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 ────────────────
{
"compared_with_test": {
"full_name": "linux.clang.integration.release_debug_no_symbols",
"name": "integration.release_debug_no_symbols",
"platform": {
"compiler": "clang",
"extras": [],
"os": "linux"
},
"platform_as_string": "linux.clang",
"revision": {
"branch": "main",
"revision_id": 62149
},
"state": "failed",
"test_id": 852263
},
"summary": {
"failed": 6,
"failed_tests": [
"ligand_motif_identification",
"real_motif_analysis",
"include_cc_check",
"ligand_motif_discovery",
"features",
"remove_duplicate_motifs"
],
"total": 806
},
"tests": {
"AddConstraintsToCurrentConformationMover": {
"log": "",
"state": "passed"
},
"AlignPDBInfoToSequences": {
"log": "",
"state": "passed"
},
"AlterSpecDisruption": {
"log": "",
"state": "passed"
},
"AnchorFinder": {
"log": "",
"state": "passed"
},
"AnchoredDesign": {
"log": "",
"state": "passed"
},
"AnchoredPDBCreator": {
"log": "",
"state": "passed"
},
"BFactorSelector": {
"log": "",
"state": "passed"
},
"BuildPeptide": {
"log": "",
"state": "passed"
},
"CCD_loop_closure": {
"log": "",
"state": "passed"
},
"CCS_PARCS": {
"log": "",
"state": "passed"
},
"ConsensusLoopDesign": {
"log": "",
"state": "passed"
},
"ContactMolecularSurface": {
"log": "",
"state": "passed"
},
"DARC_electrostatics": {
"log": "",
"state": "passed"
},
"DARC_make_ray_files": {
"log": "",
"state": "passed"
},
"DARC_sampling_on_the_fly": {
"log": "",
"state": "passed"
},
"DARC_shapeonly": {
"log": "",
"state": "passed"
},
"DNA_methylation": {
"log": "",
"state": "passed"
},
"DumpTrajectoryEnergy": {
"log": "",
"state": "passed"
},
"DumpTrajectoryEnergy_packing": {
"log": "",
"state": "passed"
},
"Enzrevert_xml": {
"log": "",
"state": "passed"
},
"FavorSequenceProfileMover": {
"log": "",
"state": "passed"
},
"FilterReportAsPoseExtraScoresMover": {
"log": "",
"state": "passed"
},
"FlipChirality": {
"log": "",
"state": "passed"
},
"FloppyTail": {
"log": "",
"state": "passed"
},
"HDXEnergy": {
"log": "",
"state": "passed"
},
"HOW_TO_MAKE_TESTS": {
"log": "",
"state": "passed"
},
"HelixBendFilter": {
"log": "",
"state": "passed"
},
"InterfaceAnalyzer": {
"log": "",
"state": "passed"
},
"InterfaceAnalyzer_allscores": {
"log": "",
"state": "passed"
},
"InterfaceAnalyzer_bothpack": {
"log": "",
"state": "passed"
},
"InterfaceAnalyzer_ligand": {
"log": "",
"state": "passed"
},
"InterfaceAnalyzer_metrics": {
"log": "",
"state": "passed"
},
"InterfaceAnalyzer_prepack": {
"log": "",
"state": "passed"
},
"InterfaceAnalyzer_resfile": {
"log": "",
"state": "passed"
},
"InterfaceAnalyzer_tracer": {
"log": "",
"state": "passed"
},
"InterfaceDdG": {
"log": "",
"state": "passed"
},
"KIC_refine": {
"log": "",
"state": "passed"
},
"KIC_vicinity": {
"log": "",
"state": "passed"
},
"KIC_with_fragments": {
"log": "",
"state": "passed"
},
"LayerDesign": {
"log": "",
"state": "passed"
},
"LayerDesign_symm": {
"log": "",
"state": "passed"
},
"LayerSelector": {
"log": "",
"state": "passed"
},
"LoopAnalyzer": {
"log": "",
"state": "passed"
},
"LoopLengthChange": {
"log": "",
"state": "passed"
},
"ModifyVariantTypeMover": {
"log": "",
"state": "passed"
},
"MutateResidue_selector": {
"log": "",
"state": "passed"
},
"N-terminal_acetylation": {
"log": "",
"state": "passed"
},
"OversaturatedHbondAcceptorFilter": {
"log": "",
"state": "passed"
},
"PDB_diagnostic": {
"log": "",
"state": "passed"
},
"PTMPrediction": {
"log": "",
"state": "passed"
},
"PeptideCyclizeMover": {
"log": "",
"state": "passed"
},
"PeptideStubMover_prependRepeat": {
"log": "",
"state": "passed"
},
"PolarDesign2019": {
"log": "",
"state": "passed"
},
"ProQ": {
"log": "",
"state": "passed"
},
"RBOut": {
"log": "",
"state": "passed"
},
"ReadResfile_with_selector": {
"log": "",
"state": "passed"
},
"RescorePDDF": {
"log": "",
"state": "passed"
},
"RescoreSAXS": {
"log": "",
"state": "passed"
},
"ResidueDisorder": {
"log": "",
"state": "passed"
},
"RunSimpleMetric_b_factor_test": {
"log": "",
"state": "passed"
},
"SID_ERMS_prediction": {
"log": "",
"state": "passed"
},
"SID_rescore": {
"log": "",
"state": "passed"
},
"SSElementSelector": {
"log": "",
"state": "passed"
},
"SecondaryStructureFilter": {
"log": "",
"state": "passed"
},
"SnugDock": {
"log": "",
"state": "passed"
},
"StrandCurvatureByLevels": {
"log": "",
"state": "passed"
},
"StrandHelixGeometryFilter": {
"log": "",
"state": "passed"
},
"ThreadingInputter": {
"log": "",
"state": "passed"
},
"TryDisulfPermutations": {
"log": "",
"state": "passed"
},
"UBQ_E2_thioester": {
"log": "",
"state": "passed"
},
"UBQ_E2_thioester_extra_bodies": {
"log": "",
"state": "passed"
},
"UBQ_E2_thioester_two_ubiquitins": {
"log": "",
"state": "passed"
},
"UBQ_Gp_CYD-CYD": {
"log": "",
"state": "passed"
},
"UBQ_Gp_LYX-Cterm": {
"log": "",
"state": "passed"
},
"UnsatSelector": {
"log": "",
"state": "passed"
},
"Werror_check": {
"log": "",
"state": "passed"
},
"abinitio": {
"log": "",
"state": "passed"
},
"abinitio_with_trRosetta": {
"log": "",
"state": "passed"
},
"add_constraints_to_current_conformation": {
"log": "",
"state": "passed"
},
"add_helix_sequence_constraints": {
"log": "",
"state": "passed"
},
"add_helix_sequence_constraints_advanced_setup": {
"log": "",
"state": "passed"
},
"add_job_pair_data": {
"log": "",
"state": "passed"
},
"ambiguous_nmr_distance_constraint": {
"log": "",
"state": "passed"
},
"angle_recovery_stats": {
"log": "",
"state": "passed"
},
"antibody_H3": {
"log": "",
"state": "passed"
},
"antibody_H3_camelid": {
"log": "",
"state": "passed"
},
"antibody_cc": {
"log": "",
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"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",
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"log": "",
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"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",
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"rings": {
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"rna_puzzle11_H2H3H4_run3_connectU40": {
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},
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"rosetta_scripts_info": {
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"rosie_ligand_docking": {
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"rotamer_recovery": {
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"rs_flexbbmoves": {
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},
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},
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},
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},
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},
"score_jd2": {
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},
"score_only_silence": {
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},
"sdf_reader": {
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},
"secondary_structure_output": {
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},
"seed_ensemble_JD2_JI": {
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},
"select_best_unique_ligand_poses": {
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},
"selected_residue_count_metric": {
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},
"sequence_profile_constraints": {
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},
"sequence_recovery": {
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},
"sequence_tolerance": {
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},
"set_torsion": {
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},
"shobuns": {
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},
"silent2frag": {
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},
"sim_cryo": {
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},
"simple_cycpep_predict": {
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},
"simple_cycpep_predict_1_4_bbmb": {
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},
"simple_cycpep_predict_angle": {
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},
"simple_cycpep_predict_anglelength": {
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},
"simple_cycpep_predict_beta_thioether_lariat": {
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},
"simple_cycpep_predict_bondangle_bondlength": {
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},
"simple_cycpep_predict_cartesian": {
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},
"simple_cycpep_predict_cispro": {
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},
"simple_cycpep_predict_cterm_isopeptide_lariat": {
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},
"simple_cycpep_predict_cterm_isopeptide_lariat_tailless": {
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},
"simple_cycpep_predict_design": {
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},
"simple_cycpep_predict_lanthionine": {
"log": "",
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},
"simple_cycpep_predict_nmethyl": {
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},
"simple_cycpep_predict_nterm_isopeptide_lariat": {
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},
"simple_cycpep_predict_nterm_isopeptide_lariat_tailless": {
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},
"simple_cycpep_predict_octahedral_metal": {
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},
"simple_cycpep_predict_peptoid": {
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},
"simple_cycpep_predict_setting": {
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},
"simple_cycpep_predict_sidechain_isopeptide": {
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},
"simple_cycpep_predict_sidechain_isopeptide_reverse": {
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},
"simple_cycpep_predict_square_planar_metal": {
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},
"simple_cycpep_predict_square_pyramidal_metal": {
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},
"simple_cycpep_predict_symm_gly": {
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},
"simple_cycpep_predict_symmetric_sampling": {
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},
"simple_cycpep_predict_tbmb": {
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},
"simple_cycpep_predict_terminal_disulfide": {
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},
"simple_cycpep_predict_terminal_disulfide_internal_permutations": {
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},
"simple_cycpep_predict_terminal_disulfide_tails": {
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},
"simple_cycpep_predict_terminal_disulfide_tails_2": {
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},
"simple_cycpep_predict_tetrahedral_metal": {
"log": "",
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},
"simple_cycpep_predict_tetrahedral_metal_asp": {
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},
"simple_cycpep_predict_thioether_cis_sampling": {
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},
"simple_cycpep_predict_thioether_lariat": {
"log": "",
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},
"simple_cycpep_predict_tma": {
"log": "",
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},
"simple_cycpep_predict_trigonal_planar_metal": {
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},
"simple_cycpep_predict_trigonal_pyramidal_metal": {
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},
"simple_dna_test": {
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},
"simple_glycosylation": {
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},
"simple_glycosylation_alternate_AAs": {
"log": "",
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},
"simple_grafting_movers": {
"log": "",
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},
"simple_hbondstoatom": {
"log": "",
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},
"simple_metric_cache": {
"log": "",
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},
"simple_metric_features": {
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},
"simple_metric_filter": {
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},
"simple_metrics": {
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},
"simple_metrics_b_factor": {
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},
"simple_metrics_in_protocols": {
"log": "",
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},
"simple_metrics_per_residue": {
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},
"site_constraint": {
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},
"small_molecule_lattice_dock": {
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},
"smallmover_resselector": {
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},
"smart_annealer": {
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},
"splice_in_4loops_longer": {
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},
"splice_in_4loops_shorter": {
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},
"splice_out_H1_H2_longer": {
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},
"splice_out_H1_H2_same": {
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},
"splice_out_H1_H2_shorter": {
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},
"splice_out_H3_longer": {
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},
"splice_out_H3_same": {
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},
"splice_out_H3_shorter": {
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},
"splice_out_L1_L2_longer": {
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},
"splice_out_L1_L2_same": {
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},
"splice_out_L1_L2_shorter": {
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},
"splice_out_L3_longer": {
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},
"splice_out_L3_same": {
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},
"splice_out_L3_shorter": {
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},
"startfrom_file": {
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},
"stepwise_lores": {
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},
"stored_residue_subset": {
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},
"struc_set_fragment_picker": {
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},
"super_aln": {
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},
"supercharge": {
"log": "",
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},
"surface_docking": {
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},
"swa_protein_CCDclose": {
"log": "",
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},
"swa_protein_build_at_Cterminus": {
"log": "",
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},
"swa_protein_build_at_Nterminus": {
"log": "",
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},
"swa_protein_cluster": {
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},
"swa_protein_combine_loops": {
"log": "",
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},
"swa_protein_loop_sampler": {
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},
"swa_protein_prepack": {
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},
"swa_rna_erraser": {
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},
"swa_rna_gagu_01_append": {
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},
"swa_rna_gagu_02_prepend": {
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},
"swa_rna_gagu_03_append_to_silent": {
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},
"swa_rna_gagu_04_clustering": {
"log": "",
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},
"swa_rna_gagu_05_prepend_to_5primeterminus": {
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},
"swa_rna_gagu_06_append_to_3primeterminus": {
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},
"swa_rna_gagu_07_prepend_dinucleotide": {
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},
"swa_rna_gagu_08_append_dinucleotide": {
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},
"swa_rna_gagu_09_sample_virtual_ribose": {
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},
"swa_rna_gagu_10_prepend_and_ccd_close": {
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},
"swa_rna_gagu_11_append_and_ccd_close": {
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},
"swa_rna_gagu_12_helix_addition": {
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},
"swa_rna_gagu_13_chunk_combination_and_closure": {
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},
"swa_rna_gagu_14_combine_long_loop_filtering": {
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},
"swa_rna_gagu_15_combine_long_loop_sampling": {
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},
"swa_rna_gagu_16_prepend_dinucleotide_on_dinucleotide": {
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},
"swa_rna_gagu_17_append_floating_base": {
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},
"swa_rna_gagu_18_rebuild_bulge": {
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},
"swa_rna_gagu_19_prepend_floating_base_by_jump": {
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},
"swa_rna_gagu_20_append_floating_base_by_jump": {
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},
"swa_rna_gagu_21_prepend_dinucleotide_on_dinucleotide_by_jump": {
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},
"swa_rna_gagu_22_prepend_and_kic_close": {
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},
"swa_rna_gagu_23_append_and_kic_close": {
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},
"swa_rna_loop_clusterer": {
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},
"swa_rna_loop_sampler": {
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},
"sweep_respair_energies": {
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},
"swm_add_rosettascripts": {
"log": "",
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},
"swm_beta_peptide_loop": {
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},
"swm_build_full_model": {
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},
"swm_dna_bridge": {
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},
"swm_dna_loop": {
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},
"swm_general_polymer_sampler": {
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},
"swm_l_rna": {
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},
"swm_protein_CCDmove": {
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},
"swm_protein_from_scratch": {
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},
"swm_protein_loop_sampler": {
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},
"swm_protein_move_inside_coiledcoil_by_bond": {
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},
"swm_protein_move_inside_helix_by_bond": {
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},
"swm_protein_preminimize": {
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},
"swm_rna_base_pair_constraints": {
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},
"swm_rna_checkpoint_partition": {
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},
"swm_rna_fourwayjunction": {
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},
"swm_rna_loop_design": {
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},
"swm_rna_move_align_dock": {
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},
"swm_rna_move_inside_helix_by_bond": {
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},
"swm_rna_move_inside_helix_by_jump": {
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},
"swm_rna_move_two_strands": {
"log": "",
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},
"swm_rna_nickedhelix": {
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},
"swm_rna_protonated_adenosine": {
"log": "",
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},
"swm_rna_singleloop": {
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},
"swm_rna_srl_triplet": {
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},
"symm_disulfidize": {
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},
"symm_rotamer_boltzmann": {
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},
"symmetric_cycpep_align_and_symmetrize": {
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},
"symmetric_docking": {
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},
"symmetrical_residue_selector": {
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},
"symmetry_data_resource": {
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},
"symmetry_multicomponent": {
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},
"target_clash": {
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},
"task_selector": {
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"state": "passed"
},
"tcrmodel": {
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},
"template_features": {
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"state": "passed"
},
"tensorflow_connection_test": {
"log": "",
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},
"tensorflow_manager": {
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},
"tensorflow_simple_model_load_and_evaluate": {
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"state": "passed"
},
"test1_benchmark": {
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},
"test_computed_saxs_spectrum": {
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},
"test_d_l_readin": {
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},
"test_degreaser": {
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},
"test_energy_method_options": {
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"state": "passed"
},
"test_idealize": {
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"state": "passed"
},
"test_rosetta_thread_manager_advanced_API": {
"log": "",
"state": "passed"
},
"test_rosetta_thread_manager_basic_API": {
"log": "",
"state": "passed"
},
"thermal_sampler": {
"log": "",
"state": "passed"
},
"thread_local_tracers_check": {
"log": "",
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},
"threefold_symm_peptide_design": {
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},
"threefoldlinkermover_tbmb": {
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},
"threefoldlinkermover_tbmb_symmetric": {
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},
"tna_base_pairs": {
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},
"torsion_restricted_sampling": {
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"state": "passed"
},
"trRosetta": {
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"state": "passed"
},
"trRosettaConstraintGenerator": {
"log": "",
"state": "passed"
},
"trRosettaConstraintGenerator_rosettascripts": {
"log": "",
"state": "passed"
},
"trRosettaProtocolMover": {
"log": "",
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},
"trRosettaProtocolMover_rosettascripts": {
"log": "",
"state": "passed"
},
"trRosettaProtocolMover_rosettascripts_diskwrite": {
"log": "",
"state": "passed"
},
"trRosettaProtocolMover_rosettascripts_diskwrite_only": {
"log": "",
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},
"trRosetta_test_predict": {
"log": "",
"state": "passed"
},
"trRosetta_test_predict_ubiquitin": {
"log": "",
"state": "passed"
},
"trRosetta_test_predict_ubiquitin_cst_file_write": {
"log": "",
"state": "passed"
},
"trRosetta_test_predict_ubiquitin_cst_file_write_only": {
"log": "",
"state": "passed"
},
"trRosetta_test_predict_ubiquitin_init_by_bins": {
"log": "",
"state": "passed"
},
"unfolded_state_energy_calc": {
"log": "",
"state": "passed"
},
"validate_database": {
"log": "",
"state": "passed"
},
"vancomycin": {
"log": "",
"state": "passed"
},
"vip": {
"log": "",
"state": "passed"
},
"voids_penalty_energy_design": {
"log": "",
"state": "passed"
},
"voids_penalty_energy_design_symmetry": {
"log": "",
"state": "passed"
},
"write_mol_file": {
"log": "",
"state": "passed"
},
"zinc_heterodimer": {
"log": "",
"state": "passed"
},
"zinc_homodimer_design": {
"log": "",
"state": "passed"
},
"zinc_homodimer_setup": {
"log": "",
"state": "passed"
}
}
}