOM k: 21 Name: C16 < apps.pilot.ligand_motifs: Connected triplet is: 21, type is CH2; 20, type is CH2; 21, type is CH2 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 22 < apps.pilot.ligand_motifs: atom name is C17 < apps.pilot.ligand_motifs: ATOM j: 6 Name: O2 < apps.pilot.ligand_motifs: ATOM k: 22 Name: C17 < apps.pilot.ligand_motifs: Connected triplet is: 22, type is COO; 6, type is ONH2; 22, type is COO < apps.pilot.ligand_motifs: ATOM j: 8 Name: N3 < apps.pilot.ligand_motifs: ATOM k: 18 Name: C12 < apps.pilot.ligand_motifs: Connected triplet is: 22, type is COO; 8, type is Nhis; 18, type is CH2 < apps.pilot.ligand_motifs: atom_i: 22 < apps.pilot.ligand_motifs: atom_i to atom_j: 8 < apps.pilot.ligand_motifs: atom_j to atom_k: 18 < apps.pilot.ligand_motifs: ATOM k: 19 Name: C14 < apps.pilot.ligand_motifs: Connected triplet is: 22, type is COO; 8, type is Nhis; 19, type is CH1 < apps.pilot.ligand_motifs: atom_i: 22 < apps.pilot.ligand_motifs: atom_i to atom_j: 8 < apps.pilot.ligand_motifs: atom_j to atom_k: 19 < apps.pilot.ligand_motifs: ATOM k: 22 Name: C17 < apps.pilot.ligand_motifs: Connected triplet is: 22, type is COO; 8, type is Nhis; 22, type is COO < apps.pilot.ligand_motifs: ATOM j: 23 Name: C19 < apps.pilot.ligand_motifs: ATOM k: 22 Name: C17 < apps.pilot.ligand_motifs: Connected triplet is: 22, type is COO; 23, type is aroC; 22, type is COO < apps.pilot.ligand_motifs: ATOM k: 24 Name: C20 < apps.pilot.ligand_motifs: Connected triplet is: 22, type is COO; 23, type is aroC; 24, type is aroC < apps.pilot.ligand_motifs: atom_i: 22 < apps.pilot.ligand_motifs: atom_i to atom_j: 23 < apps.pilot.ligand_motifs: atom_j to atom_k: 24 < apps.pilot.ligand_motifs: ATOM k: 28 Name: C24 < apps.pilot.ligand_motifs: Connected triplet is: 22, type is COO; 23, type is aroC; 28, type is aroC < apps.pilot.ligand_motifs: atom_i: 22 < apps.pilot.ligand_motifs: atom_i to atom_j: 23 < apps.pilot.ligand_motifs: atom_j to atom_k: 28 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 23 < apps.pilot.ligand_motifs: atom name is C19 < apps.pilot.ligand_motifs: ATOM j: 22 Name: C17 < apps.pilot.ligand_motifs: ATOM k: 6 Name: O2 < apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 22, type is COO; 6, type is ONH2 < apps.pilot.ligand_motifs: atom_i: 23 < apps.pilot.ligand_motifs: atom_i to atom_j: 22 < apps.pilot.ligand_motifs: atom_j to atom_k: 6 < apps.pilot.ligand_motifs: ATOM k: 8 Name: N3 < apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 22, type is COO; 8, type is Nhis < apps.pilot.ligand_motifs: atom_i: 23 < apps.pilot.ligand_motifs: atom_i to atom_j: 22 < apps.pilot.ligand_motifs: atom_j to atom_k: 8 < apps.pilot.ligand_motifs: ATOM k: 23 Name: C19 < apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 22, type is COO; 23, type is aroC < apps.pilot.ligand_motifs: ATOM j: 24 Name: C20 < apps.pilot.ligand_motifs: ATOM k: 10 Name: N4 < apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 24, type is aroC; 10, type is Nhis < apps.pilot.ligand_motifs: atom_i: 23 < apps.pilot.ligand_motifs: atom_i to atom_j: 24 < apps.pilot.ligand_motifs: atom_j to atom_k: 10 < apps.pilot.ligand_motifs: ATOM k: 23 Name: C19 < apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 24, type is aroC; 23, type is aroC < apps.pilot.ligand_motifs: ATOM k: 25 Name: C21 < apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 24, type is aroC; 25, type is aroC < apps.pilot.ligand_motifs: atom_i: 23 < apps.pilot.ligand_motifs: atom_i to atom_j: 24 < apps.pilot.ligand_motifs: atom_j to atom_k: 25 < apps.pilot.ligand_motifs: ATOM j: 28 Name: C24 < apps.pilot.ligand_motifs: ATOM k: 23 Name: C19 < apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 28, type is aroC; 23, type is aroC < apps.pilot.ligand_motifs: ATOM k: 27 Name: C23 < apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 28, type is aroC; 27, type is aroC < apps.pilot.ligand_motifs: atom_i: 23 < apps.pilot.ligand_motifs: atom_i to atom_j: 28 < apps.pilot.ligand_motifs: atom_j to atom_k: 27 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 24 < apps.pilot.ligand_motifs: atom name is C20 < apps.pilot.ligand_motifs: ATOM j: 10 Name: N4 < apps.pilot.ligand_motifs: ATOM k: 12 Name: N5 < apps.pilot.ligand_motifs: Connected triplet is: 24, type is aroC; 10, type is Nhis; 12, type is Nhis < apps.pilot.ligand_motifs: atom_i: 24 < apps.pilot.ligand_motifs: atom_i to atom_j: 10 < apps.pilot.ligand_motifs: atom_j to atom_k: 12 < apps.pilot.ligand_motifs: ATOM k: 14 Name: N6 < apps.pilot.ligand_motifs: Connected triplet is: 24, type is aroC; 10, type is Nhis; 14, type is Nhis < apps.pilot.ligand_motifs: atom_i: 24 < apps.pilot.ligand_motifs: atom_i to atom_j: 10 < apps.pilot.ligand_motifs: atom_j to atom_k: 14 < apps.pilot.ligand_motifs: ATOM k: 24 Name: C20 < apps.pilot.ligand_motifs: Connected triplet is: 24, type is aroC; 10, type is Nhis; 24, type is aroC < apps.pilot.ligand_motifs: ATOM j: 23 Name: C19 < apps.pilot.ligand_motifs: ATOM k: 22 Name: C17 < apps.pilot.ligand_motifs: Connected triplet is: 24, type is aroC; 23, type is aroC; 22, type is COO < apps.pilot.ligand_motifs: atom_i: 24 < apps.pilot.ligand_motifs: atom_i to atom_j: 23 < apps.pilot.ligand_motifs: atom_j to atom_k: 22 < apps.pilot.ligand_motifs: ATOM k: 24 Name: C20 < apps.pilot.ligand_motifs: Connected triplet is: 24, type is aroC; 23, type is aroC; 24, type is aroC < apps.pilot.ligand_motifs: ATOM k: 28 Name: C24 < apps.pilot.ligand_motifs: Connected triplet is: 24, type is aroC; 23, type is aroC; 28, type is aroC < apps.pilot.ligand_motifs: atom_i: 24 < apps.pilot.ligand_motifs: atom_i to atom_j: 23 < apps.pilot.ligand_motifs: atom_j to atom_k: 28 < apps.pilot.ligand_motifs: ATOM j: 25 Name: C21 < apps.pilot.ligand_motifs: ATOM k: 24 Name: C20 < apps.pilot.ligand_motifs: Connected triplet is: 24, type is aroC; 25, type is aroC; 24, type is aroC < apps.pilot.ligand_motifs: ATOM k: 26 Name: C22 < apps.pilot.ligand_motifs: Connected triplet is: 24, type is aroC; 25, type is aroC; 26, type is aroC < apps.pilot.ligand_motifs: atom_i: 24 < apps.pilot.ligand_motifs: atom_i to atom_j: 25 < apps.pilot.ligand_motifs: atom_j to atom_k: 26 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 25 < apps.pilot.ligand_motifs: atom name is C21 < apps.pilot.ligand_motifs: ATOM j: 24 Name: C20 < apps.pilot.ligand_motifs: ATOM k: 10 Name: N4 < apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 24, type is aroC; 10, type is Nhis < apps.pilot.ligand_motifs: atom_i: 25 < apps.pilot.ligand_motifs: atom_i to atom_j: 24 < apps.pilot.ligand_motifs: atom_j to atom_k: 10 < apps.pilot.ligand_motifs: ATOM k: 23 Name: C19 < apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 24, type is aroC; 23, type is aroC < apps.pilot.ligand_motifs: atom_i: 25 < apps.pilot.ligand_motifs: atom_i to atom_j: 24 < apps.pilot.ligand_motifs: atom_j to atom_k: 23 < apps.pilot.ligand_motifs: ATOM k: 25 Name: C21 < apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 24, type is aroC; 25, type is aroC < apps.pilot.ligand_motifs: ATOM j: 26 Name: C22 < apps.pilot.ligand_motifs: ATOM k: 25 Name: C21 < apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 26, type is aroC; 25, type is aroC < apps.pilot.ligand_motifs: ATOM k: 27 Name: C23 < apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 26, type is aroC; 27, type is aroC < apps.pilot.ligand_motifs: atom_i: 25 < apps.pilot.ligand_motifs: atom_i to atom_j: 26 < apps.pilot.ligand_motifs: atom_j to atom_k: 27 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 26 < apps.pilot.ligand_motifs: atom name is C22 < apps.pilot.ligand_motifs: ATOM j: 25 Name: C21 < apps.pilot.ligand_motifs: ATOM k: 24 Name: C20 < apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 25, type is aroC; 24, type is aroC < apps.pilot.ligand_motifs: atom_i: 26 < apps.pilot.ligand_motifs: atom_i to atom_j: 25 < apps.pilot.ligand_motifs: atom_j to atom_k: 24 < apps.pilot.ligand_motifs: ATOM k: 26 Name: C22 < apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 25, type is aroC; 26, type is aroC < apps.pilot.ligand_motifs: ATOM j: 27 Name: C23 < apps.pilot.ligand_motifs: ATOM k: 26 Name: C22 < apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 27, type is aroC; 26, type is aroC < apps.pilot.ligand_motifs: ATOM k: 28 Name: C24 < apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 27, type is aroC; 28, type is aroC < apps.pilot.ligand_motifs: atom_i: 26 < apps.pilot.ligand_motifs: atom_i to atom_j: 27 < apps.pilot.ligand_motifs: atom_j to atom_k: 28 < apps.pilot.ligand_motifs: ATOM k: 31 Name: C29 < apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 27, type is aroC; 31, type is CH3 < apps.pilot.ligand_motifs: atom_i: 26 < apps.pilot.ligand_motifs: atom_i to atom_j: 27 < apps.pilot.ligand_motifs: atom_j to atom_k: 31 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 27 < apps.pilot.ligand_motifs: atom name is C23 < apps.pilot.ligand_motifs: ATOM j: 26 Name: C22 < apps.pilot.ligand_motifs: ATOM k: 25 Name: C21 < apps.pilot.ligand_motifs: Connected triplet is: 27, type is aroC; 26, type is aroC; 25, type is aroC < apps.pilot.ligand_motifs: atom_i: 27 < apps.pilot.ligand_motifs: atom_i to atom_j: 26 < apps.pilot.ligand_motifs: atom_j to atom_k: 25 < apps.pilot.ligand_motifs: ATOM k: 27 Name: C23 < apps.pilot.ligand_motifs: Connected triplet is: 27, type is aroC; 26, type is aroC; 27, type is aroC < apps.pilot.ligand_motifs: ATOM j: 28 Name: C24 < apps.pilot.ligand_motifs: ATOM k: 23 Name: C19 < apps.pilot.ligand_motifs: Connected triplet is: 27, type is aroC; 28, type is aroC; 23, type is aroC < apps.pilot.ligand_motifs: atom_i: 27 < apps.pilot.ligand_motifs: atom_i to atom_j: 28 < apps.pilot.ligand_motifs: atom_j to atom_k: 23 < apps.pilot.ligand_motifs: ATOM k: 27 Name: C23 < apps.pilot.ligand_motifs: Connected triplet is: 27, type is aroC; 28, type is aroC; 27, type is aroC < apps.pilot.ligand_motifs: ATOM j: 31 Name: C29 < apps.pilot.ligand_motifs: ATOM k: 27 Name: C23 < apps.pilot.ligand_motifs: Connected triplet is: 27, type is aroC; 31, type is CH3; 27, type is aroC < apps.pilot.ligand_motifs: in atom iterate block, atom num is 28 < apps.pilot.ligand_motifs: atom name is C24 < apps.pilot.ligand_motifs: ATOM j: 23 Name: C19 < apps.pilot.ligand_motifs: ATOM k: 22 Name: C17 < apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 23, type is aroC; 22, type is COO < apps.pilot.ligand_motifs: atom_i: 28 < apps.pilot.ligand_motifs: atom_i to atom_j: 23 < apps.pilot.ligand_motifs: atom_j to atom_k: 22 < apps.pilot.ligand_motifs: ATOM k: 24 Name: C20 < apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 23, type is aroC; 24, type is aroC < apps.pilot.ligand_motifs: atom_i: 28 < apps.pilot.ligand_motifs: atom_i to atom_j: 23 < apps.pilot.ligand_motifs: atom_j to atom_k: 24 < apps.pilot.ligand_motifs: ATOM k: 28 Name: C24 < apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 23, type is aroC; 28, type is aroC < apps.pilot.ligand_motifs: ATOM j: 27 Name: C23 < apps.pilot.ligand_motifs: ATOM k: 26 Name: C22 < apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 27, type is aroC; 26, type is aroC < apps.pilot.ligand_motifs: atom_i: 28 < apps.pilot.ligand_motifs: atom_i to atom_j: 27 < apps.pilot.ligand_motifs: atom_j to atom_k: 26 < apps.pilot.ligand_motifs: ATOM k: 28 Name: C24 < apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 27, type is aroC; 28, type is aroC < apps.pilot.ligand_motifs: ATOM k: 31 Name: C29 < apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 27, type is aroC; 31, type is CH3 < apps.pilot.ligand_motifs: atom_i: 28 < apps.pilot.ligand_motifs: atom_i to atom_j: 27 < apps.pilot.ligand_motifs: atom_j to atom_k: 31 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 29 < apps.pilot.ligand_motifs: atom name is C27 < apps.pilot.ligand_motifs: ATOM j: 12 Name: N5 < apps.pilot.ligand_motifs: ATOM k: 10 Name: N4 < apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 12, type is Nhis; 10, type is Nhis < apps.pilot.ligand_motifs: atom_i: 29 < apps.pilot.ligand_motifs: atom_i to atom_j: 12 < apps.pilot.ligand_motifs: atom_j to atom_k: 10 < apps.pilot.ligand_motifs: ATOM k: 29 Name: C27 < apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 12, type is Nhis; 29, type is aroC < apps.pilot.ligand_motifs: ATOM j: 30 Name: C28 < apps.pilot.ligand_motifs: ATOM k: 14 Name: N6 < apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 30, type is aroC; 14, type is Nhis < apps.pilot.ligand_motifs: atom_i: 29 < apps.pilot.ligand_motifs: atom_i to atom_j: 30 < apps.pilot.ligand_motifs: atom_j to atom_k: 14 < apps.pilot.ligand_motifs: ATOM k: 29 Name: C27 < apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 30, type is aroC; 29, type is aroC < apps.pilot.ligand_motifs: in atom iterate block, atom num is 30 < apps.pilot.ligand_motifs: atom name is C28 < apps.pilot.ligand_motifs: ATOM j: 14 Name: N6 < apps.pilot.ligand_motifs: ATOM k: 10 Name: N4 < apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 14, type is Nhis; 10, type is Nhis < apps.pilot.ligand_motifs: atom_i: 30 < apps.pilot.ligand_motifs: atom_i to atom_j: 14 < apps.pilot.ligand_motifs: atom_j to atom_k: 10 < apps.pilot.ligand_motifs: ATOM k: 30 Name: C28 < apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 14, type is Nhis; 30, type is aroC < apps.pilot.ligand_motifs: ATOM j: 29 Name: C27 < apps.pilot.ligand_motifs: ATOM k: 12 Name: N5 < apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 29, type is aroC; 12, type is Nhis < apps.pilot.ligand_motifs: atom_i: 30 < apps.pilot.ligand_motifs: atom_i to atom_j: 29 < apps.pilot.ligand_motifs: atom_j to atom_k: 12 < apps.pilot.ligand_motifs: ATOM k: 30 Name: C28 < apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 29, type is aroC; 30, type is aroC < apps.pilot.ligand_motifs: in atom iterate block, atom num is 31 < apps.pilot.ligand_motifs: atom name is C29 < apps.pilot.ligand_motifs: ATOM j: 27 Name: C23 < apps.pilot.ligand_motifs: ATOM k: 26 Name: C22 < apps.pilot.ligand_motifs: Connected triplet is: 31, type is CH3; 27, type is aroC; 26, type is aroC < apps.pilot.ligand_motifs: atom_i: 31 < apps.pilot.ligand_motifs: atom_i to atom_j: 27 < apps.pilot.ligand_motifs: atom_j to atom_k: 26 < apps.pilot.ligand_motifs: ATOM k: 28 Name: C24 < apps.pilot.ligand_motifs: Connected triplet is: 31, type is CH3; 27, type is aroC; 28, type is aroC < apps.pilot.ligand_motifs: atom_i: 31 < apps.pilot.ligand_motifs: atom_i to atom_j: 27 < apps.pilot.ligand_motifs: atom_j to atom_k: 28 < apps.pilot.ligand_motifs: ATOM k: 31 Name: C29 < apps.pilot.ligand_motifs: Connected triplet is: 31, type is CH3; 27, type is aroC; 31, type is CH3 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 32 < apps.pilot.ligand_motifs: atom name is C30 < apps.pilot.ligand_motifs: ATOM j: 19 Name: C14 < apps.pilot.ligand_motifs: ATOM k: 8 Name: N3 < apps.pilot.ligand_motifs: Connected triplet is: 32, type is CH3; 19, type is CH1; 8, type is Nhis < apps.pilot.ligand_motifs: atom_i: 32 < apps.pilot.ligand_motifs: atom_i to atom_j: 19 < apps.pilot.ligand_motifs: atom_j to atom_k: 8 < apps.pilot.ligand_motifs: ATOM k: 20 Name: C15 < apps.pilot.ligand_motifs: Connected triplet is: 32, type is CH3; 19, type is CH1; 20, type is CH2 < apps.pilot.ligand_motifs: atom_i: 32 < apps.pilot.ligand_motifs: atom_i to atom_j: 19 < apps.pilot.ligand_motifs: atom_j to atom_k: 20 < apps.pilot.ligand_motifs: ATOM k: 32 Name: C30 < apps.pilot.ligand_motifs: Connected triplet is: 32, type is CH3; 19, type is CH1; 32, type is CH3 < apps.pilot.ligand_motifs: Total 3 atoms in pruned indices list is: 52 < apps.pilot.ligand_motifs: Total 3 atoms in unpruned indices list is: 104 < apps.pilot.ligand_motifs: Residue 62 passed energy cut with pack score: -1.95141, hbond score: 0, for a total score of: -1.95141 < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Top triplets contains 1 items. < apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1 < apps.pilot.ligand_motifs: Size of this_triplet: 3 928,971c73 < apps.pilot.ligand_motifs: 34: 13-15-16Writing THR111A_Z2001_Ligatoms_13_15_16_A_4s0v.pdb < apps.pilot.ligand_motifs: Residue 82 passed energy cut with pack score: -2.33653, hbond score: 0, for a total score of: -2.33653 < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Top triplets contains 1 items. < apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1 < apps.pilot.ligand_motifs: Size of this_triplet: 3 --- > protocols.motifs.IdentifyLigandMotifs: Writing THR111A_Z2001_Ligatoms_13_15_16_A_4s0v.pdb 976,1010c78 < apps.pilot.ligand_motifs: 11: 3-16-15Writing PRO131A_Z2001_Ligatoms_3_16_15_A_4s0v.pdb < apps.pilot.ligand_motifs: Residue 85 passed energy cut with pack score: -5.02867, hbond score: 0, for a total score of: -5.02867 < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Top triplets contains 1 items. < apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1 < apps.pilot.ligand_motifs: Size of this_triplet: 3 --- > protocols.motifs.IdentifyLigandMotifs: Writing PRO131A_Z2001_Ligatoms_3_16_15_A_4s0v.pdb 1015,1065c83 < apps.pilot.ligand_motifs: 49: 25-26-27Writing GLN134A_Z2001_Ligatoms_25_26_27_A_4s0v.pdb < apps.pilot.ligand_motifs: Residue 86 passed energy cut with pack score: -1.00987, hbond score: 0, for a total score of: -1.00987 < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Top triplets contains 1 items. < apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1 < apps.pilot.ligand_motifs: Size of this_triplet: 3 --- > protocols.motifs.IdentifyLigandMotifs: Writing GLN134A_Z2001_Ligatoms_25_26_27_A_4s0v.pdb 1070,1120c88 < apps.pilot.ligand_motifs: 37: 17-2-21Writing THR135A_Z2001_Ligatoms_17_2_21_A_4s0v.pdb < apps.pilot.ligand_motifs: Residue 134 passed energy cut with pack score: -1.96699, hbond score: 0, for a total score of: -1.96699 < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Top triplets contains 1 items. < apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1 < apps.pilot.ligand_motifs: Size of this_triplet: 3 --- > protocols.motifs.IdentifyLigandMotifs: Writing THR135A_Z2001_Ligatoms_17_2_21_A_4s0v.pdb 1125,1178c93 < apps.pilot.ligand_motifs: 42: 20-19-32Writing GLN187A_Z2001_Ligatoms_20_19_32_A_4s0v.pdb < apps.pilot.ligand_motifs: Residue 169 passed energy cut with pack score: -1.6689, hbond score: 0, for a total score of: -1.6689 < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Top triplets contains 1 items. < apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1 < apps.pilot.ligand_motifs: Size of this_triplet: 3 --- > protocols.motifs.IdentifyLigandMotifs: Writing GLN187A_Z2001_Ligatoms_20_19_32_A_4s0v.pdb 1183,1231c98 < apps.pilot.ligand_motifs: 36: 14-30-29Writing PHE227A_Z2001_Ligatoms_14_30_29_A_4s0v.pdb < apps.pilot.ligand_motifs: Residue 419 passed energy cut with pack score: -3.13989, hbond score: 0, for a total score of: -3.13989 < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Top triplets contains 1 items. < apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1 < apps.pilot.ligand_motifs: Size of this_triplet: 3 --- > protocols.motifs.IdentifyLigandMotifs: Writing PHE227A_Z2001_Ligatoms_14_30_29_A_4s0v.pdb 1236,1275c103 < apps.pilot.ligand_motifs: 36: 14-30-29Writing ILE320A_Z2001_Ligatoms_14_30_29_A_4s0v.pdb < apps.pilot.ligand_motifs: Residue 423 passed energy cut with pack score: -2.42951, hbond score: -0.70592, for a total score of: -3.13543 < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Top triplets contains 1 items. < apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1 < apps.pilot.ligand_motifs: Size of this_triplet: 3 --- > protocols.motifs.IdentifyLigandMotifs: Writing ILE320A_Z2001_Ligatoms_14_30_29_A_4s0v.pdb 1280,1329c108 < apps.pilot.ligand_motifs: 17: 6-22-23Writing ASN324A_Z2001_Ligatoms_6_22_23_A_4s0v.pdb < apps.pilot.ligand_motifs: Residue 447 passed energy cut with pack score: -2.65175, hbond score: 0, for a total score of: -2.65175 < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Top triplets contains 1 items. < apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1 < apps.pilot.ligand_motifs: Size of this_triplet: 3 --- > protocols.motifs.IdentifyLigandMotifs: Writing ASN324A_Z2001_Ligatoms_6_22_23_A_4s0v.pdb 1334,1386c113 < apps.pilot.ligand_motifs: 52: 28-27-31Writing HIS350A_Z2001_Ligatoms_28_27_31_A_4s0v.pdb < apps.pilot.ligand_motifs: Residue 450 passed energy cut with pack score: -1.31505, hbond score: 0, for a total score of: -1.31505 < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Top triplets contains 1 items. < apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1 < apps.pilot.ligand_motifs: Size of this_triplet: 3 --- > protocols.motifs.IdentifyLigandMotifs: Writing HIS350A_Z2001_Ligatoms_28_27_31_A_4s0v.pdb 1391,1445c118 < apps.pilot.ligand_motifs: 49: 25-26-27Writing VAL353A_Z2001_Ligatoms_25_26_27_A_4s0v.pdb < apps.pilot.ligand_motifs: Residue 451 passed energy cut with pack score: -1.379, hbond score: 0, for a total score of: -1.379 < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Top triplets contains 1 items. < apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1 < apps.pilot.ligand_motifs: Size of this_triplet: 3 --- > protocols.motifs.IdentifyLigandMotifs: Writing VAL353A_Z2001_Ligatoms_25_26_27_A_4s0v.pdb 1450,1866c123 < apps.pilot.ligand_motifs: 52: 28-27-31Writing TYR354A_Z2001_Ligatoms_28_27_31_A_4s0v.pdb < apps.pilot.ligand_motifs: Motif index contains: 1-2-17 < apps.pilot.ligand_motifs: Motif index contains: 1-2-21 < apps.pilot.ligand_motifs: Motif index contains: 1-3-16 < apps.pilot.ligand_motifs: Motif index contains: 1-5-7 < apps.pilot.ligand_motifs: Motif index contains: 2-1-3 < apps.pilot.ligand_motifs: Motif index contains: 2-1-5 < apps.pilot.ligand_motifs: Motif index contains: 2-17-18 < apps.pilot.ligand_motifs: Motif index contains: 2-21-20 < apps.pilot.ligand_motifs: Motif index contains: 3-1-5 < apps.pilot.ligand_motifs: Motif index contains: 3-16-7 < apps.pilot.ligand_motifs: Motif index contains: 3-16-15 < apps.pilot.ligand_motifs: Motif index contains: 4-11-9 < apps.pilot.ligand_motifs: Motif index contains: 4-11-13 < apps.pilot.ligand_motifs: Motif index contains: 5-7-9 < apps.pilot.ligand_motifs: Motif index contains: 5-7-16 < apps.pilot.ligand_motifs: Motif index contains: 6-22-8 < apps.pilot.ligand_motifs: Motif index contains: 6-22-23 < apps.pilot.ligand_motifs: Motif index contains: 7-9-11 < apps.pilot.ligand_motifs: Motif index contains: 7-16-15 < apps.pilot.ligand_motifs: Motif index contains: 8-18-17 < apps.pilot.ligand_motifs: Motif index contains: 8-19-20 < apps.pilot.ligand_motifs: Motif index contains: 8-19-32 < apps.pilot.ligand_motifs: Motif index contains: 8-22-23 < apps.pilot.ligand_motifs: Motif index contains: 9-7-16 < apps.pilot.ligand_motifs: Motif index contains: 9-11-13 < apps.pilot.ligand_motifs: Motif index contains: 10-12-29 < apps.pilot.ligand_motifs: Motif index contains: 10-14-30 < apps.pilot.ligand_motifs: Motif index contains: 10-24-23 < apps.pilot.ligand_motifs: Motif index contains: 10-24-25 < apps.pilot.ligand_motifs: Motif index contains: 11-13-15 < apps.pilot.ligand_motifs: Motif index contains: 12-10-14 < apps.pilot.ligand_motifs: Motif index contains: 12-10-24 < apps.pilot.ligand_motifs: Motif index contains: 12-29-30 < apps.pilot.ligand_motifs: Motif index contains: 13-15-16 < apps.pilot.ligand_motifs: Motif index contains: 14-10-24 < apps.pilot.ligand_motifs: Motif index contains: 14-30-29 < apps.pilot.ligand_motifs: Motif index contains: 17-2-21 < apps.pilot.ligand_motifs: Motif index contains: 18-8-19 < apps.pilot.ligand_motifs: Motif index contains: 18-8-22 < apps.pilot.ligand_motifs: Motif index contains: 19-8-22 < apps.pilot.ligand_motifs: Motif index contains: 19-20-21 < apps.pilot.ligand_motifs: Motif index contains: 20-19-32 < apps.pilot.ligand_motifs: Motif index contains: 22-23-24 < apps.pilot.ligand_motifs: Motif index contains: 22-23-28 < apps.pilot.ligand_motifs: Motif index contains: 23-24-25 < apps.pilot.ligand_motifs: Motif index contains: 23-28-27 < apps.pilot.ligand_motifs: Motif index contains: 24-23-28 < apps.pilot.ligand_motifs: Motif index contains: 24-25-26 < apps.pilot.ligand_motifs: Motif index contains: 25-26-27 < apps.pilot.ligand_motifs: Motif index contains: 26-27-28 < apps.pilot.ligand_motifs: Motif index contains: 26-27-31 < apps.pilot.ligand_motifs: Motif index contains: 28-27-31 < apps.pilot.ligand_motifs: in ligand splitter block, found my ligand, lig_pos is 480 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 1 < apps.pilot.ligand_motifs: atom name is C1 < apps.pilot.ligand_motifs: ATOM j: 2 Name: O1 < apps.pilot.ligand_motifs: ATOM k: 1 Name: C1 < apps.pilot.ligand_motifs: Connected triplet is: 1, type is COO; 2, type is OOC; 1, type is COO < apps.pilot.ligand_motifs: ATOM j: 3 Name: O2 < apps.pilot.ligand_motifs: ATOM k: 1 Name: C1 < apps.pilot.ligand_motifs: Connected triplet is: 1, type is COO; 3, type is OH; 1, type is COO < apps.pilot.ligand_motifs: ATOM j: 4 Name: C2 < apps.pilot.ligand_motifs: ATOM k: 1 Name: C1 < apps.pilot.ligand_motifs: Connected triplet is: 1, type is COO; 4, type is CH2; 1, type is COO < apps.pilot.ligand_motifs: ATOM k: 5 Name: C3 < apps.pilot.ligand_motifs: Connected triplet is: 1, type is COO; 4, type is CH2; 5, type is CH2 < apps.pilot.ligand_motifs: atom_i: 1 < apps.pilot.ligand_motifs: atom_i to atom_j: 4 < apps.pilot.ligand_motifs: atom_j to atom_k: 5 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 2 < apps.pilot.ligand_motifs: atom name is O1 < apps.pilot.ligand_motifs: ATOM j: 1 Name: C1 < apps.pilot.ligand_motifs: ATOM k: 2 Name: O1 < apps.pilot.ligand_motifs: Connected triplet is: 2, type is OOC; 1, type is COO; 2, type is OOC < apps.pilot.ligand_motifs: ATOM k: 3 Name: O2 < apps.pilot.ligand_motifs: Connected triplet is: 2, type is OOC; 1, type is COO; 3, type is OH < apps.pilot.ligand_motifs: atom_i: 2 < apps.pilot.ligand_motifs: atom_i to atom_j: 1 < apps.pilot.ligand_motifs: atom_j to atom_k: 3 < apps.pilot.ligand_motifs: ATOM k: 4 Name: C2 < apps.pilot.ligand_motifs: Connected triplet is: 2, type is OOC; 1, type is COO; 4, type is CH2 < apps.pilot.ligand_motifs: atom_i: 2 < apps.pilot.ligand_motifs: atom_i to atom_j: 1 < apps.pilot.ligand_motifs: atom_j to atom_k: 4 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 3 < apps.pilot.ligand_motifs: atom name is O2 < apps.pilot.ligand_motifs: ATOM j: 1 Name: C1 < apps.pilot.ligand_motifs: ATOM k: 2 Name: O1 < apps.pilot.ligand_motifs: Connected triplet is: 3, type is OH; 1, type is COO; 2, type is OOC < apps.pilot.ligand_motifs: atom_i: 3 < apps.pilot.ligand_motifs: atom_i to atom_j: 1 < apps.pilot.ligand_motifs: atom_j to atom_k: 2 < apps.pilot.ligand_motifs: ATOM k: 3 Name: O2 < apps.pilot.ligand_motifs: Connected triplet is: 3, type is OH; 1, type is COO; 3, type is OH < apps.pilot.ligand_motifs: ATOM k: 4 Name: C2 < apps.pilot.ligand_motifs: Connected triplet is: 3, type is OH; 1, type is COO; 4, type is CH2 < apps.pilot.ligand_motifs: atom_i: 3 < apps.pilot.ligand_motifs: atom_i to atom_j: 1 < apps.pilot.ligand_motifs: atom_j to atom_k: 4 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 4 < apps.pilot.ligand_motifs: atom name is C2 < apps.pilot.ligand_motifs: ATOM j: 1 Name: C1 < apps.pilot.ligand_motifs: ATOM k: 2 Name: O1 < apps.pilot.ligand_motifs: Connected triplet is: 4, type is CH2; 1, type is COO; 2, type is OOC < apps.pilot.ligand_motifs: atom_i: 4 < apps.pilot.ligand_motifs: atom_i to atom_j: 1 < apps.pilot.ligand_motifs: atom_j to atom_k: 2 < apps.pilot.ligand_motifs: ATOM k: 3 Name: O2 < apps.pilot.ligand_motifs: Connected triplet is: 4, type is CH2; 1, type is COO; 3, type is OH < apps.pilot.ligand_motifs: atom_i: 4 < apps.pilot.ligand_motifs: atom_i to atom_j: 1 < apps.pilot.ligand_motifs: atom_j to atom_k: 3 < apps.pilot.ligand_motifs: ATOM k: 4 Name: C2 < apps.pilot.ligand_motifs: Connected triplet is: 4, type is CH2; 1, type is COO; 4, type is CH2 < apps.pilot.ligand_motifs: ATOM j: 5 Name: C3 < apps.pilot.ligand_motifs: ATOM k: 4 Name: C2 < apps.pilot.ligand_motifs: Connected triplet is: 4, type is CH2; 5, type is CH2; 4, type is CH2 < apps.pilot.ligand_motifs: ATOM k: 6 Name: C4 < apps.pilot.ligand_motifs: Connected triplet is: 4, type is CH2; 5, type is CH2; 6, type is CH2 < apps.pilot.ligand_motifs: atom_i: 4 < apps.pilot.ligand_motifs: atom_i to atom_j: 5 < apps.pilot.ligand_motifs: atom_j to atom_k: 6 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 5 < apps.pilot.ligand_motifs: atom name is C3 < apps.pilot.ligand_motifs: ATOM j: 4 Name: C2 < apps.pilot.ligand_motifs: ATOM k: 1 Name: C1 < apps.pilot.ligand_motifs: Connected triplet is: 5, type is CH2; 4, type is CH2; 1, type is COO < apps.pilot.ligand_motifs: atom_i: 5 < apps.pilot.ligand_motifs: atom_i to atom_j: 4 < apps.pilot.ligand_motifs: atom_j to atom_k: 1 < apps.pilot.ligand_motifs: ATOM k: 5 Name: C3 < apps.pilot.ligand_motifs: Connected triplet is: 5, type is CH2; 4, type is CH2; 5, type is CH2 < apps.pilot.ligand_motifs: ATOM j: 6 Name: C4 < apps.pilot.ligand_motifs: ATOM k: 5 Name: C3 < apps.pilot.ligand_motifs: Connected triplet is: 5, type is CH2; 6, type is CH2; 5, type is CH2 < apps.pilot.ligand_motifs: ATOM k: 7 Name: C5 < apps.pilot.ligand_motifs: Connected triplet is: 5, type is CH2; 6, type is CH2; 7, type is CH2 < apps.pilot.ligand_motifs: atom_i: 5 < apps.pilot.ligand_motifs: atom_i to atom_j: 6 < apps.pilot.ligand_motifs: atom_j to atom_k: 7 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 6 < apps.pilot.ligand_motifs: atom name is C4 < apps.pilot.ligand_motifs: ATOM j: 5 Name: C3 < apps.pilot.ligand_motifs: ATOM k: 4 Name: C2 < apps.pilot.ligand_motifs: Connected triplet is: 6, type is CH2; 5, type is CH2; 4, type is CH2 < apps.pilot.ligand_motifs: atom_i: 6 < apps.pilot.ligand_motifs: atom_i to atom_j: 5 < apps.pilot.ligand_motifs: atom_j to atom_k: 4 < apps.pilot.ligand_motifs: ATOM k: 6 Name: C4 < apps.pilot.ligand_motifs: Connected triplet is: 6, type is CH2; 5, type is CH2; 6, type is CH2 < apps.pilot.ligand_motifs: ATOM j: 7 Name: C5 < apps.pilot.ligand_motifs: ATOM k: 6 Name: C4 < apps.pilot.ligand_motifs: Connected triplet is: 6, type is CH2; 7, type is CH2; 6, type is CH2 < apps.pilot.ligand_motifs: ATOM k: 8 Name: C6 < apps.pilot.ligand_motifs: Connected triplet is: 6, type is CH2; 7, type is CH2; 8, type is CH2 < apps.pilot.ligand_motifs: atom_i: 6 < apps.pilot.ligand_motifs: atom_i to atom_j: 7 < apps.pilot.ligand_motifs: atom_j to atom_k: 8 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 7 < apps.pilot.ligand_motifs: atom name is C5 < apps.pilot.ligand_motifs: ATOM j: 6 Name: C4 < apps.pilot.ligand_motifs: ATOM k: 5 Name: C3 < apps.pilot.ligand_motifs: Connected triplet is: 7, type is CH2; 6, type is CH2; 5, type is CH2 < apps.pilot.ligand_motifs: atom_i: 7 < apps.pilot.ligand_motifs: atom_i to atom_j: 6 < apps.pilot.ligand_motifs: atom_j to atom_k: 5 < apps.pilot.ligand_motifs: ATOM k: 7 Name: C5 < apps.pilot.ligand_motifs: Connected triplet is: 7, type is CH2; 6, type is CH2; 7, type is CH2 < apps.pilot.ligand_motifs: ATOM j: 8 Name: C6 < apps.pilot.ligand_motifs: ATOM k: 7 Name: C5 < apps.pilot.ligand_motifs: Connected triplet is: 7, type is CH2; 8, type is CH2; 7, type is CH2 < apps.pilot.ligand_motifs: ATOM k: 9 Name: C7 < apps.pilot.ligand_motifs: Connected triplet is: 7, type is CH2; 8, type is CH2; 9, type is CH2 < apps.pilot.ligand_motifs: atom_i: 7 < apps.pilot.ligand_motifs: atom_i to atom_j: 8 < apps.pilot.ligand_motifs: atom_j to atom_k: 9 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 8 < apps.pilot.ligand_motifs: atom name is C6 < apps.pilot.ligand_motifs: ATOM j: 7 Name: C5 < apps.pilot.ligand_motifs: ATOM k: 6 Name: C4 < apps.pilot.ligand_motifs: Connected triplet is: 8, type is CH2; 7, type is CH2; 6, type is CH2 < apps.pilot.ligand_motifs: atom_i: 8 < apps.pilot.ligand_motifs: atom_i to atom_j: 7 < apps.pilot.ligand_motifs: atom_j to atom_k: 6 < apps.pilot.ligand_motifs: ATOM k: 8 Name: C6 < apps.pilot.ligand_motifs: Connected triplet is: 8, type is CH2; 7, type is CH2; 8, type is CH2 < apps.pilot.ligand_motifs: ATOM j: 9 Name: C7 < apps.pilot.ligand_motifs: ATOM k: 8 Name: C6 < apps.pilot.ligand_motifs: Connected triplet is: 8, type is CH2; 9, type is CH2; 8, type is CH2 < apps.pilot.ligand_motifs: ATOM k: 10 Name: C8 < apps.pilot.ligand_motifs: Connected triplet is: 8, type is CH2; 9, type is CH2; 10, type is CH2 < apps.pilot.ligand_motifs: atom_i: 8 < apps.pilot.ligand_motifs: atom_i to atom_j: 9 < apps.pilot.ligand_motifs: atom_j to atom_k: 10 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 9 < apps.pilot.ligand_motifs: atom name is C7 < apps.pilot.ligand_motifs: ATOM j: 8 Name: C6 < apps.pilot.ligand_motifs: ATOM k: 7 Name: C5 < apps.pilot.ligand_motifs: Connected triplet is: 9, type is CH2; 8, type is CH2; 7, type is CH2 < apps.pilot.ligand_motifs: atom_i: 9 < apps.pilot.ligand_motifs: atom_i to atom_j: 8 < apps.pilot.ligand_motifs: atom_j to atom_k: 7 < apps.pilot.ligand_motifs: ATOM k: 9 Name: C7 < apps.pilot.ligand_motifs: Connected triplet is: 9, type is CH2; 8, type is CH2; 9, type is CH2 < apps.pilot.ligand_motifs: ATOM j: 10 Name: C8 < apps.pilot.ligand_motifs: ATOM k: 9 Name: C7 < apps.pilot.ligand_motifs: Connected triplet is: 9, type is CH2; 10, type is CH2; 9, type is CH2 < apps.pilot.ligand_motifs: ATOM k: 11 Name: C9 < apps.pilot.ligand_motifs: Connected triplet is: 9, type is CH2; 10, type is CH2; 11, type is aroC < apps.pilot.ligand_motifs: atom_i: 9 < apps.pilot.ligand_motifs: atom_i to atom_j: 10 < apps.pilot.ligand_motifs: atom_j to atom_k: 11 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 10 < apps.pilot.ligand_motifs: atom name is C8 < apps.pilot.ligand_motifs: ATOM j: 9 Name: C7 < apps.pilot.ligand_motifs: ATOM k: 8 Name: C6 < apps.pilot.ligand_motifs: Connected triplet is: 10, type is CH2; 9, type is CH2; 8, type is CH2 < apps.pilot.ligand_motifs: atom_i: 10 < apps.pilot.ligand_motifs: atom_i to atom_j: 9 < apps.pilot.ligand_motifs: atom_j to atom_k: 8 < apps.pilot.ligand_motifs: ATOM k: 10 Name: C8 < apps.pilot.ligand_motifs: Connected triplet is: 10, type is CH2; 9, type is CH2; 10, type is CH2 < apps.pilot.ligand_motifs: ATOM j: 11 Name: C9 < apps.pilot.ligand_motifs: ATOM k: 10 Name: C8 < apps.pilot.ligand_motifs: Connected triplet is: 10, type is CH2; 11, type is aroC; 10, type is CH2 < apps.pilot.ligand_motifs: ATOM k: 12 Name: C10 < apps.pilot.ligand_motifs: Connected triplet is: 10, type is CH2; 11, type is aroC; 12, type is aroC < apps.pilot.ligand_motifs: atom_i: 10 < apps.pilot.ligand_motifs: atom_i to atom_j: 11 < apps.pilot.ligand_motifs: atom_j to atom_k: 12 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 11 < apps.pilot.ligand_motifs: atom name is C9 < apps.pilot.ligand_motifs: ATOM j: 10 Name: C8 < apps.pilot.ligand_motifs: ATOM k: 9 Name: C7 < apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 10, type is CH2; 9, type is CH2 < apps.pilot.ligand_motifs: atom_i: 11 < apps.pilot.ligand_motifs: atom_i to atom_j: 10 < apps.pilot.ligand_motifs: atom_j to atom_k: 9 < apps.pilot.ligand_motifs: ATOM k: 11 Name: C9 < apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 10, type is CH2; 11, type is aroC < apps.pilot.ligand_motifs: ATOM j: 12 Name: C10 < apps.pilot.ligand_motifs: ATOM k: 11 Name: C9 < apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 12, type is aroC; 11, type is aroC < apps.pilot.ligand_motifs: ATOM k: 13 Name: C11 < apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 12, type is aroC; 13, type is CH2 < apps.pilot.ligand_motifs: atom_i: 11 < apps.pilot.ligand_motifs: atom_i to atom_j: 12 < apps.pilot.ligand_motifs: atom_j to atom_k: 13 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 12 < apps.pilot.ligand_motifs: atom name is C10 < apps.pilot.ligand_motifs: ATOM j: 11 Name: C9 < apps.pilot.ligand_motifs: ATOM k: 10 Name: C8 < apps.pilot.ligand_motifs: Connected triplet is: 12, type is aroC; 11, type is aroC; 10, type is CH2 < apps.pilot.ligand_motifs: atom_i: 12 < apps.pilot.ligand_motifs: atom_i to atom_j: 11 < apps.pilot.ligand_motifs: atom_j to atom_k: 10 < apps.pilot.ligand_motifs: ATOM k: 12 Name: C10 < apps.pilot.ligand_motifs: Connected triplet is: 12, type is aroC; 11, type is aroC; 12, type is aroC < apps.pilot.ligand_motifs: ATOM j: 13 Name: C11 < apps.pilot.ligand_motifs: ATOM k: 12 Name: C10 < apps.pilot.ligand_motifs: Connected triplet is: 12, type is aroC; 13, type is CH2; 12, type is aroC < apps.pilot.ligand_motifs: ATOM k: 14 Name: C12 < apps.pilot.ligand_motifs: Connected triplet is: 12, type is aroC; 13, type is CH2; 14, type is CH2 < apps.pilot.ligand_motifs: atom_i: 12 < apps.pilot.ligand_motifs: atom_i to atom_j: 13 < apps.pilot.ligand_motifs: atom_j to atom_k: 14 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 13 < apps.pilot.ligand_motifs: atom name is C11 < apps.pilot.ligand_motifs: ATOM j: 12 Name: C10 < apps.pilot.ligand_motifs: ATOM k: 11 Name: C9 < apps.pilot.ligand_motifs: Connected triplet is: 13, type is CH2; 12, type is aroC; 11, type is aroC < apps.pilot.ligand_motifs: atom_i: 13 < apps.pilot.ligand_motifs: atom_i to atom_j: 12 < apps.pilot.ligand_motifs: atom_j to atom_k: 11 < apps.pilot.ligand_motifs: ATOM k: 13 Name: C11 < apps.pilot.ligand_motifs: Connected triplet is: 13, type is CH2; 12, type is aroC; 13, type is CH2 < apps.pilot.ligand_motifs: ATOM j: 14 Name: C12 < apps.pilot.ligand_motifs: ATOM k: 13 Name: C11 < apps.pilot.ligand_motifs: Connected triplet is: 13, type is CH2; 14, type is CH2; 13, type is CH2 < apps.pilot.ligand_motifs: ATOM k: 15 Name: C13 < apps.pilot.ligand_motifs: Connected triplet is: 13, type is CH2; 14, type is CH2; 15, type is CH2 < apps.pilot.ligand_motifs: atom_i: 13 < apps.pilot.ligand_motifs: atom_i to atom_j: 14 < apps.pilot.ligand_motifs: atom_j to atom_k: 15 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 14 < apps.pilot.ligand_motifs: atom name is C12 < apps.pilot.ligand_motifs: ATOM j: 13 Name: C11 < apps.pilot.ligand_motifs: ATOM k: 12 Name: C10 < apps.pilot.ligand_motifs: Connected triplet is: 14, type is CH2; 13, type is CH2; 12, type is aroC < apps.pilot.ligand_motifs: atom_i: 14 < apps.pilot.ligand_motifs: atom_i to atom_j: 13 < apps.pilot.ligand_motifs: atom_j to atom_k: 12 < apps.pilot.ligand_motifs: ATOM k: 14 Name: C12 < apps.pilot.ligand_motifs: Connected triplet is: 14, type is CH2; 13, type is CH2; 14, type is CH2 < apps.pilot.ligand_motifs: ATOM j: 15 Name: C13 < apps.pilot.ligand_motifs: ATOM k: 14 Name: C12 < apps.pilot.ligand_motifs: Connected triplet is: 14, type is CH2; 15, type is CH2; 14, type is CH2 < apps.pilot.ligand_motifs: ATOM k: 16 Name: C14 < apps.pilot.ligand_motifs: Connected triplet is: 14, type is CH2; 15, type is CH2; 16, type is CH2 < apps.pilot.ligand_motifs: atom_i: 14 < apps.pilot.ligand_motifs: atom_i to atom_j: 15 < apps.pilot.ligand_motifs: atom_j to atom_k: 16 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 15 < apps.pilot.ligand_motifs: atom name is C13 < apps.pilot.ligand_motifs: ATOM j: 14 Name: C12 < apps.pilot.ligand_motifs: ATOM k: 13 Name: C11 < apps.pilot.ligand_motifs: Connected triplet is: 15, type is CH2; 14, type is CH2; 13, type is CH2 < apps.pilot.ligand_motifs: atom_i: 15 < apps.pilot.ligand_motifs: atom_i to atom_j: 14 < apps.pilot.ligand_motifs: atom_j to atom_k: 13 < apps.pilot.ligand_motifs: ATOM k: 15 Name: C13 < apps.pilot.ligand_motifs: Connected triplet is: 15, type is CH2; 14, type is CH2; 15, type is CH2 < apps.pilot.ligand_motifs: ATOM j: 16 Name: C14 < apps.pilot.ligand_motifs: ATOM k: 15 Name: C13 < apps.pilot.ligand_motifs: Connected triplet is: 15, type is CH2; 16, type is CH2; 15, type is CH2 < apps.pilot.ligand_motifs: ATOM k: 17 Name: C15 < apps.pilot.ligand_motifs: Connected triplet is: 15, type is CH2; 16, type is CH2; 17, type is CH2 < apps.pilot.ligand_motifs: atom_i: 15 < apps.pilot.ligand_motifs: atom_i to atom_j: 16 < apps.pilot.ligand_motifs: atom_j to atom_k: 17 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 16 < apps.pilot.ligand_motifs: atom name is C14 < apps.pilot.ligand_motifs: ATOM j: 15 Name: C13 < apps.pilot.ligand_motifs: ATOM k: 14 Name: C12 < apps.pilot.ligand_motifs: Connected triplet is: 16, type is CH2; 15, type is CH2; 14, type is CH2 < apps.pilot.ligand_motifs: atom_i: 16 < apps.pilot.ligand_motifs: atom_i to atom_j: 15 < apps.pilot.ligand_motifs: atom_j to atom_k: 14 < apps.pilot.ligand_motifs: ATOM k: 16 Name: C14 < apps.pilot.ligand_motifs: Connected triplet is: 16, type is CH2; 15, type is CH2; 16, type is CH2 < apps.pilot.ligand_motifs: ATOM j: 17 Name: C15 < apps.pilot.ligand_motifs: ATOM k: 16 Name: C14 < apps.pilot.ligand_motifs: Connected triplet is: 16, type is CH2; 17, type is CH2; 16, type is CH2 < apps.pilot.ligand_motifs: ATOM k: 18 Name: C16 < apps.pilot.ligand_motifs: Connected triplet is: 16, type is CH2; 17, type is CH2; 18, type is CH2 < apps.pilot.ligand_motifs: atom_i: 16 < apps.pilot.ligand_motifs: atom_i to atom_j: 17 < apps.pilot.ligand_motifs: atom_j to atom_k: 18 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 17 < apps.pilot.ligand_motifs: atom name is C15 < apps.pilot.ligand_motifs: ATOM j: 16 Name: C14 < apps.pilot.ligand_motifs: ATOM k: 15 Name: C13 < apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 16, type is CH2; 15, type is CH2 < apps.pilot.ligand_motifs: atom_i: 17 < apps.pilot.ligand_motifs: atom_i to atom_j: 16 < apps.pilot.ligand_motifs: atom_j to atom_k: 15 < apps.pilot.ligand_motifs: ATOM k: 17 Name: C15 < apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 16, type is CH2; 17, type is CH2 < apps.pilot.ligand_motifs: ATOM j: 18 Name: C16 < apps.pilot.ligand_motifs: ATOM k: 17 Name: C15 < apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 18, type is CH2; 17, type is CH2 < apps.pilot.ligand_motifs: ATOM k: 19 Name: C17 < apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 18, type is CH2; 19, type is CH2 < apps.pilot.ligand_motifs: atom_i: 17 < apps.pilot.ligand_motifs: atom_i to atom_j: 18 < apps.pilot.ligand_motifs: atom_j to atom_k: 19 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 18 < apps.pilot.ligand_motifs: atom name is C16 < apps.pilot.ligand_motifs: ATOM j: 17 Name: C15 < apps.pilot.ligand_motifs: ATOM k: 16 Name: C14 < apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 17, type is CH2; 16, type is CH2 < apps.pilot.ligand_motifs: atom_i: 18 < apps.pilot.ligand_motifs: atom_i to atom_j: 17 < apps.pilot.ligand_motifs: atom_j to atom_k: 16 < apps.pilot.ligand_motifs: ATOM k: 18 Name: C16 < apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 17, type is CH2; 18, type is CH2 < apps.pilot.ligand_motifs: ATOM j: 19 Name: C17 < apps.pilot.ligand_motifs: ATOM k: 18 Name: C16 < apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 19, type is CH2; 18, type is CH2 < apps.pilot.ligand_motifs: ATOM k: 20 Name: C18 < apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 19, type is CH2; 20, type is CH3 < apps.pilot.ligand_motifs: atom_i: 18 < apps.pilot.ligand_motifs: atom_i to atom_j: 19 < apps.pilot.ligand_motifs: atom_j to atom_k: 20 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 19 < apps.pilot.ligand_motifs: atom name is C17 < apps.pilot.ligand_motifs: ATOM j: 18 Name: C16 < apps.pilot.ligand_motifs: ATOM k: 17 Name: C15 < apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH2; 18, type is CH2; 17, type is CH2 < apps.pilot.ligand_motifs: atom_i: 19 < apps.pilot.ligand_motifs: atom_i to atom_j: 18 < apps.pilot.ligand_motifs: atom_j to atom_k: 17 < apps.pilot.ligand_motifs: ATOM k: 19 Name: C17 < apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH2; 18, type is CH2; 19, type is CH2 < apps.pilot.ligand_motifs: ATOM j: 20 Name: C18 < apps.pilot.ligand_motifs: ATOM k: 19 Name: C17 < apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH2; 20, type is CH3; 19, type is CH2 < apps.pilot.ligand_motifs: in atom iterate block, atom num is 20 < apps.pilot.ligand_motifs: atom name is C18 < apps.pilot.ligand_motifs: ATOM j: 19 Name: C17 < apps.pilot.ligand_motifs: ATOM k: 18 Name: C16 < apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH3; 19, type is CH2; 18, type is CH2 < apps.pilot.ligand_motifs: atom_i: 20 < apps.pilot.ligand_motifs: atom_i to atom_j: 19 < apps.pilot.ligand_motifs: atom_j to atom_k: 18 < apps.pilot.ligand_motifs: ATOM k: 20 Name: C18 < apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH3; 19, type is CH2; 20, type is CH3 < apps.pilot.ligand_motifs: Total 3 atoms in pruned indices list is: 19 < apps.pilot.ligand_motifs: Total 3 atoms in unpruned indices list is: 38 < apps.pilot.ligand_motifs: Residue 14 passed energy cut with pack score: -6.06527, hbond score: 0, for a total score of: -6.06527 < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms < apps.pilot.ligand_motifs: Top triplets contains 1 items. < apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1 < apps.pilot.ligand_motifs: Size of this_triplet: 3 --- > protocols.motifs.IdentifyLigandMotifs: Writing TYR354A_Z2001_Ligatoms_28_27_31_A_4s0v.pdb 1871,1890c128 < apps.pilot.ligand_motifs: 19: 18-19-20Writing ILE63A_Z2002_Ligatoms_18_19_20_A_4s0v.pdb < apps.pilot.ligand_motifs: Motif index contains: 1-4-5 < apps.pilot.ligand_motifs: Motif index contains: 2-1-3 < apps.pilot.ligand_motifs: Motif index contains: 2-1-4 < apps.pilot.ligand_motifs: Motif index contains: 3-1-4 < apps.pilot.ligand_motifs: Motif index contains: 4-5-6 < apps.pilot.ligand_motifs: Motif index contains: 5-6-7 < apps.pilot.ligand_motifs: Motif index contains: 6-7-8 < apps.pilot.ligand_motifs: Motif index contains: 7-8-9 < apps.pilot.ligand_motifs: Motif index contains: 8-9-10 < apps.pilot.ligand_motifs: Motif index contains: 9-10-11 < apps.pilot.ligand_motifs: Motif index contains: 10-11-12 < apps.pilot.ligand_motifs: Motif index contains: 11-12-13 < apps.pilot.ligand_motifs: Motif index contains: 12-13-14 < apps.pilot.ligand_motifs: Motif index contains: 13-14-15 < apps.pilot.ligand_motifs: Motif index contains: 14-15-16 < apps.pilot.ligand_motifs: Motif index contains: 15-16-17 < apps.pilot.ligand_motifs: Motif index contains: 16-17-18 < apps.pilot.ligand_motifs: Motif index contains: 17-18-19 < apps.pilot.ligand_motifs: Motif index contains: 18-19-20 --- > protocols.motifs.IdentifyLigandMotifs: Writing ILE63A_Z2002_Ligatoms_18_19_20_A_4s0v.pdb
Brief Diff: diff: /home/benchmark/working_dir/main:62149/real_motif_analysis: No such file or directory Compare(...): Marking as "Script failed" due to presense of .test_did_not_run.log or .test_got_timeout_kill.log file!
Brief Diff: diff: /home/benchmark/working_dir/main:62149/remove_duplicate_motifs: No such file or directory Compare(...): Marking as "Script failed" due to presense of .test_did_not_run.log or .test_got_timeout_kill.log file!
AddConstraintsToCurrentConformationMover AlignPDBInfoToSequences AlterSpecDisruption AnchorFinder AnchoredDesign AnchoredPDBCreator BFactorSelector BuildPeptide CCD_loop_closure CCS_PARCS ConsensusLoopDesign ContactMolecularSurface DARC_electrostatics DARC_make_ray_files DARC_sampling_on_the_fly DARC_shapeonly DNA_methylation DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FavorSequenceProfileMover FilterReportAsPoseExtraScoresMover FlipChirality FloppyTail HDXEnergy HOW_TO_MAKE_TESTS HelixBendFilter InterfaceAnalyzer InterfaceAnalyzer_allscores InterfaceAnalyzer_bothpack InterfaceAnalyzer_ligand InterfaceAnalyzer_metrics InterfaceAnalyzer_prepack InterfaceAnalyzer_resfile InterfaceAnalyzer_tracer InterfaceDdG KIC_refine KIC_vicinity KIC_with_fragments LayerDesign LayerDesign_symm LayerSelector LoopAnalyzer LoopLengthChange ModifyVariantTypeMover MutateResidue_selector N-terminal_acetylation OversaturatedHbondAcceptorFilter PDB_diagnostic PTMPrediction PeptideCyclizeMover PeptideStubMover_prependRepeat PolarDesign2019 ProQ RBOut ReadResfile_with_selector RescorePDDF RescoreSAXS ResidueDisorder RunSimpleMetric_b_factor_test SID_ERMS_prediction SID_rescore SSElementSelector SecondaryStructureFilter SnugDock StrandCurvatureByLevels StrandHelixGeometryFilter ThreadingInputter TryDisulfPermutations UBQ_E2_thioester UBQ_E2_thioester_extra_bodies UBQ_E2_thioester_two_ubiquitins UBQ_Gp_CYD-CYD UBQ_Gp_LYX-Cterm UnsatSelector Werror_check abinitio abinitio_with_trRosetta add_constraints_to_current_conformation add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data ambiguous_nmr_distance_constraint angle_recovery_stats antibody_H3 antibody_H3_camelid antibody_cc antibody_designer antibody_designer_camelid antibody_designer_xml antibody_graft antibody_numbering_converter app_exception_handling assemble_domains_jd2 auto-drrafter_final_results auto-drrafter_setup_run_R1 auto-drrafter_setup_run_R2 auto-drrafter_setup_run_R3 autoNOE_rosetta autosetup_metals_centroid backbonegridsampler backbonegridsampler_multiresidue backbonegridsampler_nstruct_mode backrub backrub_interface_ddG backrub_pilot balancedKIC basic_gcn_tensorflow_test batch_relax bcl_fragment_mutate beta_strand_homodimer bin_initialization bin_perturbation binselector binselector_probins blob_finder broker broker_membrane bundlegridsampler bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_multirepeat bundlegridsampler_z0_offset bundlegridsampler_z1_offset bundlereporter_filter burial_measure_centroid buried_area_filter buried_unsat_kinemage buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm c-term_conjugation calculate_sasa carbohydrates cart_min_glycans cartesianddg case_sensitive_filenames ccd_ends_graft_mover_rs central_class_modification centroid_disulfide_scores centroid_from_fullatom cl_complex_rescore classic_relax_1a19 cleanAlignment cluster cluster_alns cluster_calibur cluster_filter cmaes_minimizer coarse_rna_scoring code_template_tests_app code_template_tests_citations code_template_tests_src code_template_tests_unit coenzymes combine_silent composition_energy_layers constel constraints_metric contactMap control_flow_rs copy_rotamer_mover count_cycpep_sequences coupled_moves crankshaft_flip create_clash-based_repack_shell create_sequence_motif crossaln crosslinkermover_1_4_bbmb_asymm crosslinkermover_1_4_bbmb_c2_symmetry crosslinkermover_1_4_bbmb_s2_symm crosslinkermover_lanthionine crosslinkermover_methyllanthionine crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_thioether crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cs_rosetta_rna cst_info cstfile_to_theozyme_pdb custom_basetype_packer_palette cyclization cycpep_design_pipeline cycpep_rdkit_metric cycpep_rigid_body_permutation_mover cycpep_symmetry_filter d_workflow database_jd2_compact_io database_jd2_io database_md5 database_session_resource ddG_ensemble ddG_of_mutation ddG_scan ddG_sym dehydro_aa_patch density_denovo density_refine density_refine_symm density_tools design_glycans design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA dgdp_aio dgdp_script dihedral_constraint_generator distances disulfidize_beta_cys dna_interface_design dock_glycans dock_with_hotspot_place_simultaneously 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favor_coupling_tensor favor_native_residue features features_database_schema features_parallel features_pdb features_pdb_mpi features_postgres features_scientific_benchmark fiber_diffraction fiber_diffraction_fad fit_helixparams fit_helixparams_a3b fit_helixparams_rms fix_alignment_to_match_pdb fixbb flexpepdock flexpepdock_abinitio fold_and_dock fold_cst_new fold_from_loops fragment_picker fragmentpicker_integration_demo fuzzy ga_ligand_dock ga_ligand_dock_amino_acid ga_ligand_dock_macrocycle gen_apo_grids gen_lig_grids generate_6Dloopclose genkic_bin_perturbing genkic_bin_sampling genkic_bin_setting genkic_dihedral_copying genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars geometric_solvation glycan_anomers glycan_clash_check glycan_refinment glycan_relax glycan_sequon_scanner glycan_tree_relax glycomutagenesis glycopeptidedocking glycopeptidedocking_diglyco_long glycosylation grid_scores_features hbnet hbnet_asymm hbnet_energy 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ligand_dock_script ligand_motif_design ligand_motif_discovery ligand_motif_identification ligand_water_docking longest_continuous_polar_segment_filter loop_creation loop_grower_N_term_symm loop_hash loop_modeling make_and_perturb_bundle_multirepeat make_exemplar make_mainchain_potential make_mainchain_potential_symm make_mainchain_potential_symm_preproline make_rot_lib make_symmdef_file match_1c2t match_1n9l match_6cpa match_xml measure_lcaa_radii membrane_abinitio metal_setup metalloprotein_abrelax metalloprotein_broker metropolis_hastings mf_fixbb_des mf_fixbb_sc mf_flexbb_sc mg_modeler mg_modeler_lores mhc_epitope mhc_epitope_nmer_preload min_pack_min minimize_6Dloopclose minimize_with_elec_dens mirror_symm mixed_monte_carlo mm_params mmtfIO_score_test molfile_to_params molfile_to_params_polymer motif_dna_packer_design motif_extraction motif_score_filter mp_dock mp_dock_ensemble mp_dock_prepack mp_dock_setup mp_domain_assembly mp_domain_assembly_FtsQ mp_f19_relax mp_find_interface 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oop_dock_design orbitals output_schema pH_mode pepspec_anchor_dock peptiderive per_residue_energies per_residue_sc_sasa per_residue_solvent_exposure pertmin perturb_helical_bundle perturb_helical_bundle_copying_pitch perturb_helical_bundle_epsilon perturb_helical_bundle_setting perturb_helical_bundle_z_offset phiselector phosphonate phosphorylation place_simultaneously pmut_scan pna pna_base_pairs pocket_measure pocket_relax pocket_suggest_targets polyaramid_test_trivial pose_sewing posttranslationalmod_io ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk proteinMPNN_model_perplexity protocol_metric pwsho pymol_cif r_pdb2top r_rmsf ralford_dump_rotamers rama_mutation_selector range_relax_w_cst rb_recces rdkit_metrics read_polymeric_components readin_dna_rna_protein real_motif_analysis real_virt_mover recces_turner recon_design recon_design_mpi referencepose_mutateresidue relax_w_allatom_cst remodel_disulfides_rosettascripts 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sim_cryo simple_cycpep_predict simple_cycpep_predict_1_4_bbmb simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_beta_thioether_lariat simple_cycpep_predict_bondangle_bondlength simple_cycpep_predict_cartesian simple_cycpep_predict_cispro simple_cycpep_predict_cterm_isopeptide_lariat simple_cycpep_predict_cterm_isopeptide_lariat_tailless simple_cycpep_predict_design simple_cycpep_predict_lanthionine simple_cycpep_predict_nmethyl simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_octahedral_metal simple_cycpep_predict_peptoid simple_cycpep_predict_setting simple_cycpep_predict_sidechain_isopeptide simple_cycpep_predict_sidechain_isopeptide_reverse simple_cycpep_predict_square_planar_metal simple_cycpep_predict_square_pyramidal_metal simple_cycpep_predict_symm_gly simple_cycpep_predict_symmetric_sampling simple_cycpep_predict_tbmb simple_cycpep_predict_terminal_disulfide 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"passed" }, "fit_helixparams_a3b": { "log": "", "state": "passed" }, "fit_helixparams_rms": { "log": "", "state": "passed" }, "fix_alignment_to_match_pdb": { "log": "", "state": "passed" }, "fixbb": { "log": "", "state": "passed" }, "flexpepdock": { "log": "", "state": "passed" }, "flexpepdock_abinitio": { "log": "", "state": "passed" }, "fold_and_dock": { "log": "", "state": "passed" }, "fold_cst_new": { "log": "", "state": "passed" }, "fold_from_loops": { "log": "", "state": "passed" }, "fragment_picker": { "log": "", "state": "passed" }, "fragmentpicker_integration_demo": { "log": "", "state": "passed" }, "fuzzy": { "log": "", "state": "passed" }, "ga_ligand_dock": { "log": "", "state": "passed" }, "ga_ligand_dock_amino_acid": { "log": "", "state": "passed" }, "ga_ligand_dock_macrocycle": { "log": "", "state": "passed" }, "gen_apo_grids": { "log": "", "state": "passed" }, "gen_lig_grids": { "log": "", "state": "passed" }, "generate_6Dloopclose": { "log": "", "state": "passed" }, "genkic_bin_perturbing": { "log": "", "state": "passed" }, "genkic_bin_sampling": { "log": "", "state": "passed" }, "genkic_bin_setting": { "log": "", "state": "passed" }, "genkic_dihedral_copying": { "log": "", "state": "passed" }, "genkic_lowmemory_mode": { "log": "", "state": "passed" }, "genkic_rama_filter": { "log": "", "state": "passed" }, "genkic_ramaprepro_sampling": { "log": "", "state": "passed" }, "genkic_sugars": { "log": "", "state": "passed" }, "geometric_solvation": { "log": "", "state": "passed" }, "glycan_anomers": { "log": "", "state": "passed" }, "glycan_clash_check": { "log": "", "state": "passed" }, "glycan_refinment": { "log": "", "state": "passed" }, "glycan_relax": { "log": "", "state": "passed" }, "glycan_sequon_scanner": { "log": "", "state": "passed" }, "glycan_tree_relax": { "log": "", "state": "passed" }, "glycomutagenesis": { "log": "", "state": "passed" }, "glycopeptidedocking": { "log": "", "state": "passed" }, "glycopeptidedocking_diglyco_long": { "log": "", "state": "passed" }, "glycosylation": { "log": "", "state": "passed" }, "grid_scores_features": { "log": "", "state": "passed" }, "hbnet": { "log": "", "state": "passed" }, "hbnet_asymm": { "log": "", "state": "passed" }, "hbnet_energy": { "log": "", "state": "passed" }, "hbnet_energy_rosettascripts_linear": { "log": "", "state": "passed" }, "hbnet_energy_symm": { "log": "", "state": "passed" }, "hbnet_use_input_rot": { "log": "", "state": "passed" }, "hbonds": { "log": "", "state": "passed" }, "hbonds_sp2": { "log": "", "state": "passed" }, "hbondstoresidue_selector": { "log": "", "state": "passed" }, "hbs_design": { "log": "", "state": "passed" }, "header_using_check": { "log": "", "state": "passed" }, "helical_bundle": { "log": "", "state": "passed" }, "helical_bundle_nonideal": { "log": "", "state": "passed" }, "helical_bundle_predict": { "log": "", "state": "passed" }, "helical_bundle_predict_psipred": { "log": "", "state": "passed" }, "helical_bundle_predict_psipred_with_helix_globals": { "log": "", "state": "passed" }, "helical_bundle_predict_sequence": { "log": "", "state": "passed" }, "helical_bundle_predict_skipping_residues": { "log": "", "state": "passed" }, "helix_from_sequence": { "log": "", "state": "passed" }, "hierarchical_clustering": { "log": "", "state": "passed" }, "homodimer_fnd_ref2015_memb": { "log": "", "state": "passed" }, "hotspot_graft": { "log": "", "state": "passed" }, "hotspot_hashing": { "log": "", "state": "passed" }, "hotspot_stub_constraints": { "log": "", "state": "passed" }, "hshash_utils": { "log": "", "state": "passed" }, "hts_io": { "log": "", "state": "passed" }, "hybridization": { "log": "", "state": "passed" }, "hydrate": { "log": "", "state": "passed" }, "hydrate_relax": { "log": "", "state": "passed" }, "identify_cdr_clusters": { "log": "", "state": "passed" }, "ig_dump": { "log": "", "state": "passed" }, "include_cc_check": { "log": "Brief Diff:\nFiles /home/benchmark/working_dir/main:62149/include_cc_check/cc_includes.txt and /home/benchmark/working_dir/commits:20668/include_cc_check/cc_includes.txt differ\r\nOnly in /home/benchmark/working_dir/commits:20668/include_cc_check: .test_did_not_run.log\r\n\n\nFull Diff:\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62149/include_cc_check/cc_includes.txt /home/benchmark/working_dir/commits:20668/include_cc_check/cc_includes.txt\r\n0a1\r\n> [Tue Mar 25 15:36:46 EDT 2025] src/apps/public/motif_ligand_discovery/remove_duplicate_motifs.cc://#include <protocols/motifs/FindMotifPositionsOnLigandHelper.cc>\r\nOnly in /home/benchmark/working_dir/commits:20668/include_cc_check: .test_did_not_run.log\r\n\nCompare(...): Marking as \"Script failed\" due to presense of .test_did_not_run.log or .test_got_timeout_kill.log file!\n", "state": "script failed" }, "interaction_graph_summary_metric": { "log": "", "state": "passed" }, "interface_energy": { "log": "", "state": "passed" }, "inv_kin_lig_loop_design": { "log": "", "state": "passed" }, "iphold": { "log": "", "state": "passed" }, "jd2test_PDBIO": { "log": "", "state": "passed" }, "jd2test_PDBin_mmCIFout": { "log": "", "state": "passed" }, "jd2test_PDBin_mmCIFout_extra_data_separate": { "log": "", "state": "passed" }, "jd2test_mmCIFIO": { "log": "", "state": "passed" }, "jd2test_mmCIFin_PDBout": { "log": "", "state": "passed" }, "job_definition_script_vars": { "log": "", "state": "passed" }, "jrelax": { "log": "", "state": "passed" }, "jscore": { "log": "", "state": "passed" }, "kinemage_grid_output": { "log": "", "state": "passed" }, "kinematic_looprelax": { "log": "", "state": "passed" }, "ld_converter": { "log": "", "state": "passed" }, "ligand_database_io": { "log": "", "state": "passed" }, "ligand_dock_7cpa": { "log": "", "state": "passed" }, "ligand_dock_cholesterol": { "log": "", "state": "passed" }, "ligand_dock_ensemble": { "log": "", "state": "passed" }, "ligand_dock_grid": { "log": "", "state": "passed" }, "ligand_dock_script": { "log": "", "state": "passed" }, "ligand_motif_design": { "log": "", "state": "passed" }, "ligand_motif_discovery": { "log": "Brief Diff:\nOnly in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 4s0v_motifs.motifs\r\nOnly in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 4s0v.pdb\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio16_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120970_SubRatio_0.803259.pdb\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio22_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120911_SubRatio_0.793778.pdb\r\nOnly in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000_rep_5.200045_atr_-19.001764_delta_-21.724721_constr_6.287128.pdb\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000_WholeRatio_0.120947_SubRatio_0.802667.pdb\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio46_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120951_SubRatio_0.776593.pdb\r\nOnly in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000_rep_5.346809_atr_-18.851113_delta_-21.657672_constr_0.245685.pdb\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000_WholeRatio_0.120987_SubRatio_0.801185.pdb\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio97_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120951_SubRatio_0.802667.pdb\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_suv_0.pdb\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_suv_1.pdb\r\nOnly in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 6h4q_motifs.motifs\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: empty_WholeRatio_0.119936_SubRatio_0.645037.pdb\r\nFiles /home/benchmark/working_dir/main:62149/ligand_motif_discovery/flags and /home/benchmark/working_dir/commits:20668/ligand_motif_discovery/flags differ\r\nFiles /home/benchmark/working_dir/main:62149/ligand_motif_discovery/log and /home/benchmark/working_dir/commits:20668/ligand_motif_discovery/log differ\r\n\n\nFull Diff:\nOnly in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 4s0v_motifs.motifs\r\nOnly in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 4s0v.pdb\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio16_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120970_SubRatio_0.803259.pdb\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio22_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120911_SubRatio_0.793778.pdb\r\nOnly in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000_rep_5.200045_atr_-19.001764_delta_-21.724721_constr_6.287128.pdb\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000_WholeRatio_0.120947_SubRatio_0.802667.pdb\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio46_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120951_SubRatio_0.776593.pdb\r\nOnly in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000_rep_5.346809_atr_-18.851113_delta_-21.657672_constr_0.245685.pdb\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000_WholeRatio_0.120987_SubRatio_0.801185.pdb\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio97_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120951_SubRatio_0.802667.pdb\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_suv_0.pdb\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: 4s0v_receptor_only_suv_1.pdb\r\nOnly in /home/benchmark/working_dir/main:62149/ligand_motif_discovery: 6h4q_motifs.motifs\r\nOnly in /home/benchmark/working_dir/commits:20668/ligand_motif_discovery: empty_WholeRatio_0.119936_SubRatio_0.645037.pdb\r\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62149/ligand_motif_discovery/flags /home/benchmark/working_dir/commits:20668/ligand_motif_discovery/flags\r\n0a1\r\n> #input empty receptor protein\r\n1a3,4\r\n> \r\n> #directory of ligand(s) to attempt to dock\r\n2a6,7\r\n> \r\n> #ligand motifs library\r\n3a9,10\r\n> \r\n> #index of residue(s) to dock ligands against\r\n4a12,13\r\n> \r\n> #minimum cutoffs for fa_atr, fa_rep, and combined fa_atr_rep to be under\r\n6a16,17\r\n> \r\n> #constrain coordinates\r\n7a19,53\r\n> \r\n> #optional flags for demonstrative purposes of extra features of app:\r\n> \r\n> #space fill method\r\n> #define cube-shaped binding pocket about coordinate (coordinate corresponds to within 4s0v.pdb, shifts with script)\r\n> -binding_pocket_center_sf 54,6,53\r\n> -binding_pocket_radius_sf 7\r\n> #define cutoff of how much of binding pocket volume must be filled compared to empty pocket (>15% more filled than empty when ligand is placed)\r\n> -space_fill_cutoff_differential_score_sub 0.15\r\n> \r\n> #optional export of space fill matrices to PDB (only recommended for debugging and tuning cutoffs for binding pocket)\r\n> #Including in this test, since it can help show off the feature and troubleshoot if this test breaks\r\n> -output_space_fill_matrix_pdbs true\r\n> \r\n> #placement motifs collection\r\n> -collect_motifs_from_placed_ligand true\r\n> \r\n> #motifs against residues of interest\r\n> -significant_residues_for_motifs 447,450,419,134,86,423,451,85,62\r\n> -minimum_motifs_formed_cutoff 6\r\n> -minimum_significant_motifs_formed_cutoff 1\r\n> \r\n> #mandatory at least 1 real motif\r\n> -minimum_ratio_of_real_motifs_from_ligand 0.01\r\n> \r\n> #must form a motif with ASN423\r\n> -mandatory_residues_for_motifs 423\r\n> \r\n> #check real motifs\r\n> -check_if_ligand_motifs_match_real true\r\n> -duplicate_dist_cutoff 1.2\r\n> -duplicate_angle_cutoff 0.45\r\n> \r\n> #do not output generated ligand motifs as pdbs\r\n> -output_motifs_as_pdb false\r\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62149/ligand_motif_discovery/log /home/benchmark/working_dir/commits:20668/ligand_motif_discovery/log\r\n19,21d18\r\n< LigandDiscoverySearch_get_motif_sublibrary_by_aa: Created motif sub-library for residue ASN with 24 motifs in it.\r\n< LDS_app: Running discovery for 4s0v_receptor_only\r\n< LigandDiscoverySearch_get_motif_sublibrary_by_aa: Created motif sub-library for residue ASN with 24 motifs in it.\r\n41,341c38\r\n< core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\r\n< basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\r\n< LigandDiscoverySearch_create_protein_matrix: Creating protein clash coordinate matrix. Dimensions of matrix are 88,53,113\r\n< LigandDiscoverySearch_out: Using user-inputted fa_rep cutoff of: 500\r\n< LigandDiscoverySearch_out: Using user-inputted fa_atr cutoff of: 500\r\n< LigandDiscoverySearch_out: Starting to iterate through all ligands\r\n< LigandDiscoverySearch_out: On ligand suv\r\n< LigandDiscoverySearch_out: NBR_RADIUS of ligand is: 9.77457\r\n< LigandDiscoverySearch_out: Finding all atom trios\r\n< LigandDiscoverySearch_out: Looking through all atom trios\r\n< LigandDiscoverySearch_out: #trios = 104\r\n< LigandDiscoverySearch_out: On trio # 1\r\n< LigandDiscoverySearch_out: Trio is C9 N3 C13\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 2\r\n< LigandDiscoverySearch_out: Trio is C9 N3 C10\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 3\r\n< LigandDiscoverySearch_out: Trio is C9 C8 N1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 4\r\n< LigandDiscoverySearch_out: Trio is N3 C9 C8 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 5\r\n< LigandDiscoverySearch_out: Trio is N3 C13 C14\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 6\r\n< LigandDiscoverySearch_out: Trio is N3 C13 O2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 7\r\n< LigandDiscoverySearch_out: Trio is N3 C10 C23\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 8\r\n< LigandDiscoverySearch_out: Trio is N3 C10 C11\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 9\r\n< LigandDiscoverySearch_out: Trio is C13 N3 C9 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 10\r\n< LigandDiscoverySearch_out: Trio is C13 N3 C10\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 11\r\n< LigandDiscoverySearch_out: Trio is C13 C14 C15\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 12\r\n< LigandDiscoverySearch_out: Trio is C13 C14 C19\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 13\r\n< LigandDiscoverySearch_out: Trio is C14 C13 N3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 14\r\n< LigandDiscoverySearch_out: Trio is C14 C13 O2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 15\r\n< LigandDiscoverySearch_out: Trio is C14 C15 N4 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 16\r\n< LigandDiscoverySearch_out: Trio is C14 C15 C16\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: 62, 65, 66, 71, 79, 81, 82, 83, 85, 86, 89, 134, 137, 138, 139, 151, 153, 154, 155, 156, 161, 162, 163, 165, 166, 169, 170, 173, 174, 416, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 436, 439, 440, 442, 443, 444, 446, 447, 450, 451, Made minipose of size 56\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 1\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 1\r\n< LigandDiscoverySearch_out: On trio # 17\r\n< LigandDiscoverySearch_out: Trio is C14 C19 C18\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 18\r\n< LigandDiscoverySearch_out: Trio is C15 C14 C13\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 19\r\n< LigandDiscoverySearch_out: Trio is C15 C14 C19\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 20\r\n< LigandDiscoverySearch_out: Trio is C15 N4 N5 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 21\r\n< LigandDiscoverySearch_out: Trio is C15 N4 N6 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 22\r\n< LigandDiscoverySearch_out: Trio is C15 C16 C17\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 1\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 1\r\n< LigandDiscoverySearch_out: On trio # 23\r\n< LigandDiscoverySearch_out: Trio is N4 C15 C14\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 24\r\n< LigandDiscoverySearch_out: Trio is N4 C15 C16\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 25\r\n< LigandDiscoverySearch_out: Trio is N4 N5 C20\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 26\r\n< LigandDiscoverySearch_out: Trio is N4 N6 C21\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 27\r\n< LigandDiscoverySearch_out: Trio is N5 N4 C15\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 28\r\n< LigandDiscoverySearch_out: Trio is N5 N4 N6 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 29\r\n< LigandDiscoverySearch_out: Trio is N5 C20 C21\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 30\r\n< LigandDiscoverySearch_out: Trio is C20 N5 N4 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 31\r\n< LigandDiscoverySearch_out: Trio is C20 C21 N6 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 32\r\n< LigandDiscoverySearch_out: Trio is C21 C20 N5 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 33\r\n< LigandDiscoverySearch_out: Trio is C21 N6 N4 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 34\r\n< LigandDiscoverySearch_out: Trio is N6 N4 C15\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 35\r\n< LigandDiscoverySearch_out: Trio is N6 N4 N5 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 36\r\n< LigandDiscoverySearch_out: Trio is N6 C21 C20\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\r\n< core.scoring.elec.util: Read 40 countpair representative atoms\r\n< basic.io.database: Database file opened: scoring/score_functions/disulfides/fa_SS_distance_score\r\n< core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\r\n< LigandDiscoverySearch_out: Pre-move delta score = 109.803, fa_atr = -16.397, fa_rep = 163.157, coordinate_constraint = 0\r\n---\r\n> LDS_app: Running discovery for 4s0v_receptor_only\r\n345a43,48\r\n> protocols.motifs.LigandDiscoverySearch.discover: Current anchor residue position: 423\r\n> protocols.motifs.LigandDiscoverySearch.create_protein_matrix_space_fill: binding_pocket_dimensions: 7,7,7\r\n> protocols.motifs.LigandDiscoverySearch.create_protein_matrix_space_fill: binding_pocket_dimensions: 7,7,7\r\n> protocols.motifs.LigandDiscoverySearch.create_protein_matrix_space_fill: Sub-region stats without placed region, bound by adjusted coordinates: x(47->61) y(19->33) z(74->88)\r\n> protocols.motifs.LigandDiscoverySearch.discover: Starting to iterate through all ligands\r\n> protocols.motifs.LigandDiscoverySearch.discover: On ligand suv\r\n352,917c55,154\r\n< protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -815.271 -815.271\r\n< LigandDiscoverySearch_out: Post-dock delta score = -21.7247, fa_atr = -19.0018, fa_rep = 5.20004, coordinate_constraint = 6.28713\r\n< LigandDiscoverySearch_out: Making pdb file for: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000_rep_5.200045_atr_-19.001764_delta_-21.724721_constr_6.287128.pdb\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 1\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 1\r\n< LigandDiscoverySearch_out: On trio # 37\r\n< LigandDiscoverySearch_out: Trio is C16 C15 C14\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 38\r\n< LigandDiscoverySearch_out: Trio is C16 C15 N4 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 39\r\n< LigandDiscoverySearch_out: Trio is C16 C17 C18\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 40\r\n< LigandDiscoverySearch_out: Trio is C17 C16 C15\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 41\r\n< LigandDiscoverySearch_out: Trio is C17 C18 C19\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 42\r\n< LigandDiscoverySearch_out: Trio is C17 C18 C22\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 43\r\n< LigandDiscoverySearch_out: Trio is C18 C17 C16\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 44\r\n< LigandDiscoverySearch_out: Trio is C18 C19 C14\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 45\r\n< LigandDiscoverySearch_out: Trio is C19 C14 C13\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 46\r\n< LigandDiscoverySearch_out: Trio is C19 C14 C15\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 1\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 1\r\n< LigandDiscoverySearch_out: On trio # 47\r\n< LigandDiscoverySearch_out: Trio is C19 C18 C17\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 48\r\n< LigandDiscoverySearch_out: Trio is C19 C18 C22\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 49\r\n< LigandDiscoverySearch_out: Trio is C22 C18 C17\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 50\r\n< LigandDiscoverySearch_out: Trio is C22 C18 C19\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 51\r\n< LigandDiscoverySearch_out: Trio is O2 C13 N3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 52\r\n< LigandDiscoverySearch_out: Trio is O2 C13 C14\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: Pre-move delta score = -19.2048, fa_atr = -18.8845, fa_rep = 8.53383, coordinate_constraint = 0\r\n< protocols.ligand_docking.ligand_options.Protocol: Initializing options: \r\n< protocols.ligand_docking.ligand_options.Protocol: allow_minimization_: 1\r\n< protocols.ligand_docking.ligand_options.Protocol: allow_repacking_: 1\r\n< protocols.ligand_docking.ligand_options.Protocol: all_residues_: 0\r\n< core.pack.task: Packer task: initialize from command line() \r\n< core.pack.task: Packer task: initialize from command line() \r\n< core.pack.task: Packer task: initialize from command line() \r\n< protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -815.681 -815.681\r\n< LigandDiscoverySearch_out: Post-dock delta score = -21.6577, fa_atr = -18.8511, fa_rep = 5.34681, coordinate_constraint = 0.245685\r\n< LigandDiscoverySearch_out: Making pdb file for: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000_rep_5.346809_atr_-18.851113_delta_-21.657672_constr_0.245685.pdb\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 1\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 1\r\n< LigandDiscoverySearch_out: On trio # 53\r\n< LigandDiscoverySearch_out: Trio is C10 N3 C9 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 54\r\n< LigandDiscoverySearch_out: Trio is C10 N3 C13\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 55\r\n< LigandDiscoverySearch_out: Trio is C10 C11 C12\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 56\r\n< LigandDiscoverySearch_out: Trio is C23 C10 N3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 57\r\n< LigandDiscoverySearch_out: Trio is C23 C10 C11\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 58\r\n< LigandDiscoverySearch_out: Trio is C11 C10 N3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 59\r\n< LigandDiscoverySearch_out: Trio is C11 C10 C23\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 60\r\n< LigandDiscoverySearch_out: Trio is C11 C12 N1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 61\r\n< LigandDiscoverySearch_out: Trio is C12 C11 C10\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 62\r\n< LigandDiscoverySearch_out: Trio is C12 N1 C8 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 63\r\n< LigandDiscoverySearch_out: Trio is C12 N1 C1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 64\r\n< LigandDiscoverySearch_out: Trio is N1 C12 C11\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 65\r\n< LigandDiscoverySearch_out: Trio is N1 C8 C9 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 66\r\n< LigandDiscoverySearch_out: Trio is N1 C1 O1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 67\r\n< LigandDiscoverySearch_out: Trio is N1 C1 N2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 68\r\n< LigandDiscoverySearch_out: Trio is C8 C9 N3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 69\r\n< LigandDiscoverySearch_out: Trio is C8 N1 C12\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 70\r\n< LigandDiscoverySearch_out: Trio is C8 N1 C1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 71\r\n< LigandDiscoverySearch_out: Trio is C1 N1 C12\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 72\r\n< LigandDiscoverySearch_out: Trio is C1 N1 C8 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 73\r\n< LigandDiscoverySearch_out: Trio is C1 O1 C7 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 74\r\n< LigandDiscoverySearch_out: Trio is C1 N2 C2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 75\r\n< LigandDiscoverySearch_out: Trio is O1 C1 N1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 76\r\n< LigandDiscoverySearch_out: Trio is O1 C1 N2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 77\r\n< LigandDiscoverySearch_out: Trio is O1 C7 C6 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 78\r\n< LigandDiscoverySearch_out: Trio is O1 C7 C2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 79\r\n< LigandDiscoverySearch_out: Trio is C7 O1 C1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 80\r\n< LigandDiscoverySearch_out: Trio is C7 C6 C5 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 81\r\n< LigandDiscoverySearch_out: Trio is C7 C2 C3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 82\r\n< LigandDiscoverySearch_out: Trio is C7 C2 N2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 83\r\n< LigandDiscoverySearch_out: Trio is C6 C7 O1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 84\r\n< LigandDiscoverySearch_out: Trio is C6 C7 C2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 85\r\n< LigandDiscoverySearch_out: Trio is C6 C5 C4 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 86\r\n< LigandDiscoverySearch_out: Trio is C5 C6 C7 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 87\r\n< LigandDiscoverySearch_out: Trio is C5 C4 C3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 88\r\n< LigandDiscoverySearch_out: Trio is C5 C4 CL1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 89\r\n< LigandDiscoverySearch_out: Trio is C4 C5 C6 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 90\r\n< LigandDiscoverySearch_out: Trio is C4 C3 C2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 91\r\n< LigandDiscoverySearch_out: Trio is C3 C4 C5 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 92\r\n< LigandDiscoverySearch_out: Trio is C3 C4 CL1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 93\r\n< LigandDiscoverySearch_out: Trio is C3 C2 C7 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 94\r\n< LigandDiscoverySearch_out: Trio is C3 C2 N2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 95\r\n< LigandDiscoverySearch_out: Trio is C2 C7 O1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 96\r\n< LigandDiscoverySearch_out: Trio is C2 C7 C6 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 97\r\n< LigandDiscoverySearch_out: Trio is C2 C3 C4 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 1\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 1\r\n< LigandDiscoverySearch_out: On trio # 98\r\n< LigandDiscoverySearch_out: Trio is C2 N2 C1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 99\r\n< LigandDiscoverySearch_out: Trio is N2 C1 N1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 100\r\n< LigandDiscoverySearch_out: Trio is N2 C1 O1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 101\r\n< LigandDiscoverySearch_out: Trio is N2 C2 C7 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 102\r\n< LigandDiscoverySearch_out: Trio is N2 C2 C3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 1\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 103\r\n< LigandDiscoverySearch_out: Trio is CL1 C4 C5 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: On trio # 104\r\n< LigandDiscoverySearch_out: Trio is CL1 C4 C3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n< LigandDiscoverySearch_out: # passing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n< LigandDiscoverySearch_out: # post motif filter cases for this trio = 0\r\n< LigandDiscoverySearch_out: Total cases for trio: 0\r\n< LigandDiscoverySearch_out: Done iterating all trios, moving to next ligand\r\n< LigandDiscoverySearch_out: Total passing attempts for ligand is 2\r\n< LigandDiscoverySearch_out: Total clashing attempts for ligand is 4\r\n< LigandDiscoverySearch_out: Number of placements that passed all filters: 2\r\n---\r\n> protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -1945.71 -1945.71\r\n> basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\r\n> core.scoring.elec.util: Read 40 countpair representative atoms\r\n> basic.io.database: Database file opened: scoring/score_functions/disulfides/fa_SS_distance_score\r\n> core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\r\n> protocols.motifs.Motif: Res1 name is THR\r\n> protocols.motifs.Motif: atom1 name is CH2\r\n> protocols.motifs.Motif: atom2 name is aroC\r\n> protocols.motifs.Motif: atom3 name is Cl\r\n> protocols.motifs.Motif: Res1 name is PRO\r\n> protocols.motifs.Motif: atom1 name is Oaro\r\n> protocols.motifs.Motif: atom2 name is aroC\r\n> protocols.motifs.Motif: atom3 name is aroC\r\n> protocols.motifs.Motif: Res1 name is GLN\r\n> protocols.motifs.Motif: atom1 name is Oaro\r\n> protocols.motifs.Motif: atom2 name is aroC\r\n> protocols.motifs.Motif: atom3 name is aroC\r\n> protocols.motifs.Motif: Res1 name is THR\r\n> protocols.motifs.Motif: atom1 name is CH2\r\n> protocols.motifs.Motif: atom2 name is Nhis\r\n> protocols.motifs.Motif: atom3 name is aroC\r\n> protocols.motifs.Motif: Res1 name is GLN\r\n> protocols.motifs.Motif: atom1 name is CH2\r\n> protocols.motifs.Motif: atom2 name is CH2\r\n> protocols.motifs.Motif: atom3 name is Nhis\r\n> protocols.motifs.Motif: Res1 name is PHE\r\n> protocols.motifs.Motif: atom1 name is CH3\r\n> protocols.motifs.Motif: atom2 name is CH1\r\n> protocols.motifs.Motif: atom3 name is CH2\r\n> protocols.motifs.Motif: Res1 name is ILE\r\n> protocols.motifs.Motif: atom1 name is aroC\r\n> protocols.motifs.Motif: atom2 name is aroC\r\n> protocols.motifs.Motif: atom3 name is Nhis\r\n> protocols.motifs.Motif: Res1 name is ASN\r\n> protocols.motifs.Motif: atom1 name is aroC\r\n> protocols.motifs.Motif: atom2 name is COO\r\n> protocols.motifs.Motif: atom3 name is ONH2\r\n> protocols.motifs.Motif: Res1 name is HIS\r\n> protocols.motifs.Motif: atom1 name is aroC\r\n> protocols.motifs.Motif: atom2 name is aroC\r\n> protocols.motifs.Motif: atom3 name is CH3\r\n> protocols.motifs.Motif: Res1 name is VAL\r\n> protocols.motifs.Motif: atom1 name is aroC\r\n> protocols.motifs.Motif: atom2 name is aroC\r\n> protocols.motifs.Motif: atom3 name is aroC\r\n> protocols.motifs.Motif: Res1 name is TYR\r\n> protocols.motifs.Motif: atom1 name is aroC\r\n> protocols.motifs.Motif: atom2 name is aroC\r\n> protocols.motifs.Motif: atom3 name is CH3\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.task: Packer task: initialize from command line() \r\n> protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -1945.34 -1945.34\r\n> protocols.motifs.Motif: Res1 name is THR\r\n> protocols.motifs.Motif: atom1 name is CH2\r\n> protocols.motifs.Motif: atom2 name is aroC\r\n> protocols.motifs.Motif: atom3 name is Cl\r\n> protocols.motifs.Motif: Res1 name is PRO\r\n> protocols.motifs.Motif: atom1 name is Oaro\r\n> protocols.motifs.Motif: atom2 name is aroC\r\n> protocols.motifs.Motif: atom3 name is aroC\r\n> protocols.motifs.Motif: Res1 name is GLN\r\n> protocols.motifs.Motif: atom1 name is Oaro\r\n> protocols.motifs.Motif: atom2 name is aroC\r\n> protocols.motifs.Motif: atom3 name is aroC\r\n> protocols.motifs.Motif: Res1 name is THR\r\n> protocols.motifs.Motif: atom1 name is CH2\r\n> protocols.motifs.Motif: atom2 name is Nhis\r\n> protocols.motifs.Motif: atom3 name is aroC\r\n> protocols.motifs.Motif: Res1 name is GLN\r\n> protocols.motifs.Motif: atom1 name is CH2\r\n> protocols.motifs.Motif: atom2 name is CH2\r\n> protocols.motifs.Motif: atom3 name is Nhis\r\n> protocols.motifs.Motif: Res1 name is PHE\r\n> protocols.motifs.Motif: atom1 name is aroC\r\n> protocols.motifs.Motif: atom2 name is aroC\r\n> protocols.motifs.Motif: atom3 name is Nhis\r\n> protocols.motifs.Motif: Res1 name is ILE\r\n> protocols.motifs.Motif: atom1 name is aroC\r\n> protocols.motifs.Motif: atom2 name is aroC\r\n> protocols.motifs.Motif: atom3 name is Nhis\r\n> protocols.motifs.Motif: Res1 name is ASN\r\n> protocols.motifs.Motif: atom1 name is aroC\r\n> protocols.motifs.Motif: atom2 name is COO\r\n> protocols.motifs.Motif: atom3 name is ONH2\r\n> protocols.motifs.Motif: Res1 name is HIS\r\n> protocols.motifs.Motif: atom1 name is aroC\r\n> protocols.motifs.Motif: atom2 name is aroC\r\n> protocols.motifs.Motif: atom3 name is CH3\r\n> protocols.motifs.Motif: Res1 name is VAL\r\n> protocols.motifs.Motif: atom1 name is aroC\r\n> protocols.motifs.Motif: atom2 name is aroC\r\n> protocols.motifs.Motif: atom3 name is aroC\r\n> protocols.motifs.Motif: Res1 name is TYR\r\n> protocols.motifs.Motif: atom1 name is CH2\r\n> protocols.motifs.Motif: atom2 name is aroC\r\n> protocols.motifs.Motif: atom3 name is Cl\r\n> protocols.motifs.LigandDiscoverySearch.discover: Done iterating all trios, moving to next ligand\r\n> protocols.motifs.LigandDiscoverySearch.discover: Total passing attempts for ligand is 2\r\n> protocols.motifs.LigandDiscoverySearch.discover: Total clashing attempts for ligand is 2\r\n", "state": "failed" }, "ligand_motif_identification": { "log": "Brief Diff:\nFiles /home/benchmark/working_dir/main:62149/ligand_motif_identification/log and /home/benchmark/working_dir/commits:20668/ligand_motif_identification/log differ\r\n\n\nFull Diff:\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62149/ligand_motif_identification/log /home/benchmark/working_dir/commits:20668/ligand_motif_identification/log\r\n8,26d7\r\n< apps.pilot.ligand_motifs: motif_pdb_output_path_: \r\n< apps.pilot.ligand_motifs: motif_file_output_: AllMattMotifs.motifs\r\n< apps.pilot.ligand_motifs: output_motifs_: 1\r\n< apps.pilot.ligand_motifs: output_motifs_as_pdb_: 1\r\n< core.scoring.etable: Starting energy table calculation\r\n< core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\r\n< core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\r\n< core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\r\n< core.scoring.etable: Finished calculating energy tables.\r\n< basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine\r\n< basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\r\n< basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\r\n< core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\r\n< basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\r\n< basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\r\n< basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\r\n< basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\r\n< basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\r\n< basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\r\n57a39,48\r\n> core.scoring.etable: Starting energy table calculation\r\n> core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\r\n> core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\r\n> core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\r\n> core.scoring.etable: Finished calculating energy tables.\r\n> basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\r\n> basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\r\n> basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\r\n> basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\r\n> basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\r\n63a55,58\r\n> basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\r\n> basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\r\n> core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\r\n> basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\r\n71a67\r\n> basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine\r\n73,923d68\r\n< apps.pilot.ligand_motifs: in ligand splitter block, found my ligand, lig_pos is 479\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 1\r\n< apps.pilot.ligand_motifs: atom name is C1\r\n< apps.pilot.ligand_motifs: ATOM j: 2 Name: N1\r\n< apps.pilot.ligand_motifs: ATOM k: 1 Name: C1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 1, type is aroC; 2, type is Nhis; 1, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 17 Name: C11\r\n< apps.pilot.ligand_motifs: Connected triplet is: 1, type is aroC; 2, type is Nhis; 17, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 1\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 2\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 17\r\n< apps.pilot.ligand_motifs: ATOM k: 21 Name: C16\r\n< apps.pilot.ligand_motifs: Connected triplet is: 1, type is aroC; 2, type is Nhis; 21, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 1\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 2\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 21\r\n< apps.pilot.ligand_motifs: ATOM j: 3 Name: O1\r\n< apps.pilot.ligand_motifs: ATOM k: 1 Name: C1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 1, type is aroC; 3, type is Oaro; 1, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 16 Name: C8\r\n< apps.pilot.ligand_motifs: Connected triplet is: 1, type is aroC; 3, type is Oaro; 16, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 1\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 3\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 16\r\n< apps.pilot.ligand_motifs: ATOM j: 5 Name: N2\r\n< apps.pilot.ligand_motifs: ATOM k: 1 Name: C1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 1, type is aroC; 5, type is Nhis; 1, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 7 Name: C3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 1, type is aroC; 5, type is Nhis; 7, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 1\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 5\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 7\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 2\r\n< apps.pilot.ligand_motifs: atom name is N1\r\n< apps.pilot.ligand_motifs: ATOM j: 1 Name: C1\r\n< apps.pilot.ligand_motifs: ATOM k: 2 Name: N1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 2, type is Nhis; 1, type is aroC; 2, type is Nhis \r\n< apps.pilot.ligand_motifs: ATOM k: 3 Name: O1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 2, type is Nhis; 1, type is aroC; 3, type is Oaro \r\n< apps.pilot.ligand_motifs: atom_i: 2\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 1\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 3\r\n< apps.pilot.ligand_motifs: ATOM k: 5 Name: N2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 2, type is Nhis; 1, type is aroC; 5, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 2\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 1\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 5\r\n< apps.pilot.ligand_motifs: ATOM j: 17 Name: C11\r\n< apps.pilot.ligand_motifs: ATOM k: 2 Name: N1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 2, type is Nhis; 17, type is CH2; 2, type is Nhis \r\n< apps.pilot.ligand_motifs: ATOM k: 18 Name: C12\r\n< apps.pilot.ligand_motifs: Connected triplet is: 2, type is Nhis; 17, type is CH2; 18, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 2\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 17\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 18\r\n< apps.pilot.ligand_motifs: ATOM j: 21 Name: C16\r\n< apps.pilot.ligand_motifs: ATOM k: 2 Name: N1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 2, type is Nhis; 21, type is CH2; 2, type is Nhis \r\n< apps.pilot.ligand_motifs: ATOM k: 20 Name: C15\r\n< apps.pilot.ligand_motifs: Connected triplet is: 2, type is Nhis; 21, type is CH2; 20, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 2\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 21\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 20\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 3\r\n< apps.pilot.ligand_motifs: atom name is O1\r\n< apps.pilot.ligand_motifs: ATOM j: 1 Name: C1\r\n< apps.pilot.ligand_motifs: ATOM k: 2 Name: N1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 3, type is Oaro; 1, type is aroC; 2, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 3\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 1\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 2\r\n< apps.pilot.ligand_motifs: ATOM k: 3 Name: O1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 3, type is Oaro; 1, type is aroC; 3, type is Oaro \r\n< apps.pilot.ligand_motifs: ATOM k: 5 Name: N2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 3, type is Oaro; 1, type is aroC; 5, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 3\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 1\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 5\r\n< apps.pilot.ligand_motifs: ATOM j: 16 Name: C8\r\n< apps.pilot.ligand_motifs: ATOM k: 3 Name: O1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 3, type is Oaro; 16, type is aroC; 3, type is Oaro \r\n< apps.pilot.ligand_motifs: ATOM k: 7 Name: C3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 3, type is Oaro; 16, type is aroC; 7, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 3\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 16\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 7\r\n< apps.pilot.ligand_motifs: ATOM k: 15 Name: C7\r\n< apps.pilot.ligand_motifs: Connected triplet is: 3, type is Oaro; 16, type is aroC; 15, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 3\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 16\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 15\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 4\r\n< apps.pilot.ligand_motifs: atom name is CL1\r\n< apps.pilot.ligand_motifs: ATOM j: 11 Name: C5\r\n< apps.pilot.ligand_motifs: ATOM k: 4 Name: CL1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 4, type is Cl; 11, type is aroC; 4, type is Cl \r\n< apps.pilot.ligand_motifs: ATOM k: 9 Name: C4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 4, type is Cl; 11, type is aroC; 9, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 4\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 11\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 9\r\n< apps.pilot.ligand_motifs: ATOM k: 13 Name: C6\r\n< apps.pilot.ligand_motifs: Connected triplet is: 4, type is Cl; 11, type is aroC; 13, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 4\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 11\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 13\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 5\r\n< apps.pilot.ligand_motifs: atom name is N2\r\n< apps.pilot.ligand_motifs: ATOM j: 1 Name: C1\r\n< apps.pilot.ligand_motifs: ATOM k: 2 Name: N1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 5, type is Nhis; 1, type is aroC; 2, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 5\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 1\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 2\r\n< apps.pilot.ligand_motifs: ATOM k: 3 Name: O1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 5, type is Nhis; 1, type is aroC; 3, type is Oaro \r\n< apps.pilot.ligand_motifs: atom_i: 5\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 1\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 3\r\n< apps.pilot.ligand_motifs: ATOM k: 5 Name: N2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 5, type is Nhis; 1, type is aroC; 5, type is Nhis \r\n< apps.pilot.ligand_motifs: ATOM j: 7 Name: C3\r\n< apps.pilot.ligand_motifs: ATOM k: 5 Name: N2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 5, type is Nhis; 7, type is aroC; 5, type is Nhis \r\n< apps.pilot.ligand_motifs: ATOM k: 9 Name: C4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 5, type is Nhis; 7, type is aroC; 9, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 5\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 7\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 9\r\n< apps.pilot.ligand_motifs: ATOM k: 16 Name: C8\r\n< apps.pilot.ligand_motifs: Connected triplet is: 5, type is Nhis; 7, type is aroC; 16, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 5\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 7\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 16\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 6\r\n< apps.pilot.ligand_motifs: atom name is O2\r\n< apps.pilot.ligand_motifs: ATOM j: 22 Name: C17\r\n< apps.pilot.ligand_motifs: ATOM k: 6 Name: O2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 6, type is ONH2; 22, type is COO; 6, type is ONH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 8 Name: N3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 6, type is ONH2; 22, type is COO; 8, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 6\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 22\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 8\r\n< apps.pilot.ligand_motifs: ATOM k: 23 Name: C19\r\n< apps.pilot.ligand_motifs: Connected triplet is: 6, type is ONH2; 22, type is COO; 23, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 6\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 22\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 23\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 7\r\n< apps.pilot.ligand_motifs: atom name is C3\r\n< apps.pilot.ligand_motifs: ATOM j: 5 Name: N2\r\n< apps.pilot.ligand_motifs: ATOM k: 1 Name: C1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 7, type is aroC; 5, type is Nhis; 1, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 7\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 5\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 1\r\n< apps.pilot.ligand_motifs: ATOM k: 7 Name: C3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 7, type is aroC; 5, type is Nhis; 7, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 9 Name: C4\r\n< apps.pilot.ligand_motifs: ATOM k: 7 Name: C3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 7, type is aroC; 9, type is aroC; 7, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 11 Name: C5\r\n< apps.pilot.ligand_motifs: Connected triplet is: 7, type is aroC; 9, type is aroC; 11, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 7\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 9\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 11\r\n< apps.pilot.ligand_motifs: ATOM j: 16 Name: C8\r\n< apps.pilot.ligand_motifs: ATOM k: 3 Name: O1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 7, type is aroC; 16, type is aroC; 3, type is Oaro \r\n< apps.pilot.ligand_motifs: atom_i: 7\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 16\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 3\r\n< apps.pilot.ligand_motifs: ATOM k: 7 Name: C3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 7, type is aroC; 16, type is aroC; 7, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 15 Name: C7\r\n< apps.pilot.ligand_motifs: Connected triplet is: 7, type is aroC; 16, type is aroC; 15, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 7\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 16\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 15\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 8\r\n< apps.pilot.ligand_motifs: atom name is N3\r\n< apps.pilot.ligand_motifs: ATOM j: 18 Name: C12\r\n< apps.pilot.ligand_motifs: ATOM k: 8 Name: N3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 8, type is Nhis; 18, type is CH2; 8, type is Nhis \r\n< apps.pilot.ligand_motifs: ATOM k: 17 Name: C11\r\n< apps.pilot.ligand_motifs: Connected triplet is: 8, type is Nhis; 18, type is CH2; 17, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 8\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 18\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 17\r\n< apps.pilot.ligand_motifs: ATOM j: 19 Name: C14\r\n< apps.pilot.ligand_motifs: ATOM k: 8 Name: N3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 8, type is Nhis; 19, type is CH1; 8, type is Nhis \r\n< apps.pilot.ligand_motifs: ATOM k: 20 Name: C15\r\n< apps.pilot.ligand_motifs: Connected triplet is: 8, type is Nhis; 19, type is CH1; 20, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 8\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 19\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 20\r\n< apps.pilot.ligand_motifs: ATOM k: 32 Name: C30\r\n< apps.pilot.ligand_motifs: Connected triplet is: 8, type is Nhis; 19, type is CH1; 32, type is CH3 \r\n< apps.pilot.ligand_motifs: atom_i: 8\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 19\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 32\r\n< apps.pilot.ligand_motifs: ATOM j: 22 Name: C17\r\n< apps.pilot.ligand_motifs: ATOM k: 6 Name: O2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 8, type is Nhis; 22, type is COO; 6, type is ONH2 \r\n< apps.pilot.ligand_motifs: atom_i: 8\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 22\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 6\r\n< apps.pilot.ligand_motifs: ATOM k: 8 Name: N3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 8, type is Nhis; 22, type is COO; 8, type is Nhis \r\n< apps.pilot.ligand_motifs: ATOM k: 23 Name: C19\r\n< apps.pilot.ligand_motifs: Connected triplet is: 8, type is Nhis; 22, type is COO; 23, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 8\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 22\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 23\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 9\r\n< apps.pilot.ligand_motifs: atom name is C4\r\n< apps.pilot.ligand_motifs: ATOM j: 7 Name: C3\r\n< apps.pilot.ligand_motifs: ATOM k: 5 Name: N2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 7, type is aroC; 5, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 9\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 7\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 5\r\n< apps.pilot.ligand_motifs: ATOM k: 9 Name: C4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 7, type is aroC; 9, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 16 Name: C8\r\n< apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 7, type is aroC; 16, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 9\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 7\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 16\r\n< apps.pilot.ligand_motifs: ATOM j: 11 Name: C5\r\n< apps.pilot.ligand_motifs: ATOM k: 4 Name: CL1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 11, type is aroC; 4, type is Cl \r\n< apps.pilot.ligand_motifs: atom_i: 9\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 11\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 4\r\n< apps.pilot.ligand_motifs: ATOM k: 9 Name: C4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 11, type is aroC; 9, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 13 Name: C6\r\n< apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 11, type is aroC; 13, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 9\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 11\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 13\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 10\r\n< apps.pilot.ligand_motifs: atom name is N4\r\n< apps.pilot.ligand_motifs: ATOM j: 12 Name: N5\r\n< apps.pilot.ligand_motifs: ATOM k: 10 Name: N4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 12, type is Nhis; 10, type is Nhis \r\n< apps.pilot.ligand_motifs: ATOM k: 29 Name: C27\r\n< apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 12, type is Nhis; 29, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 10\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 12\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 29\r\n< apps.pilot.ligand_motifs: ATOM j: 14 Name: N6\r\n< apps.pilot.ligand_motifs: ATOM k: 10 Name: N4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 14, type is Nhis; 10, type is Nhis \r\n< apps.pilot.ligand_motifs: ATOM k: 30 Name: C28\r\n< apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 14, type is Nhis; 30, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 10\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 14\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 30\r\n< apps.pilot.ligand_motifs: ATOM j: 24 Name: C20\r\n< apps.pilot.ligand_motifs: ATOM k: 10 Name: N4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 24, type is aroC; 10, type is Nhis \r\n< apps.pilot.ligand_motifs: ATOM k: 23 Name: C19\r\n< apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 24, type is aroC; 23, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 10\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 24\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 23\r\n< apps.pilot.ligand_motifs: ATOM k: 25 Name: C21\r\n< apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 24, type is aroC; 25, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 10\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 24\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 25\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 11\r\n< apps.pilot.ligand_motifs: atom name is C5\r\n< apps.pilot.ligand_motifs: ATOM j: 4 Name: CL1\r\n< apps.pilot.ligand_motifs: ATOM k: 11 Name: C5\r\n< apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 4, type is Cl; 11, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 9 Name: C4\r\n< apps.pilot.ligand_motifs: ATOM k: 7 Name: C3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 9, type is aroC; 7, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 11\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 9\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 7\r\n< apps.pilot.ligand_motifs: ATOM k: 11 Name: C5\r\n< apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 9, type is aroC; 11, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 13 Name: C6\r\n< apps.pilot.ligand_motifs: ATOM k: 11 Name: C5\r\n< apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 13, type is aroC; 11, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 15 Name: C7\r\n< apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 13, type is aroC; 15, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 11\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 13\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 15\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 12\r\n< apps.pilot.ligand_motifs: atom name is N5\r\n< apps.pilot.ligand_motifs: ATOM j: 10 Name: N4\r\n< apps.pilot.ligand_motifs: ATOM k: 12 Name: N5\r\n< apps.pilot.ligand_motifs: Connected triplet is: 12, type is Nhis; 10, type is Nhis; 12, type is Nhis \r\n< apps.pilot.ligand_motifs: ATOM k: 14 Name: N6\r\n< apps.pilot.ligand_motifs: Connected triplet is: 12, type is Nhis; 10, type is Nhis; 14, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 12\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 10\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 14\r\n< apps.pilot.ligand_motifs: ATOM k: 24 Name: C20\r\n< apps.pilot.ligand_motifs: Connected triplet is: 12, type is Nhis; 10, type is Nhis; 24, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 12\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 10\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 24\r\n< apps.pilot.ligand_motifs: ATOM j: 29 Name: C27\r\n< apps.pilot.ligand_motifs: ATOM k: 12 Name: N5\r\n< apps.pilot.ligand_motifs: Connected triplet is: 12, type is Nhis; 29, type is aroC; 12, type is Nhis \r\n< apps.pilot.ligand_motifs: ATOM k: 30 Name: C28\r\n< apps.pilot.ligand_motifs: Connected triplet is: 12, type is Nhis; 29, type is aroC; 30, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 12\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 29\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 30\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 13\r\n< apps.pilot.ligand_motifs: atom name is C6\r\n< apps.pilot.ligand_motifs: ATOM j: 11 Name: C5\r\n< apps.pilot.ligand_motifs: ATOM k: 4 Name: CL1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 11, type is aroC; 4, type is Cl \r\n< apps.pilot.ligand_motifs: atom_i: 13\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 11\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 4\r\n< apps.pilot.ligand_motifs: ATOM k: 9 Name: C4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 11, type is aroC; 9, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 13\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 11\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 9\r\n< apps.pilot.ligand_motifs: ATOM k: 13 Name: C6\r\n< apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 11, type is aroC; 13, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 15 Name: C7\r\n< apps.pilot.ligand_motifs: ATOM k: 13 Name: C6\r\n< apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 15, type is aroC; 13, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 16 Name: C8\r\n< apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 15, type is aroC; 16, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 13\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 15\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 16\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 14\r\n< apps.pilot.ligand_motifs: atom name is N6\r\n< apps.pilot.ligand_motifs: ATOM j: 10 Name: N4\r\n< apps.pilot.ligand_motifs: ATOM k: 12 Name: N5\r\n< apps.pilot.ligand_motifs: Connected triplet is: 14, type is Nhis; 10, type is Nhis; 12, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 14\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 10\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 12\r\n< apps.pilot.ligand_motifs: ATOM k: 14 Name: N6\r\n< apps.pilot.ligand_motifs: Connected triplet is: 14, type is Nhis; 10, type is Nhis; 14, type is Nhis \r\n< apps.pilot.ligand_motifs: ATOM k: 24 Name: C20\r\n< apps.pilot.ligand_motifs: Connected triplet is: 14, type is Nhis; 10, type is Nhis; 24, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 14\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 10\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 24\r\n< apps.pilot.ligand_motifs: ATOM j: 30 Name: C28\r\n< apps.pilot.ligand_motifs: ATOM k: 14 Name: N6\r\n< apps.pilot.ligand_motifs: Connected triplet is: 14, type is Nhis; 30, type is aroC; 14, type is Nhis \r\n< apps.pilot.ligand_motifs: ATOM k: 29 Name: C27\r\n< apps.pilot.ligand_motifs: Connected triplet is: 14, type is Nhis; 30, type is aroC; 29, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 14\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 30\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 29\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 15\r\n< apps.pilot.ligand_motifs: atom name is C7\r\n< apps.pilot.ligand_motifs: ATOM j: 13 Name: C6\r\n< apps.pilot.ligand_motifs: ATOM k: 11 Name: C5\r\n< apps.pilot.ligand_motifs: Connected triplet is: 15, type is aroC; 13, type is aroC; 11, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 15\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 13\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 11\r\n< apps.pilot.ligand_motifs: ATOM k: 15 Name: C7\r\n< apps.pilot.ligand_motifs: Connected triplet is: 15, type is aroC; 13, type is aroC; 15, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 16 Name: C8\r\n< apps.pilot.ligand_motifs: ATOM k: 3 Name: O1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 15, type is aroC; 16, type is aroC; 3, type is Oaro \r\n< apps.pilot.ligand_motifs: atom_i: 15\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 16\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 3\r\n< apps.pilot.ligand_motifs: ATOM k: 7 Name: C3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 15, type is aroC; 16, type is aroC; 7, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 15\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 16\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 7\r\n< apps.pilot.ligand_motifs: ATOM k: 15 Name: C7\r\n< apps.pilot.ligand_motifs: Connected triplet is: 15, type is aroC; 16, type is aroC; 15, type is aroC \r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 16\r\n< apps.pilot.ligand_motifs: atom name is C8\r\n< apps.pilot.ligand_motifs: ATOM j: 3 Name: O1\r\n< apps.pilot.ligand_motifs: ATOM k: 1 Name: C1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 16, type is aroC; 3, type is Oaro; 1, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 16\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 3\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 1\r\n< apps.pilot.ligand_motifs: ATOM k: 16 Name: C8\r\n< apps.pilot.ligand_motifs: Connected triplet is: 16, type is aroC; 3, type is Oaro; 16, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 7 Name: C3\r\n< apps.pilot.ligand_motifs: ATOM k: 5 Name: N2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 16, type is aroC; 7, type is aroC; 5, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 16\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 7\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 5\r\n< apps.pilot.ligand_motifs: ATOM k: 9 Name: C4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 16, type is aroC; 7, type is aroC; 9, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 16\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 7\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 9\r\n< apps.pilot.ligand_motifs: ATOM k: 16 Name: C8\r\n< apps.pilot.ligand_motifs: Connected triplet is: 16, type is aroC; 7, type is aroC; 16, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 15 Name: C7\r\n< apps.pilot.ligand_motifs: ATOM k: 13 Name: C6\r\n< apps.pilot.ligand_motifs: Connected triplet is: 16, type is aroC; 15, type is aroC; 13, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 16\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 15\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 13\r\n< apps.pilot.ligand_motifs: ATOM k: 16 Name: C8\r\n< apps.pilot.ligand_motifs: Connected triplet is: 16, type is aroC; 15, type is aroC; 16, type is aroC \r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 17\r\n< apps.pilot.ligand_motifs: atom name is C11\r\n< apps.pilot.ligand_motifs: ATOM j: 2 Name: N1\r\n< apps.pilot.ligand_motifs: ATOM k: 1 Name: C1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 2, type is Nhis; 1, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 17\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 2\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 1\r\n< apps.pilot.ligand_motifs: ATOM k: 17 Name: C11\r\n< apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 2, type is Nhis; 17, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 21 Name: C16\r\n< apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 2, type is Nhis; 21, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 17\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 2\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 21\r\n< apps.pilot.ligand_motifs: ATOM j: 18 Name: C12\r\n< apps.pilot.ligand_motifs: ATOM k: 8 Name: N3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 18, type is CH2; 8, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 17\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 18\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 8\r\n< apps.pilot.ligand_motifs: ATOM k: 17 Name: C11\r\n< apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 18, type is CH2; 17, type is CH2 \r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 18\r\n< apps.pilot.ligand_motifs: atom name is C12\r\n< apps.pilot.ligand_motifs: ATOM j: 8 Name: N3\r\n< apps.pilot.ligand_motifs: ATOM k: 18 Name: C12\r\n< apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 8, type is Nhis; 18, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 19 Name: C14\r\n< apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 8, type is Nhis; 19, type is CH1 \r\n< apps.pilot.ligand_motifs: atom_i: 18\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 8\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 19\r\n< apps.pilot.ligand_motifs: ATOM k: 22 Name: C17\r\n< apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 8, type is Nhis; 22, type is COO \r\n< apps.pilot.ligand_motifs: atom_i: 18\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 8\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 22\r\n< apps.pilot.ligand_motifs: ATOM j: 17 Name: C11\r\n< apps.pilot.ligand_motifs: ATOM k: 2 Name: N1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 17, type is CH2; 2, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 18\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 17\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 2\r\n< apps.pilot.ligand_motifs: ATOM k: 18 Name: C12\r\n< apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 17, type is CH2; 18, type is CH2 \r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 19\r\n< apps.pilot.ligand_motifs: atom name is C14\r\n< apps.pilot.ligand_motifs: ATOM j: 8 Name: N3\r\n< apps.pilot.ligand_motifs: ATOM k: 18 Name: C12\r\n< apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH1; 8, type is Nhis; 18, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 19\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 8\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 18\r\n< apps.pilot.ligand_motifs: ATOM k: 19 Name: C14\r\n< apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH1; 8, type is Nhis; 19, type is CH1 \r\n< apps.pilot.ligand_motifs: ATOM k: 22 Name: C17\r\n< apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH1; 8, type is Nhis; 22, type is COO \r\n< apps.pilot.ligand_motifs: atom_i: 19\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 8\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 22\r\n< apps.pilot.ligand_motifs: ATOM j: 20 Name: C15\r\n< apps.pilot.ligand_motifs: ATOM k: 19 Name: C14\r\n< apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH1; 20, type is CH2; 19, type is CH1 \r\n< apps.pilot.ligand_motifs: ATOM k: 21 Name: C16\r\n< apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH1; 20, type is CH2; 21, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 19\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 20\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 21\r\n< apps.pilot.ligand_motifs: ATOM j: 32 Name: C30\r\n< apps.pilot.ligand_motifs: ATOM k: 19 Name: C14\r\n< apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH1; 32, type is CH3; 19, type is CH1 \r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 20\r\n< apps.pilot.ligand_motifs: atom name is C15\r\n< apps.pilot.ligand_motifs: ATOM j: 19 Name: C14\r\n< apps.pilot.ligand_motifs: ATOM k: 8 Name: N3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 19, type is CH1; 8, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 20\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 19\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 8\r\n< apps.pilot.ligand_motifs: ATOM k: 20 Name: C15\r\n< apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 19, type is CH1; 20, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 32 Name: C30\r\n< apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 19, type is CH1; 32, type is CH3 \r\n< apps.pilot.ligand_motifs: atom_i: 20\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 19\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 32\r\n< apps.pilot.ligand_motifs: ATOM j: 21 Name: C16\r\n< apps.pilot.ligand_motifs: ATOM k: 2 Name: N1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 21, type is CH2; 2, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 20\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 21\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 2\r\n< apps.pilot.ligand_motifs: ATOM k: 20 Name: C15\r\n< apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 21, type is CH2; 20, type is CH2 \r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 21\r\n< apps.pilot.ligand_motifs: atom name is C16\r\n< apps.pilot.ligand_motifs: ATOM j: 2 Name: N1\r\n< apps.pilot.ligand_motifs: ATOM k: 1 Name: C1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 21, type is CH2; 2, type is Nhis; 1, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 21\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 2\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 1\r\n< apps.pilot.ligand_motifs: ATOM k: 17 Name: C11\r\n< apps.pilot.ligand_motifs: Connected triplet is: 21, type is CH2; 2, type is Nhis; 17, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 21\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 2\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 17\r\n< apps.pilot.ligand_motifs: ATOM k: 21 Name: C16\r\n< apps.pilot.ligand_motifs: Connected triplet is: 21, type is CH2; 2, type is Nhis; 21, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM j: 20 Name: C15\r\n< apps.pilot.ligand_motifs: ATOM k: 19 Name: C14\r\n< apps.pilot.ligand_motifs: Connected triplet is: 21, type is CH2; 20, type is CH2; 19, type is CH1 \r\n< apps.pilot.ligand_motifs: atom_i: 21\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 20\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 19\r\n< apps.pilot.ligand_motifs: ATOM k: 21 Name: C16\r\n< apps.pilot.ligand_motifs: Connected triplet is: 21, type is CH2; 20, type is CH2; 21, type is CH2 \r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 22\r\n< apps.pilot.ligand_motifs: atom name is C17\r\n< apps.pilot.ligand_motifs: ATOM j: 6 Name: O2\r\n< apps.pilot.ligand_motifs: ATOM k: 22 Name: C17\r\n< apps.pilot.ligand_motifs: Connected triplet is: 22, type is COO; 6, type is ONH2; 22, type is COO \r\n< apps.pilot.ligand_motifs: ATOM j: 8 Name: N3\r\n< apps.pilot.ligand_motifs: ATOM k: 18 Name: C12\r\n< apps.pilot.ligand_motifs: Connected triplet is: 22, type is COO; 8, type is Nhis; 18, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 22\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 8\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 18\r\n< apps.pilot.ligand_motifs: ATOM k: 19 Name: C14\r\n< apps.pilot.ligand_motifs: Connected triplet is: 22, type is COO; 8, type is Nhis; 19, type is CH1 \r\n< apps.pilot.ligand_motifs: atom_i: 22\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 8\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 19\r\n< apps.pilot.ligand_motifs: ATOM k: 22 Name: C17\r\n< apps.pilot.ligand_motifs: Connected triplet is: 22, type is COO; 8, type is Nhis; 22, type is COO \r\n< apps.pilot.ligand_motifs: ATOM j: 23 Name: C19\r\n< apps.pilot.ligand_motifs: ATOM k: 22 Name: C17\r\n< apps.pilot.ligand_motifs: Connected triplet is: 22, type is COO; 23, type is aroC; 22, type is COO \r\n< apps.pilot.ligand_motifs: ATOM k: 24 Name: C20\r\n< apps.pilot.ligand_motifs: Connected triplet is: 22, type is COO; 23, type is aroC; 24, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 22\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 23\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 24\r\n< apps.pilot.ligand_motifs: ATOM k: 28 Name: C24\r\n< apps.pilot.ligand_motifs: Connected triplet is: 22, type is COO; 23, type is aroC; 28, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 22\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 23\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 28\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 23\r\n< apps.pilot.ligand_motifs: atom name is C19\r\n< apps.pilot.ligand_motifs: ATOM j: 22 Name: C17\r\n< apps.pilot.ligand_motifs: ATOM k: 6 Name: O2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 22, type is COO; 6, type is ONH2 \r\n< apps.pilot.ligand_motifs: atom_i: 23\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 22\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 6\r\n< apps.pilot.ligand_motifs: ATOM k: 8 Name: N3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 22, type is COO; 8, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 23\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 22\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 8\r\n< apps.pilot.ligand_motifs: ATOM k: 23 Name: C19\r\n< apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 22, type is COO; 23, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 24 Name: C20\r\n< apps.pilot.ligand_motifs: ATOM k: 10 Name: N4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 24, type is aroC; 10, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 23\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 24\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 10\r\n< apps.pilot.ligand_motifs: ATOM k: 23 Name: C19\r\n< apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 24, type is aroC; 23, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 25 Name: C21\r\n< apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 24, type is aroC; 25, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 23\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 24\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 25\r\n< apps.pilot.ligand_motifs: ATOM j: 28 Name: C24\r\n< apps.pilot.ligand_motifs: ATOM k: 23 Name: C19\r\n< apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 28, type is aroC; 23, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 27 Name: C23\r\n< apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 28, type is aroC; 27, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 23\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 28\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 27\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 24\r\n< apps.pilot.ligand_motifs: atom name is C20\r\n< apps.pilot.ligand_motifs: ATOM j: 10 Name: N4\r\n< apps.pilot.ligand_motifs: ATOM k: 12 Name: N5\r\n< apps.pilot.ligand_motifs: Connected triplet is: 24, type is aroC; 10, type is Nhis; 12, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 24\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 10\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 12\r\n< apps.pilot.ligand_motifs: ATOM k: 14 Name: N6\r\n< apps.pilot.ligand_motifs: Connected triplet is: 24, type is aroC; 10, type is Nhis; 14, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 24\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 10\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 14\r\n< apps.pilot.ligand_motifs: ATOM k: 24 Name: C20\r\n< apps.pilot.ligand_motifs: Connected triplet is: 24, type is aroC; 10, type is Nhis; 24, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 23 Name: C19\r\n< apps.pilot.ligand_motifs: ATOM k: 22 Name: C17\r\n< apps.pilot.ligand_motifs: Connected triplet is: 24, type is aroC; 23, type is aroC; 22, type is COO \r\n< apps.pilot.ligand_motifs: atom_i: 24\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 23\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 22\r\n< apps.pilot.ligand_motifs: ATOM k: 24 Name: C20\r\n< apps.pilot.ligand_motifs: Connected triplet is: 24, type is aroC; 23, type is aroC; 24, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 28 Name: C24\r\n< apps.pilot.ligand_motifs: Connected triplet is: 24, type is aroC; 23, type is aroC; 28, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 24\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 23\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 28\r\n< apps.pilot.ligand_motifs: ATOM j: 25 Name: C21\r\n< apps.pilot.ligand_motifs: ATOM k: 24 Name: C20\r\n< apps.pilot.ligand_motifs: Connected triplet is: 24, type is aroC; 25, type is aroC; 24, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 26 Name: C22\r\n< apps.pilot.ligand_motifs: Connected triplet is: 24, type is aroC; 25, type is aroC; 26, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 24\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 25\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 26\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 25\r\n< apps.pilot.ligand_motifs: atom name is C21\r\n< apps.pilot.ligand_motifs: ATOM j: 24 Name: C20\r\n< apps.pilot.ligand_motifs: ATOM k: 10 Name: N4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 24, type is aroC; 10, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 25\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 24\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 10\r\n< apps.pilot.ligand_motifs: ATOM k: 23 Name: C19\r\n< apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 24, type is aroC; 23, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 25\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 24\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 23\r\n< apps.pilot.ligand_motifs: ATOM k: 25 Name: C21\r\n< apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 24, type is aroC; 25, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 26 Name: C22\r\n< apps.pilot.ligand_motifs: ATOM k: 25 Name: C21\r\n< apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 26, type is aroC; 25, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 27 Name: C23\r\n< apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 26, type is aroC; 27, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 25\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 26\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 27\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 26\r\n< apps.pilot.ligand_motifs: atom name is C22\r\n< apps.pilot.ligand_motifs: ATOM j: 25 Name: C21\r\n< apps.pilot.ligand_motifs: ATOM k: 24 Name: C20\r\n< apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 25, type is aroC; 24, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 26\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 25\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 24\r\n< apps.pilot.ligand_motifs: ATOM k: 26 Name: C22\r\n< apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 25, type is aroC; 26, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 27 Name: C23\r\n< apps.pilot.ligand_motifs: ATOM k: 26 Name: C22\r\n< apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 27, type is aroC; 26, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 28 Name: C24\r\n< apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 27, type is aroC; 28, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 26\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 27\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 28\r\n< apps.pilot.ligand_motifs: ATOM k: 31 Name: C29\r\n< apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 27, type is aroC; 31, type is CH3 \r\n< apps.pilot.ligand_motifs: atom_i: 26\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 27\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 31\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 27\r\n< apps.pilot.ligand_motifs: atom name is C23\r\n< apps.pilot.ligand_motifs: ATOM j: 26 Name: C22\r\n< apps.pilot.ligand_motifs: ATOM k: 25 Name: C21\r\n< apps.pilot.ligand_motifs: Connected triplet is: 27, type is aroC; 26, type is aroC; 25, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 27\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 26\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 25\r\n< apps.pilot.ligand_motifs: ATOM k: 27 Name: C23\r\n< apps.pilot.ligand_motifs: Connected triplet is: 27, type is aroC; 26, type is aroC; 27, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 28 Name: C24\r\n< apps.pilot.ligand_motifs: ATOM k: 23 Name: C19\r\n< apps.pilot.ligand_motifs: Connected triplet is: 27, type is aroC; 28, type is aroC; 23, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 27\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 28\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 23\r\n< apps.pilot.ligand_motifs: ATOM k: 27 Name: C23\r\n< apps.pilot.ligand_motifs: Connected triplet is: 27, type is aroC; 28, type is aroC; 27, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 31 Name: C29\r\n< apps.pilot.ligand_motifs: ATOM k: 27 Name: C23\r\n< apps.pilot.ligand_motifs: Connected triplet is: 27, type is aroC; 31, type is CH3; 27, type is aroC \r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 28\r\n< apps.pilot.ligand_motifs: atom name is C24\r\n< apps.pilot.ligand_motifs: ATOM j: 23 Name: C19\r\n< apps.pilot.ligand_motifs: ATOM k: 22 Name: C17\r\n< apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 23, type is aroC; 22, type is COO \r\n< apps.pilot.ligand_motifs: atom_i: 28\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 23\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 22\r\n< apps.pilot.ligand_motifs: ATOM k: 24 Name: C20\r\n< apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 23, type is aroC; 24, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 28\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 23\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 24\r\n< apps.pilot.ligand_motifs: ATOM k: 28 Name: C24\r\n< apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 23, type is aroC; 28, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 27 Name: C23\r\n< apps.pilot.ligand_motifs: ATOM k: 26 Name: C22\r\n< apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 27, type is aroC; 26, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 28\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 27\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 26\r\n< apps.pilot.ligand_motifs: ATOM k: 28 Name: C24\r\n< apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 27, type is aroC; 28, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 31 Name: C29\r\n< apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 27, type is aroC; 31, type is CH3 \r\n< apps.pilot.ligand_motifs: atom_i: 28\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 27\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 31\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 29\r\n< apps.pilot.ligand_motifs: atom name is C27\r\n< apps.pilot.ligand_motifs: ATOM j: 12 Name: N5\r\n< apps.pilot.ligand_motifs: ATOM k: 10 Name: N4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 12, type is Nhis; 10, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 29\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 12\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 10\r\n< apps.pilot.ligand_motifs: ATOM k: 29 Name: C27\r\n< apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 12, type is Nhis; 29, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 30 Name: C28\r\n< apps.pilot.ligand_motifs: ATOM k: 14 Name: N6\r\n< apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 30, type is aroC; 14, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 29\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 30\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 14\r\n< apps.pilot.ligand_motifs: ATOM k: 29 Name: C27\r\n< apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 30, type is aroC; 29, type is aroC \r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 30\r\n< apps.pilot.ligand_motifs: atom name is C28\r\n< apps.pilot.ligand_motifs: ATOM j: 14 Name: N6\r\n< apps.pilot.ligand_motifs: ATOM k: 10 Name: N4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 14, type is Nhis; 10, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 30\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 14\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 10\r\n< apps.pilot.ligand_motifs: ATOM k: 30 Name: C28\r\n< apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 14, type is Nhis; 30, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 29 Name: C27\r\n< apps.pilot.ligand_motifs: ATOM k: 12 Name: N5\r\n< apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 29, type is aroC; 12, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 30\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 29\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 12\r\n< apps.pilot.ligand_motifs: ATOM k: 30 Name: C28\r\n< apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 29, type is aroC; 30, type is aroC \r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 31\r\n< apps.pilot.ligand_motifs: atom name is C29\r\n< apps.pilot.ligand_motifs: ATOM j: 27 Name: C23\r\n< apps.pilot.ligand_motifs: ATOM k: 26 Name: C22\r\n< apps.pilot.ligand_motifs: Connected triplet is: 31, type is CH3; 27, type is aroC; 26, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 31\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 27\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 26\r\n< apps.pilot.ligand_motifs: ATOM k: 28 Name: C24\r\n< apps.pilot.ligand_motifs: Connected triplet is: 31, type is CH3; 27, type is aroC; 28, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 31\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 27\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 28\r\n< apps.pilot.ligand_motifs: ATOM k: 31 Name: C29\r\n< apps.pilot.ligand_motifs: Connected triplet is: 31, type is CH3; 27, type is aroC; 31, type is CH3 \r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 32\r\n< apps.pilot.ligand_motifs: atom name is C30\r\n< apps.pilot.ligand_motifs: ATOM j: 19 Name: C14\r\n< apps.pilot.ligand_motifs: ATOM k: 8 Name: N3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 32, type is CH3; 19, type is CH1; 8, type is Nhis \r\n< apps.pilot.ligand_motifs: atom_i: 32\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 19\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 8\r\n< apps.pilot.ligand_motifs: ATOM k: 20 Name: C15\r\n< apps.pilot.ligand_motifs: Connected triplet is: 32, type is CH3; 19, type is CH1; 20, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 32\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 19\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 20\r\n< apps.pilot.ligand_motifs: ATOM k: 32 Name: C30\r\n< apps.pilot.ligand_motifs: Connected triplet is: 32, type is CH3; 19, type is CH1; 32, type is CH3 \r\n< apps.pilot.ligand_motifs: Total 3 atoms in pruned indices list is: 52\r\n< apps.pilot.ligand_motifs: Total 3 atoms in unpruned indices list is: 104\r\n< apps.pilot.ligand_motifs: Residue 62 passed energy cut with pack score: -1.95141, hbond score: 0, for a total score of: -1.95141\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Top triplets contains 1 items.\r\n< apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1\r\n< apps.pilot.ligand_motifs: Size of this_triplet: 3\r\n928,971c73\r\n< apps.pilot.ligand_motifs: 34: 13-15-16Writing THR111A_Z2001_Ligatoms_13_15_16_A_4s0v.pdb\r\n< apps.pilot.ligand_motifs: Residue 82 passed energy cut with pack score: -2.33653, hbond score: 0, for a total score of: -2.33653\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Top triplets contains 1 items.\r\n< apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1\r\n< apps.pilot.ligand_motifs: Size of this_triplet: 3\r\n---\r\n> protocols.motifs.IdentifyLigandMotifs: Writing THR111A_Z2001_Ligatoms_13_15_16_A_4s0v.pdb\r\n976,1010c78\r\n< apps.pilot.ligand_motifs: 11: 3-16-15Writing PRO131A_Z2001_Ligatoms_3_16_15_A_4s0v.pdb\r\n< apps.pilot.ligand_motifs: Residue 85 passed energy cut with pack score: -5.02867, hbond score: 0, for a total score of: -5.02867\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Top triplets contains 1 items.\r\n< apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1\r\n< apps.pilot.ligand_motifs: Size of this_triplet: 3\r\n---\r\n> protocols.motifs.IdentifyLigandMotifs: Writing PRO131A_Z2001_Ligatoms_3_16_15_A_4s0v.pdb\r\n1015,1065c83\r\n< apps.pilot.ligand_motifs: 49: 25-26-27Writing GLN134A_Z2001_Ligatoms_25_26_27_A_4s0v.pdb\r\n< apps.pilot.ligand_motifs: Residue 86 passed energy cut with pack score: -1.00987, hbond score: 0, for a total score of: -1.00987\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Top triplets contains 1 items.\r\n< apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1\r\n< apps.pilot.ligand_motifs: Size of this_triplet: 3\r\n---\r\n> protocols.motifs.IdentifyLigandMotifs: Writing GLN134A_Z2001_Ligatoms_25_26_27_A_4s0v.pdb\r\n1070,1120c88\r\n< apps.pilot.ligand_motifs: 37: 17-2-21Writing THR135A_Z2001_Ligatoms_17_2_21_A_4s0v.pdb\r\n< apps.pilot.ligand_motifs: Residue 134 passed energy cut with pack score: -1.96699, hbond score: 0, for a total score of: -1.96699\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Top triplets contains 1 items.\r\n< apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1\r\n< apps.pilot.ligand_motifs: Size of this_triplet: 3\r\n---\r\n> protocols.motifs.IdentifyLigandMotifs: Writing THR135A_Z2001_Ligatoms_17_2_21_A_4s0v.pdb\r\n1125,1178c93\r\n< apps.pilot.ligand_motifs: 42: 20-19-32Writing GLN187A_Z2001_Ligatoms_20_19_32_A_4s0v.pdb\r\n< apps.pilot.ligand_motifs: Residue 169 passed energy cut with pack score: -1.6689, hbond score: 0, for a total score of: -1.6689\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Top triplets contains 1 items.\r\n< apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1\r\n< apps.pilot.ligand_motifs: Size of this_triplet: 3\r\n---\r\n> protocols.motifs.IdentifyLigandMotifs: Writing GLN187A_Z2001_Ligatoms_20_19_32_A_4s0v.pdb\r\n1183,1231c98\r\n< apps.pilot.ligand_motifs: 36: 14-30-29Writing PHE227A_Z2001_Ligatoms_14_30_29_A_4s0v.pdb\r\n< apps.pilot.ligand_motifs: Residue 419 passed energy cut with pack score: -3.13989, hbond score: 0, for a total score of: -3.13989\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Top triplets contains 1 items.\r\n< apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1\r\n< apps.pilot.ligand_motifs: Size of this_triplet: 3\r\n---\r\n> protocols.motifs.IdentifyLigandMotifs: Writing PHE227A_Z2001_Ligatoms_14_30_29_A_4s0v.pdb\r\n1236,1275c103\r\n< apps.pilot.ligand_motifs: 36: 14-30-29Writing ILE320A_Z2001_Ligatoms_14_30_29_A_4s0v.pdb\r\n< apps.pilot.ligand_motifs: Residue 423 passed energy cut with pack score: -2.42951, hbond score: -0.70592, for a total score of: -3.13543\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Top triplets contains 1 items.\r\n< apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1\r\n< apps.pilot.ligand_motifs: Size of this_triplet: 3\r\n---\r\n> protocols.motifs.IdentifyLigandMotifs: Writing ILE320A_Z2001_Ligatoms_14_30_29_A_4s0v.pdb\r\n1280,1329c108\r\n< apps.pilot.ligand_motifs: 17: 6-22-23Writing ASN324A_Z2001_Ligatoms_6_22_23_A_4s0v.pdb\r\n< apps.pilot.ligand_motifs: Residue 447 passed energy cut with pack score: -2.65175, hbond score: 0, for a total score of: -2.65175\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Top triplets contains 1 items.\r\n< apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1\r\n< apps.pilot.ligand_motifs: Size of this_triplet: 3\r\n---\r\n> protocols.motifs.IdentifyLigandMotifs: Writing ASN324A_Z2001_Ligatoms_6_22_23_A_4s0v.pdb\r\n1334,1386c113\r\n< apps.pilot.ligand_motifs: 52: 28-27-31Writing HIS350A_Z2001_Ligatoms_28_27_31_A_4s0v.pdb\r\n< apps.pilot.ligand_motifs: Residue 450 passed energy cut with pack score: -1.31505, hbond score: 0, for a total score of: -1.31505\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Top triplets contains 1 items.\r\n< apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1\r\n< apps.pilot.ligand_motifs: Size of this_triplet: 3\r\n---\r\n> protocols.motifs.IdentifyLigandMotifs: Writing HIS350A_Z2001_Ligatoms_28_27_31_A_4s0v.pdb\r\n1391,1445c118\r\n< apps.pilot.ligand_motifs: 49: 25-26-27Writing VAL353A_Z2001_Ligatoms_25_26_27_A_4s0v.pdb\r\n< apps.pilot.ligand_motifs: Residue 451 passed energy cut with pack score: -1.379, hbond score: 0, for a total score of: -1.379\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Top triplets contains 1 items.\r\n< apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1\r\n< apps.pilot.ligand_motifs: Size of this_triplet: 3\r\n---\r\n> protocols.motifs.IdentifyLigandMotifs: Writing VAL353A_Z2001_Ligatoms_25_26_27_A_4s0v.pdb\r\n1450,1866c123\r\n< apps.pilot.ligand_motifs: 52: 28-27-31Writing TYR354A_Z2001_Ligatoms_28_27_31_A_4s0v.pdb\r\n< apps.pilot.ligand_motifs: Motif index contains: 1-2-17\r\n< apps.pilot.ligand_motifs: Motif index contains: 1-2-21\r\n< apps.pilot.ligand_motifs: Motif index contains: 1-3-16\r\n< apps.pilot.ligand_motifs: Motif index contains: 1-5-7\r\n< apps.pilot.ligand_motifs: Motif index contains: 2-1-3\r\n< apps.pilot.ligand_motifs: Motif index contains: 2-1-5\r\n< apps.pilot.ligand_motifs: Motif index contains: 2-17-18\r\n< apps.pilot.ligand_motifs: Motif index contains: 2-21-20\r\n< apps.pilot.ligand_motifs: Motif index contains: 3-1-5\r\n< apps.pilot.ligand_motifs: Motif index contains: 3-16-7\r\n< apps.pilot.ligand_motifs: Motif index contains: 3-16-15\r\n< apps.pilot.ligand_motifs: Motif index contains: 4-11-9\r\n< apps.pilot.ligand_motifs: Motif index contains: 4-11-13\r\n< apps.pilot.ligand_motifs: Motif index contains: 5-7-9\r\n< apps.pilot.ligand_motifs: Motif index contains: 5-7-16\r\n< apps.pilot.ligand_motifs: Motif index contains: 6-22-8\r\n< apps.pilot.ligand_motifs: Motif index contains: 6-22-23\r\n< apps.pilot.ligand_motifs: Motif index contains: 7-9-11\r\n< apps.pilot.ligand_motifs: Motif index contains: 7-16-15\r\n< apps.pilot.ligand_motifs: Motif index contains: 8-18-17\r\n< apps.pilot.ligand_motifs: Motif index contains: 8-19-20\r\n< apps.pilot.ligand_motifs: Motif index contains: 8-19-32\r\n< apps.pilot.ligand_motifs: Motif index contains: 8-22-23\r\n< apps.pilot.ligand_motifs: Motif index contains: 9-7-16\r\n< apps.pilot.ligand_motifs: Motif index contains: 9-11-13\r\n< apps.pilot.ligand_motifs: Motif index contains: 10-12-29\r\n< apps.pilot.ligand_motifs: Motif index contains: 10-14-30\r\n< apps.pilot.ligand_motifs: Motif index contains: 10-24-23\r\n< apps.pilot.ligand_motifs: Motif index contains: 10-24-25\r\n< apps.pilot.ligand_motifs: Motif index contains: 11-13-15\r\n< apps.pilot.ligand_motifs: Motif index contains: 12-10-14\r\n< apps.pilot.ligand_motifs: Motif index contains: 12-10-24\r\n< apps.pilot.ligand_motifs: Motif index contains: 12-29-30\r\n< apps.pilot.ligand_motifs: Motif index contains: 13-15-16\r\n< apps.pilot.ligand_motifs: Motif index contains: 14-10-24\r\n< apps.pilot.ligand_motifs: Motif index contains: 14-30-29\r\n< apps.pilot.ligand_motifs: Motif index contains: 17-2-21\r\n< apps.pilot.ligand_motifs: Motif index contains: 18-8-19\r\n< apps.pilot.ligand_motifs: Motif index contains: 18-8-22\r\n< apps.pilot.ligand_motifs: Motif index contains: 19-8-22\r\n< apps.pilot.ligand_motifs: Motif index contains: 19-20-21\r\n< apps.pilot.ligand_motifs: Motif index contains: 20-19-32\r\n< apps.pilot.ligand_motifs: Motif index contains: 22-23-24\r\n< apps.pilot.ligand_motifs: Motif index contains: 22-23-28\r\n< apps.pilot.ligand_motifs: Motif index contains: 23-24-25\r\n< apps.pilot.ligand_motifs: Motif index contains: 23-28-27\r\n< apps.pilot.ligand_motifs: Motif index contains: 24-23-28\r\n< apps.pilot.ligand_motifs: Motif index contains: 24-25-26\r\n< apps.pilot.ligand_motifs: Motif index contains: 25-26-27\r\n< apps.pilot.ligand_motifs: Motif index contains: 26-27-28\r\n< apps.pilot.ligand_motifs: Motif index contains: 26-27-31\r\n< apps.pilot.ligand_motifs: Motif index contains: 28-27-31\r\n< apps.pilot.ligand_motifs: in ligand splitter block, found my ligand, lig_pos is 480\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 1\r\n< apps.pilot.ligand_motifs: atom name is C1\r\n< apps.pilot.ligand_motifs: ATOM j: 2 Name: O1\r\n< apps.pilot.ligand_motifs: ATOM k: 1 Name: C1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 1, type is COO; 2, type is OOC; 1, type is COO \r\n< apps.pilot.ligand_motifs: ATOM j: 3 Name: O2\r\n< apps.pilot.ligand_motifs: ATOM k: 1 Name: C1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 1, type is COO; 3, type is OH; 1, type is COO \r\n< apps.pilot.ligand_motifs: ATOM j: 4 Name: C2\r\n< apps.pilot.ligand_motifs: ATOM k: 1 Name: C1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 1, type is COO; 4, type is CH2; 1, type is COO \r\n< apps.pilot.ligand_motifs: ATOM k: 5 Name: C3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 1, type is COO; 4, type is CH2; 5, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 1\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 4\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 5\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 2\r\n< apps.pilot.ligand_motifs: atom name is O1\r\n< apps.pilot.ligand_motifs: ATOM j: 1 Name: C1\r\n< apps.pilot.ligand_motifs: ATOM k: 2 Name: O1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 2, type is OOC; 1, type is COO; 2, type is OOC \r\n< apps.pilot.ligand_motifs: ATOM k: 3 Name: O2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 2, type is OOC; 1, type is COO; 3, type is OH \r\n< apps.pilot.ligand_motifs: atom_i: 2\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 1\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 3\r\n< apps.pilot.ligand_motifs: ATOM k: 4 Name: C2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 2, type is OOC; 1, type is COO; 4, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 2\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 1\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 4\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 3\r\n< apps.pilot.ligand_motifs: atom name is O2\r\n< apps.pilot.ligand_motifs: ATOM j: 1 Name: C1\r\n< apps.pilot.ligand_motifs: ATOM k: 2 Name: O1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 3, type is OH; 1, type is COO; 2, type is OOC \r\n< apps.pilot.ligand_motifs: atom_i: 3\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 1\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 2\r\n< apps.pilot.ligand_motifs: ATOM k: 3 Name: O2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 3, type is OH; 1, type is COO; 3, type is OH \r\n< apps.pilot.ligand_motifs: ATOM k: 4 Name: C2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 3, type is OH; 1, type is COO; 4, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 3\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 1\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 4\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 4\r\n< apps.pilot.ligand_motifs: atom name is C2\r\n< apps.pilot.ligand_motifs: ATOM j: 1 Name: C1\r\n< apps.pilot.ligand_motifs: ATOM k: 2 Name: O1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 4, type is CH2; 1, type is COO; 2, type is OOC \r\n< apps.pilot.ligand_motifs: atom_i: 4\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 1\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 2\r\n< apps.pilot.ligand_motifs: ATOM k: 3 Name: O2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 4, type is CH2; 1, type is COO; 3, type is OH \r\n< apps.pilot.ligand_motifs: atom_i: 4\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 1\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 3\r\n< apps.pilot.ligand_motifs: ATOM k: 4 Name: C2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 4, type is CH2; 1, type is COO; 4, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM j: 5 Name: C3\r\n< apps.pilot.ligand_motifs: ATOM k: 4 Name: C2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 4, type is CH2; 5, type is CH2; 4, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 6 Name: C4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 4, type is CH2; 5, type is CH2; 6, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 4\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 5\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 6\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 5\r\n< apps.pilot.ligand_motifs: atom name is C3\r\n< apps.pilot.ligand_motifs: ATOM j: 4 Name: C2\r\n< apps.pilot.ligand_motifs: ATOM k: 1 Name: C1\r\n< apps.pilot.ligand_motifs: Connected triplet is: 5, type is CH2; 4, type is CH2; 1, type is COO \r\n< apps.pilot.ligand_motifs: atom_i: 5\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 4\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 1\r\n< apps.pilot.ligand_motifs: ATOM k: 5 Name: C3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 5, type is CH2; 4, type is CH2; 5, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM j: 6 Name: C4\r\n< apps.pilot.ligand_motifs: ATOM k: 5 Name: C3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 5, type is CH2; 6, type is CH2; 5, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 7 Name: C5\r\n< apps.pilot.ligand_motifs: Connected triplet is: 5, type is CH2; 6, type is CH2; 7, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 5\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 6\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 7\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 6\r\n< apps.pilot.ligand_motifs: atom name is C4\r\n< apps.pilot.ligand_motifs: ATOM j: 5 Name: C3\r\n< apps.pilot.ligand_motifs: ATOM k: 4 Name: C2\r\n< apps.pilot.ligand_motifs: Connected triplet is: 6, type is CH2; 5, type is CH2; 4, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 6\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 5\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 4\r\n< apps.pilot.ligand_motifs: ATOM k: 6 Name: C4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 6, type is CH2; 5, type is CH2; 6, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM j: 7 Name: C5\r\n< apps.pilot.ligand_motifs: ATOM k: 6 Name: C4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 6, type is CH2; 7, type is CH2; 6, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 8 Name: C6\r\n< apps.pilot.ligand_motifs: Connected triplet is: 6, type is CH2; 7, type is CH2; 8, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 6\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 7\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 8\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 7\r\n< apps.pilot.ligand_motifs: atom name is C5\r\n< apps.pilot.ligand_motifs: ATOM j: 6 Name: C4\r\n< apps.pilot.ligand_motifs: ATOM k: 5 Name: C3\r\n< apps.pilot.ligand_motifs: Connected triplet is: 7, type is CH2; 6, type is CH2; 5, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 7\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 6\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 5\r\n< apps.pilot.ligand_motifs: ATOM k: 7 Name: C5\r\n< apps.pilot.ligand_motifs: Connected triplet is: 7, type is CH2; 6, type is CH2; 7, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM j: 8 Name: C6\r\n< apps.pilot.ligand_motifs: ATOM k: 7 Name: C5\r\n< apps.pilot.ligand_motifs: Connected triplet is: 7, type is CH2; 8, type is CH2; 7, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 9 Name: C7\r\n< apps.pilot.ligand_motifs: Connected triplet is: 7, type is CH2; 8, type is CH2; 9, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 7\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 8\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 9\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 8\r\n< apps.pilot.ligand_motifs: atom name is C6\r\n< apps.pilot.ligand_motifs: ATOM j: 7 Name: C5\r\n< apps.pilot.ligand_motifs: ATOM k: 6 Name: C4\r\n< apps.pilot.ligand_motifs: Connected triplet is: 8, type is CH2; 7, type is CH2; 6, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 8\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 7\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 6\r\n< apps.pilot.ligand_motifs: ATOM k: 8 Name: C6\r\n< apps.pilot.ligand_motifs: Connected triplet is: 8, type is CH2; 7, type is CH2; 8, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM j: 9 Name: C7\r\n< apps.pilot.ligand_motifs: ATOM k: 8 Name: C6\r\n< apps.pilot.ligand_motifs: Connected triplet is: 8, type is CH2; 9, type is CH2; 8, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 10 Name: C8\r\n< apps.pilot.ligand_motifs: Connected triplet is: 8, type is CH2; 9, type is CH2; 10, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 8\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 9\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 10\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 9\r\n< apps.pilot.ligand_motifs: atom name is C7\r\n< apps.pilot.ligand_motifs: ATOM j: 8 Name: C6\r\n< apps.pilot.ligand_motifs: ATOM k: 7 Name: C5\r\n< apps.pilot.ligand_motifs: Connected triplet is: 9, type is CH2; 8, type is CH2; 7, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 9\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 8\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 7\r\n< apps.pilot.ligand_motifs: ATOM k: 9 Name: C7\r\n< apps.pilot.ligand_motifs: Connected triplet is: 9, type is CH2; 8, type is CH2; 9, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM j: 10 Name: C8\r\n< apps.pilot.ligand_motifs: ATOM k: 9 Name: C7\r\n< apps.pilot.ligand_motifs: Connected triplet is: 9, type is CH2; 10, type is CH2; 9, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 11 Name: C9\r\n< apps.pilot.ligand_motifs: Connected triplet is: 9, type is CH2; 10, type is CH2; 11, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 9\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 10\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 11\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 10\r\n< apps.pilot.ligand_motifs: atom name is C8\r\n< apps.pilot.ligand_motifs: ATOM j: 9 Name: C7\r\n< apps.pilot.ligand_motifs: ATOM k: 8 Name: C6\r\n< apps.pilot.ligand_motifs: Connected triplet is: 10, type is CH2; 9, type is CH2; 8, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 10\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 9\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 8\r\n< apps.pilot.ligand_motifs: ATOM k: 10 Name: C8\r\n< apps.pilot.ligand_motifs: Connected triplet is: 10, type is CH2; 9, type is CH2; 10, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM j: 11 Name: C9\r\n< apps.pilot.ligand_motifs: ATOM k: 10 Name: C8\r\n< apps.pilot.ligand_motifs: Connected triplet is: 10, type is CH2; 11, type is aroC; 10, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 12 Name: C10\r\n< apps.pilot.ligand_motifs: Connected triplet is: 10, type is CH2; 11, type is aroC; 12, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 10\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 11\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 12\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 11\r\n< apps.pilot.ligand_motifs: atom name is C9\r\n< apps.pilot.ligand_motifs: ATOM j: 10 Name: C8\r\n< apps.pilot.ligand_motifs: ATOM k: 9 Name: C7\r\n< apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 10, type is CH2; 9, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 11\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 10\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 9\r\n< apps.pilot.ligand_motifs: ATOM k: 11 Name: C9\r\n< apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 10, type is CH2; 11, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 12 Name: C10\r\n< apps.pilot.ligand_motifs: ATOM k: 11 Name: C9\r\n< apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 12, type is aroC; 11, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 13 Name: C11\r\n< apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 12, type is aroC; 13, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 11\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 12\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 13\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 12\r\n< apps.pilot.ligand_motifs: atom name is C10\r\n< apps.pilot.ligand_motifs: ATOM j: 11 Name: C9\r\n< apps.pilot.ligand_motifs: ATOM k: 10 Name: C8\r\n< apps.pilot.ligand_motifs: Connected triplet is: 12, type is aroC; 11, type is aroC; 10, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 12\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 11\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 10\r\n< apps.pilot.ligand_motifs: ATOM k: 12 Name: C10\r\n< apps.pilot.ligand_motifs: Connected triplet is: 12, type is aroC; 11, type is aroC; 12, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM j: 13 Name: C11\r\n< apps.pilot.ligand_motifs: ATOM k: 12 Name: C10\r\n< apps.pilot.ligand_motifs: Connected triplet is: 12, type is aroC; 13, type is CH2; 12, type is aroC \r\n< apps.pilot.ligand_motifs: ATOM k: 14 Name: C12\r\n< apps.pilot.ligand_motifs: Connected triplet is: 12, type is aroC; 13, type is CH2; 14, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 12\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 13\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 14\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 13\r\n< apps.pilot.ligand_motifs: atom name is C11\r\n< apps.pilot.ligand_motifs: ATOM j: 12 Name: C10\r\n< apps.pilot.ligand_motifs: ATOM k: 11 Name: C9\r\n< apps.pilot.ligand_motifs: Connected triplet is: 13, type is CH2; 12, type is aroC; 11, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 13\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 12\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 11\r\n< apps.pilot.ligand_motifs: ATOM k: 13 Name: C11\r\n< apps.pilot.ligand_motifs: Connected triplet is: 13, type is CH2; 12, type is aroC; 13, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM j: 14 Name: C12\r\n< apps.pilot.ligand_motifs: ATOM k: 13 Name: C11\r\n< apps.pilot.ligand_motifs: Connected triplet is: 13, type is CH2; 14, type is CH2; 13, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 15 Name: C13\r\n< apps.pilot.ligand_motifs: Connected triplet is: 13, type is CH2; 14, type is CH2; 15, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 13\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 14\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 15\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 14\r\n< apps.pilot.ligand_motifs: atom name is C12\r\n< apps.pilot.ligand_motifs: ATOM j: 13 Name: C11\r\n< apps.pilot.ligand_motifs: ATOM k: 12 Name: C10\r\n< apps.pilot.ligand_motifs: Connected triplet is: 14, type is CH2; 13, type is CH2; 12, type is aroC \r\n< apps.pilot.ligand_motifs: atom_i: 14\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 13\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 12\r\n< apps.pilot.ligand_motifs: ATOM k: 14 Name: C12\r\n< apps.pilot.ligand_motifs: Connected triplet is: 14, type is CH2; 13, type is CH2; 14, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM j: 15 Name: C13\r\n< apps.pilot.ligand_motifs: ATOM k: 14 Name: C12\r\n< apps.pilot.ligand_motifs: Connected triplet is: 14, type is CH2; 15, type is CH2; 14, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 16 Name: C14\r\n< apps.pilot.ligand_motifs: Connected triplet is: 14, type is CH2; 15, type is CH2; 16, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 14\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 15\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 16\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 15\r\n< apps.pilot.ligand_motifs: atom name is C13\r\n< apps.pilot.ligand_motifs: ATOM j: 14 Name: C12\r\n< apps.pilot.ligand_motifs: ATOM k: 13 Name: C11\r\n< apps.pilot.ligand_motifs: Connected triplet is: 15, type is CH2; 14, type is CH2; 13, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 15\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 14\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 13\r\n< apps.pilot.ligand_motifs: ATOM k: 15 Name: C13\r\n< apps.pilot.ligand_motifs: Connected triplet is: 15, type is CH2; 14, type is CH2; 15, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM j: 16 Name: C14\r\n< apps.pilot.ligand_motifs: ATOM k: 15 Name: C13\r\n< apps.pilot.ligand_motifs: Connected triplet is: 15, type is CH2; 16, type is CH2; 15, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 17 Name: C15\r\n< apps.pilot.ligand_motifs: Connected triplet is: 15, type is CH2; 16, type is CH2; 17, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 15\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 16\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 17\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 16\r\n< apps.pilot.ligand_motifs: atom name is C14\r\n< apps.pilot.ligand_motifs: ATOM j: 15 Name: C13\r\n< apps.pilot.ligand_motifs: ATOM k: 14 Name: C12\r\n< apps.pilot.ligand_motifs: Connected triplet is: 16, type is CH2; 15, type is CH2; 14, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 16\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 15\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 14\r\n< apps.pilot.ligand_motifs: ATOM k: 16 Name: C14\r\n< apps.pilot.ligand_motifs: Connected triplet is: 16, type is CH2; 15, type is CH2; 16, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM j: 17 Name: C15\r\n< apps.pilot.ligand_motifs: ATOM k: 16 Name: C14\r\n< apps.pilot.ligand_motifs: Connected triplet is: 16, type is CH2; 17, type is CH2; 16, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 18 Name: C16\r\n< apps.pilot.ligand_motifs: Connected triplet is: 16, type is CH2; 17, type is CH2; 18, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 16\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 17\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 18\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 17\r\n< apps.pilot.ligand_motifs: atom name is C15\r\n< apps.pilot.ligand_motifs: ATOM j: 16 Name: C14\r\n< apps.pilot.ligand_motifs: ATOM k: 15 Name: C13\r\n< apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 16, type is CH2; 15, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 17\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 16\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 15\r\n< apps.pilot.ligand_motifs: ATOM k: 17 Name: C15\r\n< apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 16, type is CH2; 17, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM j: 18 Name: C16\r\n< apps.pilot.ligand_motifs: ATOM k: 17 Name: C15\r\n< apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 18, type is CH2; 17, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 19 Name: C17\r\n< apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH2; 18, type is CH2; 19, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 17\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 18\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 19\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 18\r\n< apps.pilot.ligand_motifs: atom name is C16\r\n< apps.pilot.ligand_motifs: ATOM j: 17 Name: C15\r\n< apps.pilot.ligand_motifs: ATOM k: 16 Name: C14\r\n< apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 17, type is CH2; 16, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 18\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 17\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 16\r\n< apps.pilot.ligand_motifs: ATOM k: 18 Name: C16\r\n< apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 17, type is CH2; 18, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM j: 19 Name: C17\r\n< apps.pilot.ligand_motifs: ATOM k: 18 Name: C16\r\n< apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 19, type is CH2; 18, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM k: 20 Name: C18\r\n< apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH2; 19, type is CH2; 20, type is CH3 \r\n< apps.pilot.ligand_motifs: atom_i: 18\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 19\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 20\r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 19\r\n< apps.pilot.ligand_motifs: atom name is C17\r\n< apps.pilot.ligand_motifs: ATOM j: 18 Name: C16\r\n< apps.pilot.ligand_motifs: ATOM k: 17 Name: C15\r\n< apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH2; 18, type is CH2; 17, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 19\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 18\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 17\r\n< apps.pilot.ligand_motifs: ATOM k: 19 Name: C17\r\n< apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH2; 18, type is CH2; 19, type is CH2 \r\n< apps.pilot.ligand_motifs: ATOM j: 20 Name: C18\r\n< apps.pilot.ligand_motifs: ATOM k: 19 Name: C17\r\n< apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH2; 20, type is CH3; 19, type is CH2 \r\n< apps.pilot.ligand_motifs: in atom iterate block, atom num is 20\r\n< apps.pilot.ligand_motifs: atom name is C18\r\n< apps.pilot.ligand_motifs: ATOM j: 19 Name: C17\r\n< apps.pilot.ligand_motifs: ATOM k: 18 Name: C16\r\n< apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH3; 19, type is CH2; 18, type is CH2 \r\n< apps.pilot.ligand_motifs: atom_i: 20\r\n< apps.pilot.ligand_motifs: atom_i to atom_j: 19\r\n< apps.pilot.ligand_motifs: atom_j to atom_k: 18\r\n< apps.pilot.ligand_motifs: ATOM k: 20 Name: C18\r\n< apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH3; 19, type is CH2; 20, type is CH3 \r\n< apps.pilot.ligand_motifs: Total 3 atoms in pruned indices list is: 19\r\n< apps.pilot.ligand_motifs: Total 3 atoms in unpruned indices list is: 38\r\n< apps.pilot.ligand_motifs: Residue 14 passed energy cut with pack score: -6.06527, hbond score: 0, for a total score of: -6.06527\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n< apps.pilot.ligand_motifs: Top triplets contains 1 items.\r\n< apps.pilot.ligand_motifs: Top triplets are: Size of top_triplets: 1\r\n< apps.pilot.ligand_motifs: Size of this_triplet: 3\r\n---\r\n> protocols.motifs.IdentifyLigandMotifs: Writing TYR354A_Z2001_Ligatoms_28_27_31_A_4s0v.pdb\r\n1871,1890c128\r\n< apps.pilot.ligand_motifs: 19: 18-19-20Writing ILE63A_Z2002_Ligatoms_18_19_20_A_4s0v.pdb\r\n< apps.pilot.ligand_motifs: Motif index contains: 1-4-5\r\n< apps.pilot.ligand_motifs: Motif index contains: 2-1-3\r\n< apps.pilot.ligand_motifs: Motif index contains: 2-1-4\r\n< apps.pilot.ligand_motifs: Motif index contains: 3-1-4\r\n< apps.pilot.ligand_motifs: Motif index contains: 4-5-6\r\n< apps.pilot.ligand_motifs: Motif index contains: 5-6-7\r\n< apps.pilot.ligand_motifs: Motif index contains: 6-7-8\r\n< apps.pilot.ligand_motifs: Motif index contains: 7-8-9\r\n< apps.pilot.ligand_motifs: Motif index contains: 8-9-10\r\n< apps.pilot.ligand_motifs: Motif index contains: 9-10-11\r\n< apps.pilot.ligand_motifs: Motif index contains: 10-11-12\r\n< apps.pilot.ligand_motifs: Motif index contains: 11-12-13\r\n< apps.pilot.ligand_motifs: Motif index contains: 12-13-14\r\n< apps.pilot.ligand_motifs: Motif index contains: 13-14-15\r\n< apps.pilot.ligand_motifs: Motif index contains: 14-15-16\r\n< apps.pilot.ligand_motifs: Motif index contains: 15-16-17\r\n< apps.pilot.ligand_motifs: Motif index contains: 16-17-18\r\n< apps.pilot.ligand_motifs: Motif index contains: 17-18-19\r\n< apps.pilot.ligand_motifs: Motif index contains: 18-19-20\r\n---\r\n> protocols.motifs.IdentifyLigandMotifs: Writing ILE63A_Z2002_Ligatoms_18_19_20_A_4s0v.pdb\r\n", "state": "failed" }, "ligand_water_docking": { "log": "", "state": "passed" }, "longest_continuous_polar_segment_filter": { "log": "", "state": "passed" }, "loop_creation": { "log": "", "state": "passed" }, "loop_grower_N_term_symm": { "log": "", "state": "passed" }, "loop_hash": { "log": "", "state": "passed" }, "loop_modeling": { "log": "", "state": "passed" }, "make_and_perturb_bundle_multirepeat": { "log": "", "state": "passed" }, "make_exemplar": { "log": "", "state": "passed" }, "make_mainchain_potential": { "log": "", "state": "passed" }, "make_mainchain_potential_symm": { "log": "", "state": "passed" }, "make_mainchain_potential_symm_preproline": { "log": "", "state": "passed" }, "make_rot_lib": { "log": "", "state": "passed" }, "make_symmdef_file": { "log": "", "state": "passed" }, "match_1c2t": { "log": "", "state": "passed" }, "match_1n9l": { "log": "", "state": "passed" }, "match_6cpa": { "log": "", "state": "passed" }, "match_xml": { "log": "", "state": "passed" }, "measure_lcaa_radii": { "log": "", "state": "passed" }, "membrane_abinitio": { "log": "", "state": "passed" }, "metal_setup": { "log": "", "state": "passed" }, "metalloprotein_abrelax": { "log": "", "state": "passed" }, "metalloprotein_broker": { "log": "", "state": "passed" }, "metropolis_hastings": { "log": "", "state": "passed" }, "mf_fixbb_des": { "log": "", "state": "passed" }, "mf_fixbb_sc": { "log": "", "state": "passed" }, "mf_flexbb_sc": { "log": "", "state": "passed" }, "mg_modeler": { "log": "", "state": "passed" }, "mg_modeler_lores": { "log": "", "state": "passed" }, "mhc_epitope": { "log": "", "state": "passed" }, "mhc_epitope_nmer_preload": { "log": "", "state": "passed" }, "min_pack_min": { "log": "", "state": "passed" }, "minimize_6Dloopclose": { "log": "", "state": "passed" }, "minimize_with_elec_dens": { "log": "", "state": "passed" }, "mirror_symm": { "log": "", "state": "passed" }, "mixed_monte_carlo": { "log": "", "state": "passed" }, "mm_params": { "log": "", "state": "passed" }, "mmtfIO_score_test": { "log": "", "state": "passed" }, "molfile_to_params": { "log": "", "state": "passed" }, "molfile_to_params_polymer": { "log": "", "state": "passed" }, "motif_dna_packer_design": { "log": "", "state": "passed" }, "motif_extraction": { "log": "", "state": "passed" }, "motif_score_filter": { "log": "", "state": "passed" }, "mp_dock": { "log": "", "state": "passed" }, "mp_dock_ensemble": { "log": "", "state": "passed" }, "mp_dock_prepack": { "log": "", "state": "passed" }, "mp_dock_setup": { "log": "", "state": "passed" }, "mp_domain_assembly": { "log": "", "state": "passed" }, "mp_domain_assembly_FtsQ": { "log": "", "state": "passed" }, "mp_f19_relax": { "log": "", "state": "passed" }, "mp_find_interface": { "log": "", "state": "passed" }, "mp_interface_statistics": { "log": "", "state": "passed" }, "mp_ligand_interface": { "log": "", "state": "passed" }, "mp_loadtime": { "log": "", "state": "passed" }, "mp_mutate_relax": { "log": "", "state": "passed" }, "mp_mutate_repack": { "log": "", "state": "passed" }, "mp_quick_relax": { "log": "", "state": "passed" }, "mp_quick_relax_ref2015_memb": { "log": "", "state": "passed" }, "mp_range_relax": { "log": "", "state": "passed" }, "mp_relax": { "log": "", "state": "passed" }, "mp_score_jd2": { "log": "", "state": "passed" }, "mp_span_ang_ref2015_memb": { "log": "", "state": "passed" }, "mp_span_from_pdb": { "log": "", "state": "passed" }, "mp_symdock": { "log": "", "state": "passed" }, "mp_symmetry_load": { "log": "", "state": "passed" }, "mp_transform": { "log": "", "state": "passed" }, "mp_transform_optimize": { "log": "", "state": "passed" }, "mp_vis_emb": { "log": "", "state": "passed" }, "mpi_multistate_design": { "log": "", "state": "passed" }, "mpi_simple_cycpep_predict": { "log": "", "state": "passed" }, "mpi_simple_cycpep_predict_4level": { "log": "", "state": "passed" }, "mpi_simple_cycpep_predict_computing_pnear_to_all": { "log": "", "state": "passed" }, "mpil_find_pore_ahelical": { "log": "", "state": "passed" }, "mpil_find_pore_bbarrel": { "log": "", "state": "passed" }, "mpil_load_implicit_lipids": { "log": "", "state": "passed" }, "mr_protocols": { "log": "", "state": "passed" }, "multistage_rosetta_scripts": { "log": "", "state": "passed" }, "multistage_rosetta_scripts_clustering": { "log": "", "state": "passed" }, "multithreaded_fastdesign": { "log": "", "state": "passed" }, "multithreaded_fixbb": { "log": "", "state": "passed" }, "multithreaded_interaction_graph_accuracy": { "log": "", "state": "passed" }, "multithreaded_interaction_graph_accuracy_symm": { "log": "", "state": "passed" }, "multithreaded_packrotamersmover": { "log": "", "state": "passed" }, "mutate": { "log": "", "state": "passed" }, "ncaa_fixbb": { "log": "", "state": "passed" }, "ncbb_packer_palette": { "log": "", "state": "passed" }, "netcharge_design": { "log": "", "state": "passed" }, "netcharge_design_symm": { "log": "", "state": "passed" }, "next_generation_KIC": { "log": "", "state": "passed" }, "noe_assignment": { "log": "", "state": "passed" }, "non-canonical_connectivities": { "log": "", "state": "passed" }, "nonideal_rtmin": { "log": "", "state": "passed" }, "nucleobase_sample_around": { "log": "", "state": "passed" }, "number_of_residuetypes": { "log": "", "state": "passed" }, "oligourea_design": { "log": "", "state": "passed" }, "oligourea_predict": { "log": "", "state": "passed" }, "oop_create": { "log": "", "state": "passed" }, "oop_design": { "log": "", "state": "passed" }, "oop_dock_design": { "log": "", "state": "passed" }, "orbitals": { "log": "", "state": "passed" }, "output_schema": { "log": "", "state": "passed" }, "pH_mode": { "log": "", "state": "passed" }, "pepspec_anchor_dock": { "log": "", "state": "passed" }, "peptiderive": { "log": "", "state": "passed" }, "per_residue_energies": { "log": "", "state": "passed" }, "per_residue_sc_sasa": { "log": "", "state": "passed" }, "per_residue_solvent_exposure": { "log": "", "state": "passed" }, "pertmin": { "log": "", "state": "passed" }, "perturb_helical_bundle": { "log": "", "state": "passed" }, "perturb_helical_bundle_copying_pitch": { "log": "", "state": "passed" }, "perturb_helical_bundle_epsilon": { "log": "", "state": "passed" }, "perturb_helical_bundle_setting": { "log": "", "state": "passed" }, "perturb_helical_bundle_z_offset": { "log": "", "state": "passed" }, "phiselector": { "log": "", "state": "passed" }, "phosphonate": { "log": "", "state": "passed" }, "phosphorylation": { "log": "", "state": "passed" }, "place_simultaneously": { "log": "", "state": "passed" }, "pmut_scan": { "log": "", "state": "passed" }, "pna": { "log": "", "state": "passed" }, "pna_base_pairs": { "log": "", "state": "passed" }, "pocket_measure": { "log": "", "state": "passed" }, "pocket_relax": { "log": "", "state": "passed" }, "pocket_suggest_targets": { "log": "", "state": "passed" }, "polyaramid_test_trivial": { "log": "", "state": "passed" }, "pose_sewing": { "log": "", "state": "passed" }, "posttranslationalmod_io": { "log": "", "state": "passed" }, "ppi_v3_suiteA": { "log": "", "state": "passed" }, "ppi_v3_suiteB": { "log": "", "state": "passed" }, "ppi_v3_suiteC": { "log": "", "state": "passed" }, "ppi_v3_suiteD": { "log": "", "state": "passed" }, "ppi_v3_suiteE": { "log": "", "state": "passed" }, "ppi_v3_suiteF": { "log": "", "state": "passed" }, "ppi_v3_suiteG": { "log": "", "state": "passed" }, "ppk": { "log": "", "state": "passed" }, "proteinMPNN_model_perplexity": { "log": "", "state": "passed" }, "protocol_metric": { "log": "", "state": "passed" }, "pwsho": { "log": "", "state": "passed" }, "pymol_cif": { "log": "", "state": "passed" }, "r_pdb2top": { "log": "", "state": "passed" }, "r_rmsf": { "log": "", "state": "passed" }, "ralford_dump_rotamers": { "log": "", "state": "passed" }, "rama_mutation_selector": { "log": "", "state": "passed" }, "range_relax_w_cst": { "log": "", "state": "passed" }, "rb_recces": { "log": "", "state": "passed" }, "rdkit_metrics": { "log": "", "state": "passed" }, "read_polymeric_components": { "log": "", "state": "passed" }, "readin_dna_rna_protein": { "log": "", "state": "passed" }, "real_motif_analysis": { "log": "Brief Diff:\ndiff: /home/benchmark/working_dir/main:62149/real_motif_analysis: No such file or directory\r\n\nCompare(...): Marking as \"Script failed\" due to presense of .test_did_not_run.log or .test_got_timeout_kill.log file!\n", "state": "script failed" }, "real_virt_mover": { "log": "", "state": "passed" }, "recces_turner": { "log": "", "state": "passed" }, "recon_design": { "log": "", "state": "passed" }, "recon_design_mpi": { "log": "", "state": "passed" }, "referencepose_mutateresidue": { "log": "", "state": "passed" }, "relax_w_allatom_cst": { "log": "", "state": "passed" }, "remodel_disulfides_rosettascripts": { "log": "", "state": "passed" }, "remodel_helical_repeat": { "log": "", "state": "passed" }, "remove_duplicate_motifs": { "log": "Brief Diff:\ndiff: /home/benchmark/working_dir/main:62149/remove_duplicate_motifs: No such file or directory\r\n\nCompare(...): Marking as \"Script failed\" due to presense of .test_did_not_run.log or .test_got_timeout_kill.log file!\n", "state": "script failed" }, "repack_with_elec_dens": { "log": "", "state": "passed" }, "repeat_propagate": { "log": "", "state": "passed" }, "repeat_propagate_v2": { "log": "", "state": "passed" }, "repeat_propagate_v3": { "log": "", "state": "passed" }, "repeat_relax": { "log": "", "state": "passed" }, "replica_docking": { "log": "", "state": "passed" }, "report_hbonds_for_plugin": { "log": "", "state": "passed" }, "res_lipo_ref2015_memb": { "log": "", "state": "passed" }, "residue_energy_breakdown": { "log": "", "state": "passed" }, "resource_database_locator": { "log": "", "state": "passed" }, "restype_converter": { "log": "", "state": "passed" }, "rings": { "log": "", "state": "passed" }, "rna_add_WC_stats": { "log": "", "state": "passed" }, "rna_assemble": { "log": "", "state": "passed" }, "rna_cluster": { "log": "", "state": "passed" }, "rna_denovo": { "log": "", "state": "passed" }, "rna_denovo_RNP_low_res": { "log": "", "state": "passed" }, "rna_denovo_RNP_refine_native": { "log": "", "state": "passed" }, "rna_denovo_base_pair_constraints": { "log": "", "state": "passed" }, "rna_denovo_base_pair_setup": { "log": "", "state": "passed" }, "rna_denovo_bps": { "log": "", "state": "passed" }, "rna_denovo_bps_fixed_ends": { "log": "", "state": "passed" }, "rna_denovo_bps_helix_ends": { "log": "", "state": "passed" }, "rna_denovo_dna_bridge": { "log": "", "state": "passed" }, "rna_denovo_fragment_homology_exclusion": { "log": "", "state": "passed" }, "rna_denovo_grid_vdw": { "log": "", "state": "passed" }, "rna_denovo_lariat": { "log": "", "state": "passed" }, "rna_denovo_new_FT_2in_dens": { "log": "", "state": "passed" }, "rna_denovo_new_FT_5P_j12_leadzyme": { "log": "", "state": "passed" }, "rna_denovo_new_FT_RNP_2prot_dens": { "log": "", "state": "passed" }, "rna_denovo_new_FT_rna_two_chains": { "log": "", "state": "passed" }, "rna_denovo_new_libs": { "log": "", "state": "passed" }, "rna_denovo_symm_hack": { "log": "", "state": "passed" }, "rna_design": { "log": "", "state": "passed" }, "rna_farfar_block_stack": { "log": "", "state": "passed" }, "rna_farfar_noncanonical_hairpin": { "log": "", "state": "passed" }, "rna_farfar_syn_chi_res": { "log": "", "state": "passed" }, "rna_helix": { "log": "", "state": "passed" }, "rna_minimize": { "log": "", "state": "passed" }, "rna_minimize_6D_loop_close": { "log": "", "state": "passed" }, "rna_motif": { "log": 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