Compiling: find bin -type l ! -name ".*" -exec rm {} \; ; /Volumes/scratch/b3.w/prefix/mac/hikaru-2/mac/python-3.9.clang/707eb77cedeac3e91130adc5f9ccf882/bin/python3.9 ./scons.py bin mode=release cxx=clang extras= -j32
Running: unset __PYVENV_LAUNCHER__ && . /Volumes/scratch/b3.w/prefix/mac/hikaru-2/mac/python_virtual_environments/python-3.9/70fb5a411fc5470c895f6d4975b66fbe/bin/activate && cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration && python ./integration.py --mode=release --compiler=clang --extras= --timeout=480 -j32 --skip-comparison --additional_flags "-in:path:database_cache_dir /Volumes/scratch/b3.w/rosetta/commits/rosetta/.database-binaries/macclangrelease"
Running integration script...
Command line: unset __PYVENV_LAUNCHER__ && . /Volumes/scratch/b3.w/prefix/mac/hikaru-2/mac/python_virtual_environments/python-3.9/70fb5a411fc5470c895f6d4975b66fbe/bin/activate && cd /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration && python ./integration.py --mode=release --compiler=clang --extras= --timeout=480 -j32 --skip-comparison --additional_flags "-in:path:database_cache_dir /Volumes/scratch/b3.w/rosetta/commits/rosetta/.database-binaries/macclangrelease"
Using Rosetta source dir at: /Volumes/scratch/b3.w/rosetta/commits/rosetta/source
Using Rosetta database dir at:/Volumes/scratch/b3.w/rosetta/commits/rosetta/database
Current Versions Tested:
MAIN: 1298fde858856152300a5d4b072b28448924a54c
TOOLS: b0af2521cbed1f2bde597ef1c5406efa376a6f85
DEMOS: 48c9239db73b9a8c828954d9215c983b9f144c92
Python: `/Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python_virtual_environments/python-3.9/70fb5a411fc5470c895f6d4975b66fbe/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 480 && bash /Volumes/scratch/b3.w/rosetta/commits/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 480 && bash /Volumes/scratch/b3.w/rosetta/commits/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 480 && bash /Volumes/scratch/b3.w/rosetta/commits/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 960 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/app_exception_handling/command.sh
Running Test dgdp_script
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/dgdp_script/command.sh
Running Test simple_cycpep_predict_square_pyramidal_metal
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_square_pyramidal_metal/command.sh
Running Test auto-drrafter_setup_run_R2
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/auto-drrafter_setup_run_R2/command.sh
Running Test dgdp_aio
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/dgdp_aio/command.sh
Running Test database_md5
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/database_md5/command.sh
Running Test ddG_of_mutation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ddG_of_mutation/command.sh
Running Test antibody_H3
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/antibody_H3/command.sh
Running Test fast_relax_scripts
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fast_relax_scripts/command.sh
Running Test cyclization
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cyclization/command.sh
Running Test remodel
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/remodel/command.sh
Running Test ccd_ends_graft_mover_rs
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ccd_ends_graft_mover_rs/command.sh
Running Test glycopeptidedocking_diglyco_long
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/glycopeptidedocking_diglyco_long/command.sh
Running Test bundlegridsampler_composition_energy
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bundlegridsampler_composition_energy/command.sh
Running Test add_helix_sequence_constraints
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/add_helix_sequence_constraints/command.sh
Running Test glycan_tree_relax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/glycan_tree_relax/command.sh
Running Test crosslinkermover_octahedral
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_octahedral/command.sh
Running Test ligand_dock_ensemble
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ligand_dock_ensemble/command.sh
Running Test nonideal_rtmin
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/nonideal_rtmin/command.sh
Running Test ga_ligand_dock
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ga_ligand_dock/command.sh
Running Test ddG_sym
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ddG_sym/command.sh
Running Test mp_relax_w_ligand
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_relax_w_ligand/command.sh
Running Test buried_unsat_voids_hbnet_design_symm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/buried_unsat_voids_hbnet_design_symm/command.sh
Running Test add_helix_sequence_constraints_advanced_setup
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/add_helix_sequence_constraints_advanced_setup/command.sh
Running Test auto-drrafter_setup_run_R1
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/auto-drrafter_setup_run_R1/command.sh
Running Test crosslinkermover_tma
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_tma/command.sh
Running Test ppi_v3_suiteC
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ppi_v3_suiteC/command.sh
Running Test peptiderive
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/peptiderive/command.sh
Running Test drrafter_run
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/drrafter_run/command.sh
Finished real_motif_analysis in 8 seconds [~ 55 test (6.740196078431373%) started, 761 in queue, 32 running]
Running Test rna_denovo_lariat
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_lariat/command.sh
Finished remove_duplicate_motifs in 18 seconds [~ 56 test (6.862745098039215%) started, 760 in queue, 32 running]
Running Test voids_penalty_energy_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/voids_penalty_energy_design/command.sh
Finished rna_denovo_lariat in 116 seconds [~ 57 test (6.985294117647059%) started, 759 in queue, 32 running]
Running Test swm_dna_bridge
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_dna_bridge/command.sh
Finished crosslinkermover_tma in 125 seconds [~ 58 test (7.107843137254902%) started, 758 in queue, 32 running]
Running Test flexpepdock
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/flexpepdock/command.sh
Finished ppi_v3_suiteC in 125 seconds [~ 59 test (7.230392156862745%) started, 757 in queue, 32 running]
Running Test swm_rna_srl_triplet
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_rna_srl_triplet/command.sh
Finished drrafter_run in 128 seconds [~ 60 test (7.352941176470588%) started, 756 in queue, 32 running]
Running Test ga_ligand_dock_macrocycle
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ga_ligand_dock_macrocycle/command.sh
Finished buried_unsat_voids_hbnet_design_symm in 128 seconds [~ 61 test (7.4754901960784315%) started, 755 in queue, 32 running]
Running Test validate_database
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/validate_database/command.sh
Finished peptiderive in 128 seconds [~ 62 test (7.598039215686274%) started, 754 in queue, 32 running]
Running Test swa_protein_CCDclose
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_protein_CCDclose/command.sh
Finished voids_penalty_energy_design in 112 seconds [~ 63 test (7.720588235294118%) started, 753 in queue, 32 running]
Running Test ddG_ensemble
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ddG_ensemble/command.sh
Finished auto-drrafter_setup_run_R1 in 133 seconds [~ 64 test (7.8431372549019605%) started, 752 in queue, 32 running]
Running Test coupled_moves
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/coupled_moves/command.sh
Finished ddG_sym in 140 seconds [~ 65 test (7.965686274509804%) started, 751 in queue, 32 running]
Running Test job_definition_script_vars
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/job_definition_script_vars/command.sh
Finished nonideal_rtmin in 140 seconds [~ 66 test (8.088235294117647%) started, 750 in queue, 32 running]
Running Test swm_rna_base_pair_constraints
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_rna_base_pair_constraints/command.sh
Finished add_helix_sequence_constraints_advanced_setup in 144 seconds [~ 67 test (8.21078431372549%) started, 749 in queue, 32 running]
Running Test rnp_ddg_relax_command_2
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rnp_ddg_relax_command_2/command.sh
Finished crosslinkermover_octahedral in 146 seconds [~ 68 test (8.333333333333334%) started, 748 in queue, 32 running]
Running Test test1_benchmark
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/test1_benchmark/command.sh
Finished ga_ligand_dock in 149 seconds [~ 69 test (8.455882352941176%) started, 747 in queue, 32 running]
Running Test ppi_v3_suiteF
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ppi_v3_suiteF/command.sh
Finished ligand_dock_ensemble in 154 seconds [~ 70 test (8.57843137254902%) started, 746 in queue, 32 running]
Running Test glycan_relax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/glycan_relax/command.sh
Finished mp_relax_w_ligand in 155 seconds [~ 71 test (8.700980392156863%) started, 745 in queue, 32 running]
Running Test docking_ensemble_prepack
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/docking_ensemble_prepack/command.sh
Finished ccd_ends_graft_mover_rs in 158 seconds [~ 72 test (8.823529411764707%) started, 744 in queue, 32 running]
Running Test simple_cycpep_predict_trigonal_pyramidal_metal
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_trigonal_pyramidal_metal/command.sh
Finished glycan_tree_relax in 163 seconds [~ 73 test (8.946078431372548%) started, 743 in queue, 32 running]
No correct command.sh file found for esm_model_perplexity. Skipping.
Running Test auto-drrafter_setup_run_R3
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/auto-drrafter_setup_run_R3/command.sh
Finished glycopeptidedocking_diglyco_long in 165 seconds [~ 75 test (9.191176470588236%) started, 741 in queue, 32 running]
Running Test antibody_designer
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/antibody_designer/command.sh
Finished remodel in 170 seconds [~ 76 test (9.313725490196079%) started, 740 in queue, 32 running]
Running Test rna_denovo_dna_bridge
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_dna_bridge/command.sh
Finished bundlegridsampler_composition_energy in 173 seconds [~ 77 test (9.436274509803921%) started, 739 in queue, 32 running]
Running Test count_cycpep_sequences
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/count_cycpep_sequences/command.sh
Finished add_helix_sequence_constraints in 174 seconds [~ 78 test (9.558823529411764%) started, 738 in queue, 32 running]
Running Test rnp_ddg_calc_mut
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rnp_ddg_calc_mut/command.sh
Finished cyclization in 178 seconds [~ 79 test (9.681372549019608%) started, 737 in queue, 32 running]
Running Test helical_bundle_predict_psipred_with_helix_globals
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/helical_bundle_predict_psipred_with_helix_globals/command.sh
Finished fast_relax_scripts in 182 seconds [~ 80 test (9.803921568627452%) started, 736 in queue, 32 running]
Running Test simple_metrics_per_residue
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_metrics_per_residue/command.sh
Finished antibody_H3 in 186 seconds [~ 81 test (9.926470588235293%) started, 735 in queue, 32 running]
Running Test composition_energy_layers
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/composition_energy_layers/command.sh
Finished ddG_of_mutation in 187 seconds [~ 82 test (10.049019607843137%) started, 734 in queue, 32 running]
Running Test glycopeptidedocking
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/glycopeptidedocking/command.sh
Finished dgdp_aio in 212 seconds [~ 83 test (10.17156862745098%) started, 733 in queue, 32 running]
Running Test helical_bundle_predict_psipred
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/helical_bundle_predict_psipred/command.sh
Finished simple_cycpep_predict_square_pyramidal_metal in 218 seconds [~ 84 test (10.294117647058824%) started, 732 in queue, 32 running]
Running Test SnugDock
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/SnugDock/command.sh
Finished swm_dna_bridge in 98 seconds [~ 85 test (10.416666666666666%) started, 731 in queue, 32 running]
Running Test swm_dna_loop
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_dna_loop/command.sh
Finished swa_protein_CCDclose in 100 seconds [~ 86 test (10.53921568627451%) started, 730 in queue, 32 running]
Running Test rosetta_scripts_loops
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rosetta_scripts_loops/command.sh
Finished auto-drrafter_setup_run_R2 in 233 seconds [~ 87 test (10.661764705882353%) started, 729 in queue, 32 running]
Running Test antibody_designer_xml
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/antibody_designer_xml/command.sh
Finished ddG_ensemble in 102 seconds [~ 88 test (10.784313725490197%) started, 728 in queue, 32 running]
Running Test hbnet_asymm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hbnet_asymm/command.sh
Finished flexpepdock in 108 seconds [~ 89 test (10.906862745098039%) started, 727 in queue, 32 running]
Running Test voids_penalty_energy_design_symmetry
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/voids_penalty_energy_design_symmetry/command.sh
Finished swm_rna_srl_triplet in 111 seconds [~ 90 test (11.029411764705882%) started, 726 in queue, 32 running]
Running Test hydrate_relax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hydrate_relax/command.sh
Finished ga_ligand_dock_macrocycle in 109 seconds [~ 91 test (11.151960784313726%) started, 725 in queue, 32 running]
Running Test hbnet_energy
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hbnet_energy/command.sh
Finished validate_database in 110 seconds [~ 92 test (11.27450980392157%) started, 724 in queue, 32 running]
Finished coupled_moves in 105 seconds [~ 92 test (11.27450980392157%) started, 724 in queue, 31 running]
Running Test docking_ensemble
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/docking_ensemble/command.sh
Running Test crosslinkermover_square_pyramidal
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_square_pyramidal/command.sh
Finished test1_benchmark in 92 seconds [~ 94 test (11.519607843137255%) started, 722 in queue, 32 running]
Running Test bundlegridsampler_copy_pitch
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bundlegridsampler_copy_pitch/command.sh
Finished simple_cycpep_predict_trigonal_pyramidal_metal in 82 seconds [~ 95 test (11.642156862745098%) started, 721 in queue, 32 running]
Running Test dna_interface_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/dna_interface_design/command.sh
Finished rnp_ddg_relax_command_2 in 97 seconds [~ 96 test (11.764705882352942%) started, 720 in queue, 32 running]
Running Test crosslinkermover_1_4_bbmb_s2_symm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_1_4_bbmb_s2_symm/command.sh
Finished job_definition_script_vars in 103 seconds [~ 97 test (11.887254901960784%) started, 719 in queue, 32 running]
Running Test crosslinkermover_tetrahedral_metal_d2_symmetry
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_tetrahedral_metal_d2_symmetry/command.sh
Finished swm_rna_base_pair_constraints in 104 seconds [~ 98 test (12.009803921568627%) started, 718 in queue, 32 running]
Running Test vip
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/vip/command.sh
Finished glycan_relax in 94 seconds [~ 99 test (12.132352941176471%) started, 717 in queue, 32 running]
Running Test swa_rna_gagu_09_sample_virtual_ribose
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_09_sample_virtual_ribose/command.sh
Finished ppi_v3_suiteF in 99 seconds [~ 100 test (12.254901960784315%) started, 716 in queue, 32 running]
Running Test fiber_diffraction_fad
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fiber_diffraction_fad/command.sh
Finished docking_ensemble_prepack in 98 seconds [~ 101 test (12.377450980392156%) started, 715 in queue, 32 running]
Running Test supercharge
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/supercharge/command.sh
Finished rna_denovo_dna_bridge in 90 seconds [~ 102 test (12.5%) started, 714 in queue, 32 running]
Running Test molfile_to_params_polymer
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/molfile_to_params_polymer/command.sh
Finished auto-drrafter_setup_run_R3 in 97 seconds [~ 103 test (12.622549019607844%) started, 713 in queue, 32 running]
Running Test PolarDesign2019
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/PolarDesign2019/command.sh
Finished rnp_ddg_calc_mut in 88 seconds [~ 104 test (12.745098039215685%) started, 712 in queue, 32 running]
Running Test simple_glycosylation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_glycosylation/command.sh
Finished antibody_designer in 97 seconds [~ 105 test (12.867647058823529%) started, 711 in queue, 32 running]
Running Test jd2test_mmCIFin_PDBout
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/jd2test_mmCIFin_PDBout/command.sh
Finished dgdp_script in 264 seconds [~ 106 test (12.990196078431373%) started, 710 in queue, 32 running]
Running Test jd2test_mmCIFIO
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/jd2test_mmCIFIO/command.sh
Finished helical_bundle_predict_psipred_with_helix_globals in 90 seconds [~ 107 test (13.112745098039216%) started, 709 in queue, 32 running]
Running Test helical_bundle_predict
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/helical_bundle_predict/command.sh
Finished count_cycpep_sequences in 95 seconds [~ 108 test (13.235294117647058%) started, 708 in queue, 32 running]
Running Test crosslinkermover_square_planar
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_square_planar/command.sh
Finished glycopeptidedocking in 88 seconds [~ 109 test (13.357843137254902%) started, 707 in queue, 32 running]
Running Test bundlegridsampler_composition_energy_fract_range
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bundlegridsampler_composition_energy_fract_range/command.sh
Finished composition_energy_layers in 90 seconds [~ 110 test (13.480392156862745%) started, 706 in queue, 32 running]
Running Test LoopAnalyzer
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/LoopAnalyzer/command.sh
Finished simple_metrics_per_residue in 96 seconds [~ 111 test (13.602941176470589%) started, 705 in queue, 32 running]
Running Test inverse_rotamer_remodel
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/inverse_rotamer_remodel/command.sh
Finished SnugDock in 81 seconds [~ 112 test (13.72549019607843%) started, 704 in queue, 32 running]
Running Test relax_w_allatom_cst
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/relax_w_allatom_cst/command.sh
Finished helical_bundle_predict_psipred in 87 seconds [~ 113 test (13.848039215686274%) started, 703 in queue, 32 running]
Running Test helical_bundle_predict_skipping_residues
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/helical_bundle_predict_skipping_residues/command.sh
Finished rosetta_scripts_loops in 81 seconds [~ 114 test (13.970588235294118%) started, 702 in queue, 32 running]
Running Test hbnet_energy_rosettascripts_linear
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hbnet_energy_rosettascripts_linear/command.sh
Finished swm_dna_loop in 88 seconds [~ 115 test (14.093137254901961%) started, 701 in queue, 32 running]
Running Test d_workflow
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/d_workflow/command.sh
Finished voids_penalty_energy_design_symmetry in 78 seconds [~ 116 test (14.215686274509803%) started, 700 in queue, 32 running]
Running Test control_flow_rs
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/control_flow_rs/command.sh
Finished hbnet_asymm in 79 seconds [~ 117 test (14.338235294117647%) started, 699 in queue, 32 running]
Running Test simple_metrics
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_metrics/command.sh
Finished hydrate_relax in 80 seconds [~ 118 test (14.46078431372549%) started, 698 in queue, 32 running]
Running Test crosslinkermover_tma_symm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_tma_symm/command.sh
sed: 1: "/Volumes/scratch/b3.w/r ...": bad flag in substitute command: 'o'
Finished database_md5 in 318 seconds [~ 119 test (14.583333333333334%) started, 697 in queue, 32 running]
Running Test rna_denovo_base_pair_constraints
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_base_pair_constraints/command.sh
Finished antibody_designer_xml in 85 seconds [~ 120 test (14.705882352941176%) started, 696 in queue, 32 running]
Running Test hotspot_hashing
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hotspot_hashing/command.sh
Finished crosslinkermover_square_pyramidal in 80 seconds [~ 121 test (14.82843137254902%) started, 695 in queue, 32 running]
Running Test helical_bundle_predict_sequence
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/helical_bundle_predict_sequence/command.sh
Finished docking_ensemble in 81 seconds [~ 122 test (14.950980392156863%) started, 694 in queue, 32 running]
Running Test design_glycans
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/design_glycans/command.sh
Finished vip in 76 seconds [~ 123 test (15.073529411764707%) started, 693 in queue, 32 running]
Running Test ligand_water_docking
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ligand_water_docking/command.sh
Finished hbnet_energy in 83 seconds [~ 124 test (15.196078431372548%) started, 692 in queue, 32 running]
Running Test fiber_diffraction
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fiber_diffraction/command.sh
Finished bundlegridsampler_copy_pitch in 83 seconds [~ 125 test (15.318627450980392%) started, 691 in queue, 32 running]
Running Test beta_strand_homodimer
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/beta_strand_homodimer/command.sh
Finished crosslinkermover_1_4_bbmb_s2_symm in 80 seconds [~ 126 test (15.441176470588236%) started, 690 in queue, 32 running]
Running Test polyaramid_test_trivial
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/polyaramid_test_trivial/command.sh
Finished dna_interface_design in 83 seconds [~ 127 test (15.563725490196079%) started, 689 in queue, 32 running]
Running Test crosslinkermover_1_4_bbmb_asymm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_1_4_bbmb_asymm/command.sh
Finished crosslinkermover_tetrahedral_metal_d2_symmetry in 81 seconds [~ 128 test (15.686274509803921%) started, 688 in queue, 32 running]
Running Test membrane_relax_hbond
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/membrane_relax_hbond/command.sh
Finished fiber_diffraction_fad in 77 seconds [~ 129 test (15.808823529411764%) started, 687 in queue, 32 running]
Running Test mr_protocols
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mr_protocols/command.sh
Finished swa_rna_gagu_09_sample_virtual_ribose in 80 seconds [~ 130 test (15.931372549019608%) started, 686 in queue, 32 running]
Running Test membrane_relax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/membrane_relax/command.sh
Finished supercharge in 75 seconds [~ 131 test (16.05392156862745%) started, 685 in queue, 32 running]
Running Test simple_cycpep_predict_cartesian
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_cartesian/command.sh
Finished simple_glycosylation in 72 seconds [~ 132 test (16.176470588235293%) started, 684 in queue, 32 running]
Running Test AlterSpecDisruption
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/AlterSpecDisruption/command.sh
Finished PolarDesign2019 in 78 seconds [~ 133 test (16.29901960784314%) started, 683 in queue, 32 running]
Running Test mp_domain_assembly_FtsQ
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_domain_assembly_FtsQ/command.sh
Finished jd2test_mmCIFin_PDBout in 79 seconds [~ 134 test (16.42156862745098%) started, 682 in queue, 32 running]
Running Test glycomutagenesis
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/glycomutagenesis/command.sh
Finished jd2test_mmCIFIO in 78 seconds [~ 135 test (16.544117647058822%) started, 681 in queue, 32 running]
Running Test backrub
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/backrub/command.sh
Finished helical_bundle_predict in 75 seconds [~ 136 test (16.666666666666668%) started, 680 in queue, 32 running]
Running Test autoNOE_rosetta
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/autoNOE_rosetta/command.sh
Finished crosslinkermover_square_planar in 77 seconds [~ 137 test (16.78921568627451%) started, 679 in queue, 32 running]
Running Test antibody_H3_camelid
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/antibody_H3_camelid/command.sh
Finished inverse_rotamer_remodel in 70 seconds [~ 138 test (16.91176470588235%) started, 678 in queue, 32 running]
Running Test simple_cycpep_predict
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict/command.sh
Finished LoopAnalyzer in 73 seconds [~ 139 test (17.034313725490197%) started, 677 in queue, 32 running]
Running Test pertmin
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pertmin/command.sh
Finished bundlegridsampler_composition_energy_fract_range in 76 seconds [~ 140 test (17.15686274509804%) started, 676 in queue, 32 running]
Running Test crosslinkermover_tetrahedral_metal_c2_symmetry
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_tetrahedral_metal_c2_symmetry/command.sh
Finished molfile_to_params_polymer in 91 seconds [~ 141 test (17.279411764705884%) started, 675 in queue, 32 running]
Running Test rs_loophash
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rs_loophash/command.sh
Finished relax_w_allatom_cst in 70 seconds [~ 142 test (17.401960784313726%) started, 674 in queue, 32 running]
Running Test rnp_ddg_calc_wt
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rnp_ddg_calc_wt/command.sh
Finished helical_bundle_predict_skipping_residues in 73 seconds [~ 143 test (17.524509803921568%) started, 673 in queue, 32 running]
Running Test hybridization
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hybridization/command.sh
Finished d_workflow in 71 seconds [~ 144 test (17.647058823529413%) started, 672 in queue, 32 running]
Running Test hts_io
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hts_io/command.sh
Finished hbnet_energy_rosettascripts_linear in 76 seconds [~ 145 test (17.769607843137255%) started, 671 in queue, 32 running]
Running Test swa_protein_prepack
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_protein_prepack/command.sh
Finished simple_metrics in 73 seconds [~ 146 test (17.892156862745097%) started, 670 in queue, 32 running]
Running Test swa_protein_loop_sampler
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_protein_loop_sampler/command.sh
Finished ligand_water_docking in 66 seconds [~ 147 test (18.014705882352942%) started, 669 in queue, 32 running]
Running Test crosslinkermover_square_planar_d2_symm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_square_planar_d2_symm/command.sh
Finished mr_protocols in 61 seconds [~ 148 test (18.137254901960784%) started, 668 in queue, 32 running]
Running Test simple_cycpep_predict_anglelength
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_anglelength/command.sh
Finished control_flow_rs in 77 seconds [~ 149 test (18.25980392156863%) started, 667 in queue, 32 running]
Running Test rosetta_scripts_jd3
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rosetta_scripts_jd3/command.sh
Finished rna_denovo_base_pair_constraints in 71 seconds [~ 150 test (18.38235294117647%) started, 666 in queue, 32 running]
Finished polyaramid_test_trivial in 66 seconds [~ 150 test (18.38235294117647%) started, 666 in queue, 31 running]
Running Test ligand_database_io
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ligand_database_io/command.sh
Running Test simple_cycpep_predict_setting
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_setting/command.sh
Finished crosslinkermover_tma_symm in 73 seconds [~ 152 test (18.627450980392158%) started, 664 in queue, 32 running]
Running Test netcharge_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/netcharge_design/command.sh
Finished helical_bundle_predict_sequence in 71 seconds [~ 153 test (18.75%) started, 663 in queue, 32 running]
Running Test fast_relax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fast_relax/command.sh
Finished crosslinkermover_1_4_bbmb_asymm in 67 seconds [~ 154 test (18.872549019607842%) started, 662 in queue, 32 running]
Running Test pmut_scan
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pmut_scan/command.sh
Finished beta_strand_homodimer in 69 seconds [~ 155 test (18.995098039215687%) started, 661 in queue, 32 running]
Running Test hbnet
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hbnet/command.sh
Finished hotspot_hashing in 73 seconds [~ 156 test (19.11764705882353%) started, 660 in queue, 32 running]
Running Test simple_cycpep_predict_tetrahedral_metal
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_tetrahedral_metal/command.sh
Finished membrane_relax_hbond in 68 seconds [~ 157 test (19.24019607843137%) started, 659 in queue, 32 running]
Running Test simple_cycpep_predict_angle
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_angle/command.sh
Finished design_glycans in 73 seconds [~ 158 test (19.362745098039216%) started, 658 in queue, 32 running]
Running Test remodel_disulfides_rosettascripts
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/remodel_disulfides_rosettascripts/command.sh
Finished simple_cycpep_predict_cartesian in 64 seconds [~ 159 test (19.485294117647058%) started, 657 in queue, 32 running]
Running Test mirror_symm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mirror_symm/command.sh
Finished membrane_relax in 67 seconds [~ 160 test (19.607843137254903%) started, 656 in queue, 32 running]
Running Test bridge_chains
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bridge_chains/command.sh
Finished fiber_diffraction in 75 seconds [~ 161 test (19.730392156862745%) started, 655 in queue, 32 running]
Running Test swa_rna_erraser
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_erraser/command.sh
Finished AlterSpecDisruption in 64 seconds [~ 162 test (19.852941176470587%) started, 654 in queue, 32 running]
Running Test rna_denovo_fragment_homology_exclusion
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_fragment_homology_exclusion/command.sh
Finished mp_domain_assembly_FtsQ in 62 seconds [~ 163 test (19.975490196078432%) started, 653 in queue, 32 running]
Running Test perturb_helical_bundle_copying_pitch
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/perturb_helical_bundle_copying_pitch/command.sh
Finished mp_f19_relax in 404 seconds [~ 164 test (20.098039215686274%) started, 652 in queue, 32 running]
Running Test batch_relax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/batch_relax/command.sh
Finished backrub in 62 seconds [~ 165 test (20.220588235294116%) started, 651 in queue, 32 running]
Running Test swm_l_rna
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_l_rna/command.sh
Finished glycomutagenesis in 64 seconds [~ 166 test (20.34313725490196%) started, 650 in queue, 32 running]
Running Test rna_puzzle5_P15P3P8_noP4P6_4RB_G208phosphate_ligation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_puzzle5_P15P3P8_noP4P6_4RB_G208phosphate_ligation/command.sh
Finished autoNOE_rosetta in 64 seconds [~ 167 test (20.465686274509803%) started, 649 in queue, 32 running]
Running Test seed_ensemble_JD2_JI
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/seed_ensemble_JD2_JI/command.sh
Finished antibody_H3_camelid in 64 seconds [~ 168 test (20.58823529411765%) started, 648 in queue, 32 running]
Running Test symm_disulfidize
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/symm_disulfidize/command.sh
Finished rs_loophash in 57 seconds [~ 169 test (20.71078431372549%) started, 647 in queue, 32 running]
Running Test simple_cycpep_predict_trigonal_planar_metal
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_trigonal_planar_metal/command.sh
Finished simple_cycpep_predict in 62 seconds [~ 170 test (20.833333333333332%) started, 646 in queue, 32 running]
Running Test ligand_dock_script
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ligand_dock_script/command.sh
Finished pertmin in 62 seconds [~ 171 test (20.955882352941178%) started, 645 in queue, 32 running]
Running Test simple_cycpep_predict_tbmb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_tbmb/command.sh
Finished crosslinkermover_tetrahedral_metal_c2_symmetry in 61 seconds [~ 172 test (21.07843137254902%) started, 644 in queue, 32 running]
Running Test mp_dock_ensemble
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_dock_ensemble/command.sh
Finished hybridization in 52 seconds [~ 173 test (21.20098039215686%) started, 643 in queue, 32 running]
Running Test farnesyl
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/farnesyl/command.sh
Finished rnp_ddg_calc_wt in 58 seconds [~ 174 test (21.323529411764707%) started, 642 in queue, 32 running]
Running Test range_relax_w_cst
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/range_relax_w_cst/command.sh
Finished simple_cycpep_predict_setting in 50 seconds [~ 175 test (21.44607843137255%) started, 641 in queue, 32 running]
Finished simple_cycpep_predict_tetrahedral_metal in 48 seconds [~ 176 test (21.568627450980394%) started, 640 in queue, 32 running]
Running Test motif_dna_packer_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/motif_dna_packer_design/command.sh
Running Test crosslinkermover_octahedral_s2_symm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_octahedral_s2_symm/command.sh
Finished swa_protein_loop_sampler in 55 seconds [~ 177 test (21.691176470588236%) started, 639 in queue, 32 running]
Running Test KIC_with_fragments
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/KIC_with_fragments/command.sh
Finished hts_io in 59 seconds [~ 178 test (21.813725490196077%) started, 638 in queue, 32 running]
Finished hbnet in 50 seconds [~ 178 test (21.813725490196077%) started, 638 in queue, 31 running]
Running Test test_degreaser
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/test_degreaser/command.sh
Running Test repeat_relax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/repeat_relax/command.sh
Finished netcharge_design in 55 seconds [~ 180 test (22.058823529411764%) started, 636 in queue, 32 running]
Running Test remodel_helical_repeat
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/remodel_helical_repeat/command.sh
Finished swa_protein_prepack in 58 seconds [~ 181 test (22.181372549019606%) started, 635 in queue, 32 running]
Finished rosetta_scripts_jd3 in 55 seconds [~ 181 test (22.181372549019606%) started, 635 in queue, 31 running]
Running Test next_generation_KIC
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/next_generation_KIC/command.sh
Running Test splice_out_H3_longer
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/splice_out_H3_longer/command.sh
Finished simple_cycpep_predict_anglelength in 57 seconds [~ 183 test (22.426470588235293%) started, 633 in queue, 32 running]
Running Test simple_cycpep_predict_tma
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_tma/command.sh
Finished crosslinkermover_square_planar_d2_symm in 57 seconds [~ 184 test (22.54901960784314%) started, 632 in queue, 32 running]
Finished simple_cycpep_predict_angle in 53 seconds [~ 184 test (22.54901960784314%) started, 632 in queue, 31 running]
Running Test rna_puzzle12_P5P6P7_DMS
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_puzzle12_P5P6P7_DMS/command.sh
Running Test docking_local_refine
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/docking_local_refine/command.sh
Finished ligand_database_io in 57 seconds [~ 186 test (22.794117647058822%) started, 630 in queue, 32 running]
Finished bridge_chains in 50 seconds [~ 186 test (22.794117647058822%) started, 630 in queue, 31 running]
Running Test rna_denovo_symm_hack
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_symm_hack/command.sh
Running Test cycpep_rigid_body_permutation_mover
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cycpep_rigid_body_permutation_mover/command.sh
Finished fast_relax in 55 seconds [~ 188 test (23.03921568627451%) started, 628 in queue, 32 running]
Running Test zinc_heterodimer
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/zinc_heterodimer/command.sh
Finished pmut_scan in 55 seconds [~ 189 test (23.16176470588235%) started, 627 in queue, 32 running]
Running Test sdf_reader
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/sdf_reader/command.sh
Finished remodel_disulfides_rosettascripts in 54 seconds [~ 190 test (23.284313725490197%) started, 626 in queue, 32 running]
Running Test crankshaft_flip
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crankshaft_flip/command.sh
Finished mirror_symm in 54 seconds [~ 191 test (23.40686274509804%) started, 625 in queue, 32 running]
Running Test AlignPDBInfoToSequences
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/AlignPDBInfoToSequences/command.sh
Finished simple_cycpep_predict_trigonal_planar_metal in 38 seconds [~ 192 test (23.529411764705884%) started, 624 in queue, 32 running]
Running Test ga_ligand_dock_amino_acid
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ga_ligand_dock_amino_acid/command.sh
Finished swa_rna_erraser in 53 seconds [~ 193 test (23.651960784313726%) started, 623 in queue, 32 running]
Running Test simple_cycpep_predict_octahedral_metal
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_octahedral_metal/command.sh
Finished rna_denovo_fragment_homology_exclusion in 51 seconds [~ 194 test (23.774509803921568%) started, 622 in queue, 32 running]
Running Test mp_relax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_relax/command.sh
Finished perturb_helical_bundle_copying_pitch in 49 seconds [~ 195 test (23.897058823529413%) started, 621 in queue, 32 running]
Running Test ppi_v3_suiteB
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ppi_v3_suiteB/command.sh
Finished simple_cycpep_predict_tbmb in 43 seconds [~ 196 test (24.019607843137255%) started, 620 in queue, 32 running]
Running Test mp_find_interface
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_find_interface/command.sh
Finished batch_relax in 53 seconds [~ 197 test (24.142156862745097%) started, 619 in queue, 32 running]
Finished swm_l_rna in 51 seconds [~ 197 test (24.142156862745097%) started, 619 in queue, 31 running]
Running Test hotspot_graft
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hotspot_graft/command.sh
Running Test fixbb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fixbb/command.sh
Finished rna_puzzle5_P15P3P8_noP4P6_4RB_G208phosphate_ligation in 51 seconds [~ 199 test (24.387254901960784%) started, 617 in queue, 32 running]
Running Test remodel_disulfides
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/remodel_disulfides/command.sh
Finished seed_ensemble_JD2_JI in 51 seconds [~ 200 test (24.50980392156863%) started, 616 in queue, 32 running]
Finished mp_dock_ensemble in 45 seconds [~ 200 test (24.50980392156863%) started, 616 in queue, 31 running]
Running Test hbs_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hbs_design/command.sh
Running Test disulfidize_beta_cys
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/disulfidize_beta_cys/command.sh
Finished symm_disulfidize in 50 seconds [~ 202 test (24.754901960784313%) started, 614 in queue, 32 running]
Running Test buried_unsat_voids_hbnet_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/buried_unsat_voids_hbnet_design/command.sh
Finished ligand_dock_script in 50 seconds [~ 203 test (24.877450980392158%) started, 613 in queue, 32 running]
Running Test bundlegridsampler_epsilon
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bundlegridsampler_epsilon/command.sh
Finished farnesyl in 46 seconds [~ 204 test (25.0%) started, 612 in queue, 32 running]
Running Test TryDisulfPermutations
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/TryDisulfPermutations/command.sh
Finished range_relax_w_cst in 47 seconds [~ 205 test (25.122549019607842%) started, 611 in queue, 32 running]
Running Test swa_protein_combine_loops
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_protein_combine_loops/command.sh
Finished simple_cycpep_predict_tma in 35 seconds [~ 206 test (25.245098039215687%) started, 610 in queue, 32 running]
Running Test mp_symdock
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_symdock/command.sh
Finished crosslinkermover_octahedral_s2_symm in 46 seconds [~ 207 test (25.36764705882353%) started, 609 in queue, 32 running]
Running Test enzdes
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/enzdes/command.sh
Finished test_degreaser in 45 seconds [~ 208 test (25.49019607843137%) started, 608 in queue, 32 running]
Finished repeat_relax in 45 seconds [~ 208 test (25.49019607843137%) started, 608 in queue, 31 running]
Running Test entropy_correction
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/entropy_correction/command.sh
Running Test bundlereporter_filter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bundlereporter_filter/command.sh
Finished motif_dna_packer_design in 48 seconds [~ 210 test (25.735294117647058%) started, 606 in queue, 32 running]
Running Test secondary_structure_output
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/secondary_structure_output/command.sh
Finished KIC_with_fragments in 47 seconds [~ 211 test (25.857843137254903%) started, 605 in queue, 32 running]
Running Test rna_denovo_new_FT_RNP_2prot_dens
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_new_FT_RNP_2prot_dens/command.sh
Finished rna_denovo_symm_hack in 43 seconds [~ 212 test (25.980392156862745%) started, 604 in queue, 32 running]
Running Test mp_domain_assembly
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_domain_assembly/command.sh
Finished simple_cycpep_predict_octahedral_metal in 40 seconds [~ 213 test (26.102941176470587%) started, 603 in queue, 32 running]
Running Test generate_6Dloopclose
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/generate_6Dloopclose/command.sh
Finished splice_out_H3_longer in 46 seconds [~ 214 test (26.225490196078432%) started, 602 in queue, 32 running]
Running Test explicit_membrane
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/explicit_membrane/command.sh
Finished zinc_heterodimer in 45 seconds [~ 215 test (26.348039215686274%) started, 601 in queue, 32 running]
Running Test docking_distance_constraints
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/docking_distance_constraints/command.sh
Finished cycpep_rigid_body_permutation_mover in 46 seconds [~ 216 test (26.470588235294116%) started, 600 in queue, 32 running]
Finished rna_puzzle12_P5P6P7_DMS in 47 seconds [~ 217 test (26.59313725490196%) started, 599 in queue, 32 running]
Finished docking_local_refine in 47 seconds [~ 217 test (26.59313725490196%) started, 599 in queue, 31 running]
Running Test UBQ_E2_thioester_extra_bodies
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/UBQ_E2_thioester_extra_bodies/command.sh
Running Test simple_cycpep_predict_bondangle_bondlength
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_bondangle_bondlength/command.sh
Running Test mhc_epitope
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mhc_epitope/command.sh
Finished remodel_helical_repeat in 48 seconds [~ 219 test (26.83823529411765%) started, 597 in queue, 32 running]
Finished ga_ligand_dock_amino_acid in 44 seconds [~ 219 test (26.83823529411765%) started, 597 in queue, 31 running]
Running Test small_molecule_lattice_dock
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/small_molecule_lattice_dock/command.sh
Running Test rna_denovo_RNP_refine_native
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_RNP_refine_native/command.sh
Finished next_generation_KIC in 48 seconds [~ 221 test (27.083333333333332%) started, 595 in queue, 32 running]
Running Test oop_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/oop_design/command.sh
Finished crankshaft_flip in 45 seconds [~ 222 test (27.205882352941178%) started, 594 in queue, 32 running]
Finished mp_relax in 43 seconds [~ 222 test (27.205882352941178%) started, 594 in queue, 31 running]
Running Test make_symmdef_file
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/make_symmdef_file/command.sh
Running Test crosslinkermover_1_4_bbmb_c2_symmetry
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_1_4_bbmb_c2_symmetry/command.sh
Finished sdf_reader in 47 seconds [~ 224 test (27.45098039215686%) started, 592 in queue, 32 running]
Finished ppi_v3_suiteB in 43 seconds [~ 224 test (27.45098039215686%) started, 592 in queue, 31 running]
No correct command.sh file found for trRosetta. Skipping.
Running Test SID_ERMS_prediction
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/SID_ERMS_prediction/command.sh
Running Test rna_denovo_RNP_low_res
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_RNP_low_res/command.sh
Finished AlignPDBInfoToSequences in 46 seconds [~ 227 test (27.818627450980394%) started, 589 in queue, 32 running]
Running Test ppi_v3_suiteE
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ppi_v3_suiteE/command.sh
Finished mp_find_interface in 41 seconds [~ 228 test (27.941176470588236%) started, 588 in queue, 32 running]
Running Test ppi_v3_suiteA
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ppi_v3_suiteA/command.sh
Finished remodel_disulfides in 41 seconds [~ 229 test (28.063725490196077%) started, 587 in queue, 32 running]
Running Test kinematic_looprelax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/kinematic_looprelax/command.sh
Finished hotspot_graft in 41 seconds [~ 230 test (28.186274509803923%) started, 586 in queue, 32 running]
Running Test hbnet_energy_symm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hbnet_energy_symm/command.sh
Finished fixbb in 43 seconds [~ 231 test (28.308823529411764%) started, 585 in queue, 32 running]
Running Test evolution
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/evolution/command.sh
Finished hbs_design in 41 seconds [~ 232 test (28.431372549019606%) started, 584 in queue, 32 running]
Running Test UBQ_E2_thioester
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/UBQ_E2_thioester/command.sh
Finished buried_unsat_voids_hbnet_design in 41 seconds [~ 233 test (28.55392156862745%) started, 583 in queue, 32 running]
Running Test simple_cycpep_predict_terminal_disulfide_tails_2
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_terminal_disulfide_tails_2/command.sh
Finished disulfidize_beta_cys in 43 seconds [~ 234 test (28.676470588235293%) started, 582 in queue, 32 running]
Running Test homodimer_fnd_ref2015_memb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/homodimer_fnd_ref2015_memb/command.sh
Finished bundlegridsampler_epsilon in 42 seconds [~ 235 test (28.79901960784314%) started, 581 in queue, 32 running]
Running Test docking_site_constraints
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/docking_site_constraints/command.sh
Finished TryDisulfPermutations in 41 seconds [~ 236 test (28.92156862745098%) started, 580 in queue, 32 running]
Running Test cycpep_rdkit_metric
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cycpep_rdkit_metric/command.sh
Finished swa_protein_combine_loops in 40 seconds [~ 237 test (29.044117647058822%) started, 579 in queue, 32 running]
Running Test cycpep_design_pipeline
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cycpep_design_pipeline/command.sh
Finished mp_symdock in 44 seconds [~ 238 test (29.166666666666668%) started, 578 in queue, 32 running]
Running Test rna_denovo_new_libs
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_new_libs/command.sh
Finished enzdes in 40 seconds [~ 239 test (29.28921568627451%) started, 577 in queue, 32 running]
Running Test ligand_dock_cholesterol
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ligand_dock_cholesterol/command.sh
Finished rna_denovo_new_FT_RNP_2prot_dens in 38 seconds [~ 240 test (29.41176470588235%) started, 576 in queue, 32 running]
Finished mp_domain_assembly in 38 seconds [~ 240 test (29.41176470588235%) started, 576 in queue, 31 running]
Running Test dock_glycans
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/dock_glycans/command.sh
Running Test AnchoredDesign
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/AnchoredDesign/command.sh
Finished secondary_structure_output in 39 seconds [~ 242 test (29.65686274509804%) started, 574 in queue, 32 running]
Running Test symm_rotamer_boltzmann
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/symm_rotamer_boltzmann/command.sh
Finished bundlereporter_filter in 40 seconds [~ 243 test (29.779411764705884%) started, 573 in queue, 32 running]
Running Test rna_farfar_block_stack
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_farfar_block_stack/command.sh
Finished generate_6Dloopclose in 38 seconds [~ 244 test (29.901960784313726%) started, 572 in queue, 32 running]
Running Test bundlegridsampler
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bundlegridsampler/command.sh
Finished entropy_correction in 41 seconds [~ 245 test (30.024509803921568%) started, 571 in queue, 32 running]
Running Test rna_denovo_new_FT_2in_dens
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_new_FT_2in_dens/command.sh
Finished mhc_epitope in 36 seconds [~ 246 test (30.147058823529413%) started, 570 in queue, 32 running]
Running Test mixed_monte_carlo
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mixed_monte_carlo/command.sh
Finished rna_denovo_RNP_refine_native in 36 seconds [~ 247 test (30.269607843137255%) started, 569 in queue, 32 running]
Running Test features_parallel
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/features_parallel/command.sh
Finished simple_cycpep_predict_bondangle_bondlength in 37 seconds [~ 248 test (30.392156862745097%) started, 568 in queue, 32 running]
Running Test splice_out_L3_longer
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/splice_out_L3_longer/command.sh
Finished explicit_membrane in 38 seconds [~ 249 test (30.514705882352942%) started, 567 in queue, 32 running]
Finished docking_distance_constraints in 37 seconds [~ 249 test (30.514705882352942%) started, 567 in queue, 31 running]
Running Test splice_out_H1_H2_longer
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/splice_out_H1_H2_longer/command.sh
Running Test simple_cycpep_predict_beta_thioether_lariat
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_beta_thioether_lariat/command.sh
Finished oop_design in 37 seconds [~ 251 test (30.75980392156863%) started, 565 in queue, 32 running]
Running Test rotamer_probability
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rotamer_probability/command.sh
Finished ppi_v3_suiteE in 36 seconds [~ 252 test (30.88235294117647%) started, 564 in queue, 32 running]
Finished make_symmdef_file in 36 seconds [~ 253 test (31.004901960784313%) started, 563 in queue, 32 running]
Running Test iphold
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/iphold/command.sh
Running Test interaction_graph_summary_metric
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/interaction_graph_summary_metric/command.sh
Finished rna_denovo_RNP_low_res in 36 seconds [~ 254 test (31.127450980392158%) started, 562 in queue, 32 running]
Running Test genkic_sugars
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/genkic_sugars/command.sh
Finished UBQ_E2_thioester_extra_bodies in 38 seconds [~ 255 test (31.25%) started, 561 in queue, 32 running]
Finished crosslinkermover_1_4_bbmb_c2_symmetry in 37 seconds [~ 255 test (31.25%) started, 561 in queue, 31 running]
Running Test farfar_mrna
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/farfar_mrna/command.sh
Running Test backrub_pilot
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/backrub_pilot/command.sh
Finished SID_ERMS_prediction in 37 seconds [~ 257 test (31.495098039215687%) started, 559 in queue, 32 running]
Running Test task_selector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/task_selector/command.sh
Finished ppi_v3_suiteA in 36 seconds [~ 258 test (31.61764705882353%) started, 558 in queue, 32 running]
Running Test netcharge_design_symm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/netcharge_design_symm/command.sh
Finished simple_cycpep_predict_terminal_disulfide_tails_2 in 31 seconds [~ 259 test (31.74019607843137%) started, 557 in queue, 32 running]
Running Test swa_protein_build_at_Nterminus
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_protein_build_at_Nterminus/command.sh
Finished hbnet_energy_symm in 35 seconds [~ 260 test (31.862745098039216%) started, 556 in queue, 32 running]
Running Test flexpepdock_abinitio
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/flexpepdock_abinitio/command.sh
Finished kinematic_looprelax in 36 seconds [~ 261 test (31.985294117647058%) started, 555 in queue, 32 running]
Running Test favor_native_residue
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/favor_native_residue/command.sh
Finished evolution in 35 seconds [~ 262 test (32.1078431372549%) started, 554 in queue, 32 running]
Finished homodimer_fnd_ref2015_memb in 34 seconds [~ 262 test (32.1078431372549%) started, 554 in queue, 31 running]
Running Test constraints_metric
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/constraints_metric/command.sh
Running Test bundlegridsampler_design_nstruct_mode
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bundlegridsampler_design_nstruct_mode/command.sh
Finished UBQ_E2_thioester in 36 seconds [~ 264 test (32.35294117647059%) started, 552 in queue, 32 running]
Running Test swm_rna_move_inside_helix_by_jump
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_rna_move_inside_helix_by_jump/command.sh
Finished docking_site_constraints in 35 seconds [~ 265 test (32.47549019607843%) started, 551 in queue, 32 running]
Running Test splice_in_4loops_shorter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/splice_in_4loops_shorter/command.sh
Finished small_molecule_lattice_dock in 45 seconds [~ 266 test (32.59803921568628%) started, 550 in queue, 32 running]
Running Test rs_flexbbmoves
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rs_flexbbmoves/command.sh
Finished cycpep_rdkit_metric in 36 seconds [~ 267 test (32.720588235294116%) started, 549 in queue, 32 running]
Running Test ppi_v3_suiteG
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ppi_v3_suiteG/command.sh
Finished cycpep_design_pipeline in 36 seconds [~ 268 test (32.84313725490196%) started, 548 in queue, 32 running]
Running Test ppi_v3_suiteD
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ppi_v3_suiteD/command.sh
Finished rna_denovo_new_libs in 34 seconds [~ 269 test (32.96568627450981%) started, 547 in queue, 32 running]
Running Test pose_sewing
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pose_sewing/command.sh
Finished mixed_monte_carlo in 30 seconds [~ 270 test (33.088235294117645%) started, 546 in queue, 32 running]
Running Test ncaa_fixbb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ncaa_fixbb/command.sh
Finished ligand_dock_cholesterol in 33 seconds [~ 271 test (33.21078431372549%) started, 545 in queue, 32 running]
Running Test features
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/features/command.sh
Finished rna_farfar_block_stack in 32 seconds [~ 272 test (33.333333333333336%) started, 544 in queue, 32 running]
Running Test cycpep_symmetry_filter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cycpep_symmetry_filter/command.sh
Finished symm_rotamer_boltzmann in 33 seconds [~ 273 test (33.455882352941174%) started, 543 in queue, 32 running]
Finished iphold in 30 seconds [~ 273 test (33.455882352941174%) started, 543 in queue, 31 running]
Running Test cleanAlignment
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cleanAlignment/command.sh
Finished rna_denovo_new_FT_2in_dens in 32 seconds [~ 275 test (33.700980392156865%) started, 541 in queue, 32 running]
Running Test balancedKIC
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/balancedKIC/command.sh
Running Test simple_metrics_b_factor
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_metrics_b_factor/command.sh
Finished AnchoredDesign in 34 seconds [~ 276 test (33.8235294117647%) started, 540 in queue, 32 running]
Finished simple_cycpep_predict_beta_thioether_lariat in 31 seconds [~ 276 test (33.8235294117647%) started, 540 in queue, 31 running]
Running Test simple_grafting_movers
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_grafting_movers/command.sh
Running Test hbnet_use_input_rot
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hbnet_use_input_rot/command.sh
Finished splice_out_L3_longer in 32 seconds [~ 278 test (34.068627450980394%) started, 538 in queue, 32 running]
Running Test Enzrevert_xml
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/Enzrevert_xml/command.sh
Finished splice_out_H1_H2_longer in 32 seconds [~ 279 test (34.19117647058823%) started, 537 in queue, 32 running]
Running Test swm_rna_singleloop
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_rna_singleloop/command.sh
Finished dock_glycans in 35 seconds [~ 280 test (34.31372549019608%) started, 536 in queue, 32 running]
Finished bundlegridsampler in 34 seconds [~ 280 test (34.31372549019608%) started, 536 in queue, 31 running]
Running Test rosie_ligand_docking
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rosie_ligand_docking/command.sh
Running Test ligand_dock_7cpa
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ligand_dock_7cpa/command.sh
Finished features_parallel in 33 seconds [~ 282 test (34.55882352941177%) started, 534 in queue, 32 running]
Finished rotamer_probability in 32 seconds [~ 282 test (34.55882352941177%) started, 534 in queue, 31 running]
Running Test kinemage_grid_output
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/kinemage_grid_output/command.sh
Running Test fold_from_loops
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fold_from_loops/command.sh
Finished interaction_graph_summary_metric in 32 seconds [~ 284 test (34.80392156862745%) started, 532 in queue, 32 running]
Finished genkic_sugars in 32 seconds [~ 284 test (34.80392156862745%) started, 532 in queue, 31 running]
Running Test doug_dock_design_min_mod2_cal_cal
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/doug_dock_design_min_mod2_cal_cal/command.sh
No correct command.sh file found for trRosettaConstraintGenerator. Skipping.
Running Test HDXEnergy
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/HDXEnergy/command.sh
Finished backrub_pilot in 32 seconds [~ 287 test (35.17156862745098%) started, 529 in queue, 32 running]
Running Test splice_out_L1_L2_longer
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/splice_out_L1_L2_longer/command.sh
Finished task_selector in 32 seconds [~ 288 test (35.294117647058826%) started, 528 in queue, 32 running]
Finished swa_protein_build_at_Nterminus in 29 seconds [~ 288 test (35.294117647058826%) started, 528 in queue, 31 running]
Running Test splice_in_4loops_longer
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/splice_in_4loops_longer/command.sh
Running Test simple_cycpep_predict_1_4_bbmb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_1_4_bbmb/command.sh
Finished farfar_mrna in 33 seconds [~ 290 test (35.53921568627451%) started, 526 in queue, 32 running]
Running Test hydrate
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hydrate/command.sh
Finished netcharge_design_symm in 31 seconds [~ 291 test (35.661764705882355%) started, 525 in queue, 32 running]
Running Test docking_full_protocol
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/docking_full_protocol/command.sh
Finished flexpepdock_abinitio in 30 seconds [~ 292 test (35.78431372549019%) started, 524 in queue, 32 running]
Running Test dock_with_hotspot_place_simultaneously
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/dock_with_hotspot_place_simultaneously/command.sh
Finished favor_native_residue in 30 seconds [~ 293 test (35.90686274509804%) started, 523 in queue, 32 running]
Running Test UBQ_Gp_LYX-Cterm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/UBQ_Gp_LYX-Cterm/command.sh
Finished bundlegridsampler_design_nstruct_mode in 30 seconds [~ 294 test (36.029411764705884%) started, 522 in queue, 32 running]
Finished swm_rna_move_inside_helix_by_jump in 30 seconds [~ 294 test (36.029411764705884%) started, 522 in queue, 31 running]
Running Test threefold_symm_peptide_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/threefold_symm_peptide_design/command.sh
Running Test splice_out_L3_same
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/splice_out_L3_same/command.sh
Finished splice_in_4loops_shorter in 29 seconds [~ 296 test (36.27450980392157%) started, 520 in queue, 32 running]
Running Test splice_out_H1_H2_same
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/splice_out_H1_H2_same/command.sh
Finished rs_flexbbmoves in 29 seconds [~ 297 test (36.39705882352941%) started, 519 in queue, 32 running]
Running Test simple_hbondstoatom
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_hbondstoatom/command.sh
Finished constraints_metric in 32 seconds [~ 298 test (36.51960784313726%) started, 518 in queue, 32 running]
Running Test simple_cycpep_predict_thioether_cis_sampling
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_thioether_cis_sampling/command.sh
Finished simple_metrics_b_factor in 17 seconds [~ 299 test (36.6421568627451%) started, 517 in queue, 32 running]
Finished simple_grafting_movers in 16 seconds [~ 299 test (36.6421568627451%) started, 517 in queue, 31 running]
Running Test simple_cycpep_predict_symm_gly
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_symm_gly/command.sh
Running Test simple_cycpep_predict_cispro
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_cispro/command.sh
Finished ppi_v3_suiteG in 30 seconds [~ 301 test (36.88725490196079%) started, 515 in queue, 32 running]
Running Test rosetta_scripts_include
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rosetta_scripts_include/command.sh
Finished ppi_v3_suiteD in 30 seconds [~ 302 test (37.009803921568626%) started, 514 in queue, 32 running]
Running Test perturb_helical_bundle
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/perturb_helical_bundle/command.sh
Finished simple_cycpep_predict_thioether_cis_sampling in 18 seconds [~ 303 test (37.13235294117647%) started, 513 in queue, 32 running]
Running Test match_1n9l
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/match_1n9l/command.sh
Finished pose_sewing in 29 seconds [~ 304 test (37.254901960784316%) started, 512 in queue, 32 running]
Running Test genkic_lowmemory_mode
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/genkic_lowmemory_mode/command.sh
Finished ncaa_fixbb in 30 seconds [~ 305 test (37.377450980392155%) started, 511 in queue, 32 running]
Running Test KIC_refine
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/KIC_refine/command.sh
Finished HDXEnergy in 27 seconds [~ 306 test (37.5%) started, 510 in queue, 32 running]
Running Test InterfaceAnalyzer
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/InterfaceAnalyzer/command.sh
Finished hbnet_use_input_rot in 29 seconds [~ 307 test (37.622549019607845%) started, 509 in queue, 32 running]
Finished ligand_dock_7cpa in 28 seconds [~ 307 test (37.622549019607845%) started, 509 in queue, 31 running]
Running Test pocket_relax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pocket_relax/command.sh
Running Test multistage_rosetta_scripts
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/multistage_rosetta_scripts/command.sh
Finished splice_out_L1_L2_longer in 27 seconds [~ 309 test (37.86764705882353%) started, 507 in queue, 32 running]
Running Test helical_bundle_nonideal
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/helical_bundle_nonideal/command.sh
Finished swm_rna_singleloop in 29 seconds [~ 310 test (37.990196078431374%) started, 506 in queue, 32 running]
Finished rosie_ligand_docking in 29 seconds [~ 310 test (37.990196078431374%) started, 506 in queue, 31 running]
Running Test favor_coupling_tensor
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/favor_coupling_tensor/command.sh
Running Test KIC_vicinity
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/KIC_vicinity/command.sh
Finished features in 31 seconds [~ 312 test (38.23529411764706%) started, 504 in queue, 32 running]
Finished fold_from_loops in 28 seconds [~ 312 test (38.23529411764706%) started, 504 in queue, 31 running]
Finished hydrate in 27 seconds [~ 312 test (38.23529411764706%) started, 504 in queue, 30 running]
Running Test torsion_restricted_sampling
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/torsion_restricted_sampling/command.sh
Running Test sequence_profile_constraints
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/sequence_profile_constraints/command.sh
Running Test score12_docking
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/score12_docking/command.sh
Finished cleanAlignment in 30 seconds [~ 315 test (38.60294117647059%) started, 501 in queue, 32 running]
Finished splice_in_4loops_longer in 28 seconds [~ 315 test (38.60294117647059%) started, 501 in queue, 31 running]
Finished simple_cycpep_predict_1_4_bbmb in 28 seconds [~ 315 test (38.60294117647059%) started, 501 in queue, 30 running]
Running Test place_simultaneously
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/place_simultaneously/command.sh
Running Test bundlegridsampler_z1_offset
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bundlegridsampler_z1_offset/command.sh
Finished cycpep_symmetry_filter in 30 seconds [~ 318 test (38.970588235294116%) started, 498 in queue, 32 running]
Running Test bundlegridsampler_z0_offset
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bundlegridsampler_z0_offset/command.sh
Running Test auto-drrafter_final_results
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/auto-drrafter_final_results/command.sh
Finished Enzrevert_xml in 30 seconds [~ 319 test (39.09313725490196%) started, 497 in queue, 32 running]
Running Test symmetry_multicomponent
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/symmetry_multicomponent/command.sh
Finished balancedKIC in 31 seconds [~ 320 test (39.21568627450981%) started, 496 in queue, 32 running]
Running Test swm_protein_loop_sampler
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_protein_loop_sampler/command.sh
Finished kinemage_grid_output in 29 seconds [~ 321 test (39.338235294117645%) started, 495 in queue, 32 running]
Running Test swm_beta_peptide_loop
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_beta_peptide_loop/command.sh
Finished doug_dock_design_min_mod2_cal_cal in 29 seconds [~ 322 test (39.46078431372549%) started, 494 in queue, 32 running]
Running Test splice_out_L1_L2_same
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/splice_out_L1_L2_same/command.sh
Finished dock_with_hotspot_place_simultaneously in 27 seconds [~ 323 test (39.583333333333336%) started, 493 in queue, 32 running]
Running Test simple_metric_filter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_metric_filter/command.sh
Finished docking_full_protocol in 28 seconds [~ 324 test (39.705882352941174%) started, 492 in queue, 32 running]
Finished UBQ_Gp_LYX-Cterm in 27 seconds [~ 324 test (39.705882352941174%) started, 492 in queue, 31 running]
Running Test match_6cpa
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/match_6cpa/command.sh
Running Test ligand_motif_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ligand_motif_design/command.sh
Finished threefold_symm_peptide_design in 27 seconds [~ 326 test (39.950980392156865%) started, 490 in queue, 32 running]
Running Test density_refine
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/density_refine/command.sh
Finished splice_out_L3_same in 27 seconds [~ 327 test (40.0735294117647%) started, 489 in queue, 32 running]
Running Test crosslinkermover_trigonal_pyramidal
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_trigonal_pyramidal/command.sh
Finished splice_out_H1_H2_same in 27 seconds [~ 328 test (40.19607843137255%) started, 488 in queue, 32 running]
Running Test cart_min_glycans
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cart_min_glycans/command.sh
Finished simple_hbondstoatom in 27 seconds [~ 329 test (40.318627450980394%) started, 487 in queue, 32 running]
Running Test backrub_interface_ddG
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/backrub_interface_ddG/command.sh
Finished simple_cycpep_predict_cispro in 26 seconds [~ 330 test (40.44117647058823%) started, 486 in queue, 32 running]
Running Test loop_modeling
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/loop_modeling/command.sh
Finished simple_cycpep_predict_symm_gly in 27 seconds [~ 331 test (40.56372549019608%) started, 485 in queue, 32 running]
Running Test loop_grower_N_term_symm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/loop_grower_N_term_symm/command.sh
Finished rosetta_scripts_include in 27 seconds [~ 332 test (40.68627450980392%) started, 484 in queue, 32 running]
Running Test jd2test_PDBin_mmCIFout
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/jd2test_PDBin_mmCIFout/command.sh
Finished perturb_helical_bundle in 27 seconds [~ 333 test (40.80882352941177%) started, 483 in queue, 32 running]
Running Test jd2test_PDBIO
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/jd2test_PDBIO/command.sh
Finished match_1n9l in 27 seconds [~ 334 test (40.931372549019606%) started, 482 in queue, 32 running]
Running Test inv_kin_lig_loop_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/inv_kin_lig_loop_design/command.sh
Finished simple_metric_filter in 22 seconds [~ 335 test (41.05392156862745%) started, 481 in queue, 32 running]
Running Test hbonds
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hbonds/command.sh
Finished genkic_lowmemory_mode in 27 seconds [~ 336 test (41.1764705882353%) started, 480 in queue, 32 running]
Running Test design_w_custom_palette-NCAAs
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/design_w_custom_palette-NCAAs/command.sh
Finished symmetry_multicomponent in 24 seconds [~ 337 test (41.299019607843135%) started, 479 in queue, 32 running]
Running Test crosslinkermover_trigonal_planar
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_trigonal_planar/command.sh
Finished score12_docking in 25 seconds [~ 338 test (41.42156862745098%) started, 478 in queue, 32 running]
Finished swm_protein_loop_sampler in 24 seconds [~ 338 test (41.42156862745098%) started, 478 in queue, 31 running]
Running Test bin_initialization
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bin_initialization/command.sh
Running Test swm_general_polymer_sampler
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_general_polymer_sampler/command.sh
Finished pocket_relax in 26 seconds [~ 340 test (41.666666666666664%) started, 476 in queue, 32 running]
Finished KIC_vicinity in 25 seconds [~ 340 test (41.666666666666664%) started, 476 in queue, 31 running]
Running Test splice_out_L3_shorter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/splice_out_L3_shorter/command.sh
Finished torsion_restricted_sampling in 25 seconds [~ 342 test (41.911764705882355%) started, 474 in queue, 32 running]
Finished swm_beta_peptide_loop in 24 seconds [~ 342 test (41.911764705882355%) started, 474 in queue, 31 running]
Running Test simple_metric_features
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_metric_features/command.sh
Running Test simple_glycosylation_alternate_AAs
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_glycosylation_alternate_AAs/command.sh
Running Test simple_cycpep_predict_tetrahedral_metal_asp
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_tetrahedral_metal_asp/command.sh
Finished multistage_rosetta_scripts in 26 seconds [~ 344 test (42.15686274509804%) started, 472 in queue, 32 running]
Finished favor_coupling_tensor in 26 seconds [~ 344 test (42.15686274509804%) started, 472 in queue, 31 running]
Running Test simple_cycpep_predict_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_design/command.sh
Running Test score_only_silence
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/score_only_silence/command.sh
Finished KIC_refine in 27 seconds [~ 346 test (42.40196078431372%) started, 470 in queue, 32 running]
Finished sequence_profile_constraints in 26 seconds [~ 346 test (42.40196078431372%) started, 470 in queue, 31 running]
Finished bundlegridsampler_z1_offset in 25 seconds [~ 346 test (42.40196078431372%) started, 470 in queue, 30 running]
Finished bundlegridsampler_z0_offset in 25 seconds [~ 346 test (42.40196078431372%) started, 470 in queue, 29 running]
Running Test residue_energy_breakdown
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/residue_energy_breakdown/command.sh
Running Test pepspec
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pepspec/command.sh
Running Test oligourea_predict
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/oligourea_predict/command.sh
Finished match_6cpa in 24 seconds [~ 350 test (42.8921568627451%) started, 466 in queue, 32 running]
Running Test multistage_rosetta_scripts_clustering
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/multistage_rosetta_scripts_clustering/command.sh
Running Test membrane_abinitio
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/membrane_abinitio/command.sh
Finished helical_bundle_nonideal in 26 seconds [~ 351 test (43.01470588235294%) started, 465 in queue, 32 running]
Finished place_simultaneously in 26 seconds [~ 351 test (43.01470588235294%) started, 465 in queue, 31 running]
Finished splice_out_L1_L2_same in 25 seconds [~ 351 test (43.01470588235294%) started, 465 in queue, 30 running]
Running Test make_mainchain_potential
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/make_mainchain_potential/command.sh
Running Test jd2test_PDBin_mmCIFout_extra_data_separate
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/jd2test_PDBin_mmCIFout_extra_data_separate/command.sh
Running Test design_w_custom_palette-CAAs
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/design_w_custom_palette-CAAs/command.sh
Finished InterfaceAnalyzer in 27 seconds [~ 354 test (43.38235294117647%) started, 462 in queue, 32 running]
Running Test carbohydrates
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/carbohydrates/command.sh
Finished app_exception_handling in 619 seconds [~ 355 test (43.504901960784316%) started, 461 in queue, 32 running]
Running Test bundlegridsampler_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bundlegridsampler_design/command.sh
Finished ligand_motif_design in 25 seconds [~ 356 test (43.627450980392155%) started, 460 in queue, 32 running]
Finished density_refine in 24 seconds [~ 356 test (43.627450980392155%) started, 460 in queue, 31 running]
Running Test RunSimpleMetric_b_factor_test
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/RunSimpleMetric_b_factor_test/command.sh
Running Test tcrmodel
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/tcrmodel/command.sh
Finished auto-drrafter_final_results in 27 seconds [~ 358 test (43.872549019607845%) started, 458 in queue, 32 running]
Running Test splice_out_H1_H2_shorter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/splice_out_H1_H2_shorter/command.sh
Finished cart_min_glycans in 24 seconds [~ 359 test (43.995098039215684%) started, 457 in queue, 32 running]
Running Test simple_metrics_in_protocols
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_metrics_in_protocols/command.sh
Finished crosslinkermover_trigonal_pyramidal in 25 seconds [~ 360 test (44.11764705882353%) started, 456 in queue, 32 running]
Running Test simple_metric_cache
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_metric_cache/command.sh
Finished backrub_interface_ddG in 25 seconds [~ 361 test (44.240196078431374%) started, 455 in queue, 32 running]
Running Test rna_puzzle11_H2H3H4_run3_connectU40
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_puzzle11_H2H3H4_run3_connectU40/command.sh
Finished loop_modeling in 23 seconds [~ 362 test (44.36274509803921%) started, 454 in queue, 32 running]
Running Test rna_farfar_noncanonical_hairpin
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_farfar_noncanonical_hairpin/command.sh
Finished tcrmodel in 9 seconds [~ 363 test (44.48529411764706%) started, 453 in queue, 32 running]
Running Test mm_params
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mm_params/command.sh
Finished loop_grower_N_term_symm in 23 seconds [~ 364 test (44.6078431372549%) started, 452 in queue, 32 running]
Running Test minimize_with_elec_dens
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/minimize_with_elec_dens/command.sh
Finished simple_cycpep_predict_tetrahedral_metal_asp in 14 seconds [~ 365 test (44.73039215686274%) started, 451 in queue, 32 running]
Running Test enumerative_sampling
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/enumerative_sampling/command.sh
Finished jd2test_PDBin_mmCIFout in 24 seconds [~ 366 test (44.85294117647059%) started, 450 in queue, 32 running]
Running Test centroid_from_fullatom
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/centroid_from_fullatom/command.sh
Finished jd2test_PDBIO in 24 seconds [~ 367 test (44.97549019607843%) started, 449 in queue, 32 running]
Running Test antibody_designer_camelid
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/antibody_designer_camelid/command.sh
Finished inv_kin_lig_loop_design in 24 seconds [~ 368 test (45.09803921568628%) started, 448 in queue, 32 running]
Running Test AnchorFinder
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/AnchorFinder/command.sh
Finished hbonds in 24 seconds [~ 369 test (45.220588235294116%) started, 447 in queue, 32 running]
Finished simple_glycosylation_alternate_AAs in 22 seconds [~ 369 test (45.220588235294116%) started, 447 in queue, 31 running]
Running Test simple_cycpep_predict_thioether_lariat
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_thioether_lariat/command.sh
Running Test sasa_metric_options
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/sasa_metric_options/command.sh
/Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_metric_features/command.sh: line 12: dump.sql: No such file or directory
Finished simple_metric_features in 22 seconds [~ 371 test (45.46568627450981%) started, 445 in queue, 32 running]
Finished membrane_abinitio in 22 seconds [~ 371 test (45.46568627450981%) started, 445 in queue, 31 running]
Finished simple_metrics_in_protocols in 19 seconds [~ 371 test (45.46568627450981%) started, 445 in queue, 30 running]
Running Test motif_score_filter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/motif_score_filter/command.sh
Running Test mhc_epitope_nmer_preload
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mhc_epitope_nmer_preload/command.sh
Running Test mf_fixbb_des
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mf_fixbb_des/command.sh
Finished score_only_silence in 22 seconds [~ 374 test (45.833333333333336%) started, 442 in queue, 32 running]
Running Test glycan_anomers
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/glycan_anomers/command.sh
Finished splice_out_L3_shorter in 23 seconds [~ 375 test (45.955882352941174%) started, 441 in queue, 32 running]
Finished multistage_rosetta_scripts_clustering in 22 seconds [~ 375 test (45.955882352941174%) started, 441 in queue, 31 running]
Finished make_mainchain_potential in 22 seconds [~ 375 test (45.955882352941174%) started, 441 in queue, 30 running]
Running Test crosslinkermover_trigonal_pyramidal_c3_symm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_trigonal_pyramidal_c3_symm/command.sh
Running Test crosslinkermover_trigonal_planar_c3_symm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_trigonal_planar_c3_symm/command.sh
Running Test bundlegridsampler_multirepeat
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bundlegridsampler_multirepeat/command.sh
Finished oligourea_predict in 22 seconds [~ 378 test (46.3235294117647%) started, 438 in queue, 32 running]
Running Test UBQ_Gp_CYD-CYD
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/UBQ_Gp_CYD-CYD/command.sh
Finished design_w_custom_palette-NCAAs in 24 seconds [~ 379 test (46.44607843137255%) started, 437 in queue, 32 running]
Finished simple_cycpep_predict_design in 23 seconds [~ 379 test (46.44607843137255%) started, 437 in queue, 31 running]
Running Test LayerSelector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/LayerSelector/command.sh
Running Test splice_out_L1_L2_shorter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/splice_out_L1_L2_shorter/command.sh
Finished carbohydrates in 22 seconds [~ 381 test (46.69117647058823%) started, 435 in queue, 32 running]
Running Test ncbb_packer_palette
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ncbb_packer_palette/command.sh
Finished pepspec in 23 seconds [~ 382 test (46.81372549019608%) started, 434 in queue, 32 running]
Finished simple_metric_cache in 20 seconds [~ 382 test (46.81372549019608%) started, 434 in queue, 31 running]
Running Test match_xml
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/match_xml/command.sh
Running Test hbonds_sp2
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hbonds_sp2/command.sh
Finished crosslinkermover_trigonal_planar in 24 seconds [~ 384 test (47.05882352941177%) started, 432 in queue, 32 running]
Finished bin_initialization in 24 seconds [~ 384 test (47.05882352941177%) started, 432 in queue, 31 running]
Finished bundlegridsampler_design in 22 seconds [~ 384 test (47.05882352941177%) started, 432 in queue, 30 running]
Running Test crosslinkermover_methyllanthionine
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_methyllanthionine/command.sh
Running Test add_constraints_to_current_conformation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/add_constraints_to_current_conformation/command.sh
Running Test InterfaceAnalyzer_metrics
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/InterfaceAnalyzer_metrics/command.sh
Finished jd2test_PDBin_mmCIFout_extra_data_separate in 23 seconds [~ 387 test (47.4264705882353%) started, 429 in queue, 32 running]
Finished design_w_custom_palette-CAAs in 23 seconds [~ 387 test (47.4264705882353%) started, 429 in queue, 31 running]
Running Test AnchoredPDBCreator
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/AnchoredPDBCreator/command.sh
Running Test thermal_sampler
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/thermal_sampler/command.sh
Finished residue_energy_breakdown in 24 seconds [~ 389 test (47.67156862745098%) started, 427 in queue, 32 running]
Finished splice_out_H1_H2_shorter in 22 seconds [~ 389 test (47.67156862745098%) started, 427 in queue, 31 running]
Running Test swa_protein_build_at_Cterminus
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_protein_build_at_Cterminus/command.sh
Running Test splice_out_H3_same
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/splice_out_H3_same/command.sh
Finished rna_puzzle11_H2H3H4_run3_connectU40 in 21 seconds [~ 391 test (47.916666666666664%) started, 425 in queue, 32 running]
Running Test rollmover
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rollmover/command.sh
Finished swm_general_polymer_sampler in 26 seconds [~ 392 test (48.03921568627451%) started, 424 in queue, 32 running]
Running Test recon_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/recon_design/command.sh
Finished RunSimpleMetric_b_factor_test in 26 seconds [~ 393 test (48.161764705882355%) started, 423 in queue, 32 running]
Running Test metropolis_hastings
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/metropolis_hastings/command.sh
Finished mm_params in 21 seconds [~ 394 test (48.28431372549019%) started, 422 in queue, 32 running]
Running Test ligand_dock_grid
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ligand_dock_grid/command.sh
Finished rna_farfar_noncanonical_hairpin in 22 seconds [~ 395 test (48.40686274509804%) started, 421 in queue, 32 running]
Running Test density_denovo
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/density_denovo/command.sh
Finished minimize_with_elec_dens in 22 seconds [~ 396 test (48.529411764705884%) started, 420 in queue, 32 running]
Running Test broker
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/broker/command.sh
Finished enumerative_sampling in 22 seconds [~ 397 test (48.65196078431372%) started, 419 in queue, 32 running]
Running Test antibody_graft
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/antibody_graft/command.sh
Finished centroid_from_fullatom in 22 seconds [~ 398 test (48.77450980392157%) started, 418 in queue, 32 running]
Running Test UBQ_E2_thioester_two_ubiquitins
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/UBQ_E2_thioester_two_ubiquitins/command.sh
Finished antibody_designer_camelid in 21 seconds [~ 399 test (48.89705882352941%) started, 417 in queue, 32 running]
Running Test ThreadingInputter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ThreadingInputter/command.sh
Finished motif_score_filter in 20 seconds [~ 400 test (49.01960784313726%) started, 416 in queue, 32 running]
Finished thermal_sampler in 19 seconds [~ 400 test (49.01960784313726%) started, 416 in queue, 31 running]
Finished swa_protein_build_at_Cterminus in 18 seconds [~ 400 test (49.01960784313726%) started, 416 in queue, 30 running]
Running Test thread_local_tracers_check
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/thread_local_tracers_check/command.sh
Running Test simple_cycpep_predict_square_planar_metal
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_square_planar_metal/command.sh
Running Test posttranslationalmod_io
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/posttranslationalmod_io/command.sh
Finished ncbb_packer_palette in 20 seconds [~ 403 test (49.38725490196079%) started, 413 in queue, 32 running]
Running Test perturb_helical_bundle_setting
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/perturb_helical_bundle_setting/command.sh
Finished AnchorFinder in 22 seconds [~ 404 test (49.509803921568626%) started, 412 in queue, 32 running]
Running Test oligourea_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/oligourea_design/command.sh
Finished sasa_metric_options in 22 seconds [~ 405 test (49.63235294117647%) started, 411 in queue, 32 running]
Finished AnchoredPDBCreator in 19 seconds [~ 405 test (49.63235294117647%) started, 411 in queue, 31 running]
Running Test min_pack_min
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/min_pack_min/command.sh
Running Test ReadResfile_with_selector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ReadResfile_with_selector/command.sh
Finished mhc_epitope_nmer_preload in 21 seconds [~ 407 test (49.877450980392155%) started, 409 in queue, 32 running]
Finished glycan_anomers in 21 seconds [~ 407 test (49.877450980392155%) started, 409 in queue, 31 running]
Finished bundlegridsampler_multirepeat in 21 seconds [~ 407 test (49.877450980392155%) started, 409 in queue, 30 running]
Running Test LayerDesign
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/LayerDesign/command.sh
Running Test zinc_homodimer_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/zinc_homodimer_design/command.sh
Running Test startfrom_file
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/startfrom_file/command.sh
Finished UBQ_Gp_CYD-CYD in 21 seconds [~ 410 test (50.245098039215684%) started, 406 in queue, 32 running]
Finished add_constraints_to_current_conformation in 20 seconds [~ 410 test (50.245098039215684%) started, 406 in queue, 31 running]
Running Test splice_out_H3_shorter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/splice_out_H3_shorter/command.sh
Running Test simple_cycpep_predict_peptoid
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_peptoid/command.sh
Finished mf_fixbb_des in 22 seconds [~ 412 test (50.490196078431374%) started, 404 in queue, 32 running]
Finished splice_out_L1_L2_shorter in 21 seconds [~ 412 test (50.490196078431374%) started, 404 in queue, 31 running]
Finished hbonds_sp2 in 20 seconds [~ 412 test (50.490196078431374%) started, 404 in queue, 30 running]
Running Test repack_with_elec_dens
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/repack_with_elec_dens/command.sh
Running Test pna
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pna/command.sh
Running Test glycan_sequon_scanner
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/glycan_sequon_scanner/command.sh
Finished LayerSelector in 21 seconds [~ 415 test (50.8578431372549%) started, 401 in queue, 32 running]
Finished match_xml in 21 seconds [~ 415 test (50.8578431372549%) started, 401 in queue, 31 running]
Finished splice_out_H3_same in 20 seconds [~ 415 test (50.8578431372549%) started, 401 in queue, 30 running]
Running Test glycan_refinment
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/glycan_refinment/command.sh
Running Test enzscore_filter_metal_sym
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/enzscore_filter_metal_sym/command.sh
Running Test enzscore_filter_dimetal_sym
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/enzscore_filter_dimetal_sym/command.sh
Finished crosslinkermover_trigonal_pyramidal_c3_symm in 22 seconds [~ 418 test (51.22549019607843%) started, 398 in queue, 32 running]
Finished crosslinkermover_trigonal_planar_c3_symm in 22 seconds [~ 418 test (51.22549019607843%) started, 398 in queue, 31 running]
Finished crosslinkermover_methyllanthionine in 21 seconds [~ 418 test (51.22549019607843%) started, 398 in queue, 30 running]
Running Test coarse_rna_scoring
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/coarse_rna_scoring/command.sh
Running Test classic_relax_1a19
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/classic_relax_1a19/command.sh
Running Test backbonegridsampler_nstruct_mode
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/backbonegridsampler_nstruct_mode/command.sh
Finished InterfaceAnalyzer_metrics in 21 seconds [~ 421 test (51.59313725490196%) started, 395 in queue, 32 running]
Running Test PeptideCyclizeMover
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/PeptideCyclizeMover/command.sh
Finished recon_design in 19 seconds [~ 422 test (51.71568627450981%) started, 394 in queue, 32 running]
Running Test test_computed_saxs_spectrum
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/test_computed_saxs_spectrum/command.sh
Finished rollmover in 19 seconds [~ 423 test (51.838235294117645%) started, 393 in queue, 32 running]
Running Test swm_rna_checkpoint_partition
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_rna_checkpoint_partition/command.sh
Finished metropolis_hastings in 19 seconds [~ 424 test (51.96078431372549%) started, 392 in queue, 32 running]
Running Test swm_protein_move_inside_helix_by_bond
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_protein_move_inside_helix_by_bond/command.sh
Finished simple_cycpep_predict_thioether_lariat in 25 seconds [~ 425 test (52.083333333333336%) started, 391 in queue, 32 running]
Running Test simple_dna_test
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_dna_test/command.sh
Finished ligand_dock_grid in 20 seconds [~ 426 test (52.205882352941174%) started, 390 in queue, 32 running]
Running Test rosetta_scripts_hbond_options
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rosetta_scripts_hbond_options/command.sh
Finished density_denovo in 19 seconds [~ 427 test (52.32843137254902%) started, 389 in queue, 32 running]
Running Test ppk
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ppk/command.sh
sed: 1: "threadlocal_tracers.txt": undefined label 'hreadlocal_tracers.txt'
Finished thread_local_tracers_check in 10 seconds [~ 428 test (52.450980392156865%) started, 388 in queue, 32 running]
Running Test mp_ligand_interface
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_ligand_interface/command.sh
Finished broker in 20 seconds [~ 429 test (52.5735294117647%) started, 387 in queue, 32 running]
Running Test genkic_rama_filter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/genkic_rama_filter/command.sh
Finished antibody_graft in 19 seconds [~ 430 test (52.69607843137255%) started, 386 in queue, 32 running]
Running Test fuzzy
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fuzzy/command.sh
Finished UBQ_E2_thioester_two_ubiquitins in 20 seconds [~ 431 test (52.818627450980394%) started, 385 in queue, 32 running]
Running Test enzscore_filter_metal
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/enzscore_filter_metal/command.sh
Finished ThreadingInputter in 20 seconds [~ 432 test (52.94117647058823%) started, 384 in queue, 32 running]
Running Test enzscore_filter_dimetal
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/enzscore_filter_dimetal/command.sh
Finished zinc_homodimer_design in 17 seconds [~ 433 test (53.06372549019608%) started, 383 in queue, 32 running]
Running Test ddG_scan
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ddG_scan/command.sh
Finished perturb_helical_bundle_setting in 18 seconds [~ 434 test (53.18627450980392%) started, 382 in queue, 32 running]
Running Test crosslinkermover_tetrahedral_metal_asp
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_tetrahedral_metal_asp/command.sh
Finished posttranslationalmod_io in 19 seconds [~ 435 test (53.30882352941177%) started, 381 in queue, 32 running]
Finished oligourea_design in 19 seconds [~ 435 test (53.30882352941177%) started, 381 in queue, 31 running]
Finished startfrom_file in 18 seconds [~ 435 test (53.30882352941177%) started, 381 in queue, 30 running]
Finished glycan_refinment in 17 seconds [~ 435 test (53.30882352941177%) started, 381 in queue, 29 running]
Running Test crosslinkermover_lanthionine
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_lanthionine/command.sh
Running Test backbonegridsampler_multiresidue
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/backbonegridsampler_multiresidue/command.sh
Running Test symmetric_docking
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/symmetric_docking/command.sh
Running Test sim_cryo
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/sim_cryo/command.sh
Finished min_pack_min in 19 seconds [~ 439 test (53.799019607843135%) started, 377 in queue, 32 running]
Finished splice_out_H3_shorter in 18 seconds [~ 439 test (53.799019607843135%) started, 377 in queue, 31 running]
Finished repack_with_elec_dens in 18 seconds [~ 439 test (53.799019607843135%) started, 377 in queue, 30 running]
Finished glycan_sequon_scanner in 18 seconds [~ 439 test (53.799019607843135%) started, 377 in queue, 29 running]
Running Test rosetta_scripts_setup
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rosetta_scripts_setup/command.sh
Running Test rna_denovo_base_pair_setup
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_base_pair_setup/command.sh
Running Test repeat_propagate_v3
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/repeat_propagate_v3/command.sh
Running Test repeat_propagate
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/repeat_propagate/command.sh
Finished ReadResfile_with_selector in 19 seconds [~ 443 test (54.28921568627451%) started, 373 in queue, 32 running]
Finished simple_cycpep_predict_peptoid in 18 seconds [~ 443 test (54.28921568627451%) started, 373 in queue, 31 running]
Finished backbonegridsampler_nstruct_mode in 18 seconds [~ 443 test (54.28921568627451%) started, 373 in queue, 30 running]
Running Test protocol_metric
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/protocol_metric/command.sh
Running Test perturb_helical_bundle_z_offset
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/perturb_helical_bundle_z_offset/command.sh
Running Test perturb_helical_bundle_epsilon
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/perturb_helical_bundle_epsilon/command.sh
Finished simple_cycpep_predict_square_planar_metal in 20 seconds [~ 446 test (54.65686274509804%) started, 370 in queue, 32 running]
Finished LayerDesign in 19 seconds [~ 446 test (54.65686274509804%) started, 370 in queue, 31 running]
Finished enzscore_filter_metal_sym in 18 seconds [~ 446 test (54.65686274509804%) started, 370 in queue, 30 running]
Finished PeptideCyclizeMover in 17 seconds [~ 446 test (54.65686274509804%) started, 370 in queue, 29 running]
Running Test metalloprotein_abrelax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/metalloprotein_abrelax/command.sh
Running Test grid_scores_features
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/grid_scores_features/command.sh
Running Test exclusively_shared_jumps
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/exclusively_shared_jumps/command.sh
Running Test custom_basetype_packer_palette
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/custom_basetype_packer_palette/command.sh
Finished coarse_rna_scoring in 18 seconds [~ 450 test (55.14705882352941%) started, 366 in queue, 32 running]
Finished classic_relax_1a19 in 18 seconds [~ 450 test (55.14705882352941%) started, 366 in queue, 31 running]
Running Test crosslinkermover_thioether
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_thioether/command.sh
Running Test create_sequence_motif
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/create_sequence_motif/command.sh
Finished enzscore_filter_dimetal_sym in 19 seconds [~ 452 test (55.3921568627451%) started, 364 in queue, 32 running]
Finished test_computed_saxs_spectrum in 18 seconds [~ 452 test (55.3921568627451%) started, 364 in queue, 31 running]
Running Test UnsatSelector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/UnsatSelector/command.sh
Running Test LayerDesign_symm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/LayerDesign_symm/command.sh
Finished swm_rna_checkpoint_partition in 18 seconds [~ 454 test (55.63725490196079%) started, 362 in queue, 32 running]
Finished swm_protein_move_inside_helix_by_bond in 17 seconds [~ 454 test (55.63725490196079%) started, 362 in queue, 31 running]
Running Test FloppyTail
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/FloppyTail/command.sh
Running Test FlipChirality
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/FlipChirality/command.sh
Finished pna in 20 seconds [~ 456 test (55.88235294117647%) started, 360 in queue, 32 running]
Running Test ContactMolecularSurface
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ContactMolecularSurface/command.sh
Finished simple_dna_test in 17 seconds [~ 457 test (56.004901960784316%) started, 359 in queue, 32 running]
Running Test write_mol_file
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/write_mol_file/command.sh
Finished ppk in 17 seconds [~ 458 test (56.127450980392155%) started, 358 in queue, 32 running]
Running Test vancomycin
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/vancomycin/command.sh
Finished rosetta_scripts_hbond_options in 18 seconds [~ 459 test (56.25%) started, 357 in queue, 32 running]
Finished mp_ligand_interface in 17 seconds [~ 459 test (56.25%) started, 357 in queue, 31 running]
Running Test threefoldlinkermover_tbmb_symmetric
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/threefoldlinkermover_tbmb_symmetric/command.sh
Running Test threefoldlinkermover_tbmb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/threefoldlinkermover_tbmb/command.sh
Finished genkic_rama_filter in 17 seconds [~ 461 test (56.495098039215684%) started, 355 in queue, 32 running]
Running Test symmetry_data_resource
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/symmetry_data_resource/command.sh
Finished fuzzy in 18 seconds [~ 462 test (56.61764705882353%) started, 354 in queue, 32 running]
Running Test symmetric_cycpep_align_and_symmetrize
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/symmetric_cycpep_align_and_symmetrize/command.sh
Finished enzscore_filter_metal in 17 seconds [~ 463 test (56.740196078431374%) started, 353 in queue, 32 running]
Running Test sample_seq_from_probs
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/sample_seq_from_probs/command.sh
Finished enzscore_filter_dimetal in 17 seconds [~ 464 test (56.86274509803921%) started, 352 in queue, 32 running]
Running Test rotamer_recovery
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rotamer_recovery/command.sh
Finished sim_cryo in 16 seconds [~ 465 test (56.98529411764706%) started, 351 in queue, 32 running]
Running Test rna_farfar_syn_chi_res
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_farfar_syn_chi_res/command.sh
Finished repeat_propagate_v3 in 16 seconds [~ 466 test (57.1078431372549%) started, 350 in queue, 32 running]
Finished ddG_scan in 17 seconds [~ 467 test (57.23039215686274%) started, 349 in queue, 32 running]
Running Test resource_database_locator
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/resource_database_locator/command.sh
Running Test res_lipo_ref2015_memb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/res_lipo_ref2015_memb/command.sh
Finished repeat_propagate in 16 seconds [~ 468 test (57.35294117647059%) started, 348 in queue, 32 running]
Running Test repeat_propagate_v2
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/repeat_propagate_v2/command.sh
Finished rosetta_scripts_setup in 16 seconds [~ 469 test (57.47549019607843%) started, 347 in queue, 32 running]
Finished grid_scores_features in 16 seconds [~ 469 test (57.47549019607843%) started, 347 in queue, 31 running]
Running Test real_virt_mover
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/real_virt_mover/command.sh
Running Test readin_dna_rna_protein
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/readin_dna_rna_protein/command.sh
Finished protocol_metric in 16 seconds [~ 471 test (57.720588235294116%) started, 345 in queue, 32 running]
Finished perturb_helical_bundle_z_offset in 16 seconds [~ 471 test (57.720588235294116%) started, 345 in queue, 31 running]
Finished perturb_helical_bundle_epsilon in 16 seconds [~ 471 test (57.720588235294116%) started, 345 in queue, 30 running]
Running Test rdkit_metrics
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rdkit_metrics/command.sh
Running Test rama_mutation_selector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rama_mutation_selector/command.sh
Running Test pna_base_pairs
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pna_base_pairs/command.sh
Finished crosslinkermover_tetrahedral_metal_asp in 17 seconds [~ 474 test (58.088235294117645%) started, 342 in queue, 32 running]
Finished rna_denovo_base_pair_setup in 17 seconds [~ 474 test (58.088235294117645%) started, 342 in queue, 31 running]
Finished exclusively_shared_jumps in 16 seconds [~ 474 test (58.088235294117645%) started, 342 in queue, 30 running]
Finished FloppyTail in 15 seconds [~ 474 test (58.088235294117645%) started, 342 in queue, 29 running]
Running Test mp_span_ang_ref2015_memb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_span_ang_ref2015_memb/command.sh
Running Test mp_quick_relax_ref2015_memb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_quick_relax_ref2015_memb/command.sh
Running Test mf_flexbb_sc
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mf_flexbb_sc/command.sh
Running Test make_rot_lib
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/make_rot_lib/command.sh
Finished backbonegridsampler_multiresidue in 17 seconds [~ 478 test (58.57843137254902%) started, 338 in queue, 32 running]
Finished metalloprotein_abrelax in 17 seconds [~ 478 test (58.57843137254902%) started, 338 in queue, 31 running]
Finished create_sequence_motif in 17 seconds [~ 478 test (58.57843137254902%) started, 338 in queue, 30 running]
Running Test loop_creation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/loop_creation/command.sh
Running Test genkic_ramaprepro_sampling
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/genkic_ramaprepro_sampling/command.sh
Finished crosslinkermover_lanthionine in 17 seconds [~ 481 test (58.94607843137255%) started, 335 in queue, 32 running]
Finished UnsatSelector in 16 seconds [~ 481 test (58.94607843137255%) started, 335 in queue, 31 running]
Running Test features_pdb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/features_pdb/command.sh
Running Test database_session_resource
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/database_session_resource/command.sh
Running Test cst_info
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cst_info/command.sh
Finished custom_basetype_packer_palette in 17 seconds [~ 483 test (59.19117647058823%) started, 333 in queue, 32 running]
Running Test crosslinkermover_tetrahedral_metal
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_tetrahedral_metal/command.sh
Finished symmetric_docking in 18 seconds [~ 484 test (59.31372549019608%) started, 332 in queue, 32 running]
Finished LayerDesign_symm in 17 seconds [~ 484 test (59.31372549019608%) started, 332 in queue, 31 running]
Finished write_mol_file in 16 seconds [~ 484 test (59.31372549019608%) started, 332 in queue, 30 running]
Running Test bin_perturbation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bin_perturbation/command.sh
Running Test autosetup_metals_centroid
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/autosetup_metals_centroid/command.sh
Running Test RBOut
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/RBOut/command.sh
Finished crosslinkermover_thioether in 17 seconds [~ 487 test (59.681372549019606%) started, 329 in queue, 32 running]
Finished FlipChirality in 16 seconds [~ 487 test (59.681372549019606%) started, 329 in queue, 31 running]
Running Test PDB_diagnostic
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/PDB_diagnostic/command.sh
Running Test InterfaceDdG
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/InterfaceDdG/command.sh
Finished ContactMolecularSurface in 17 seconds [~ 489 test (59.9264705882353%) started, 327 in queue, 32 running]
Running Test DumpTrajectoryEnergy_packing
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/DumpTrajectoryEnergy_packing/command.sh
Finished vancomycin in 15 seconds [~ 490 test (60.049019607843135%) started, 326 in queue, 32 running]
Running Test ConsensusLoopDesign
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ConsensusLoopDesign/command.sh
Finished threefoldlinkermover_tbmb_symmetric in 16 seconds [~ 491 test (60.17156862745098%) started, 325 in queue, 32 running]
Finished threefoldlinkermover_tbmb in 16 seconds [~ 491 test (60.17156862745098%) started, 325 in queue, 31 running]
Running Test BFactorSelector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/BFactorSelector/command.sh
Running Test swm_rna_fourwayjunction
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_rna_fourwayjunction/command.sh
Finished symmetry_data_resource in 16 seconds [~ 493 test (60.416666666666664%) started, 323 in queue, 32 running]
Running Test swm_protein_move_inside_coiledcoil_by_bond
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_protein_move_inside_coiledcoil_by_bond/command.sh
Finished symmetric_cycpep_align_and_symmetrize in 15 seconds [~ 494 test (60.53921568627451%) started, 322 in queue, 32 running]
Running Test swm_protein_CCDmove
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_protein_CCDmove/command.sh
Finished rotamer_recovery in 14 seconds [~ 495 test (60.661764705882355%) started, 321 in queue, 32 running]
Running Test swa_rna_gagu_15_combine_long_loop_sampling
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_15_combine_long_loop_sampling/command.sh
Finished sample_seq_from_probs in 16 seconds [~ 496 test (60.78431372549019%) started, 320 in queue, 32 running]
Running Test smallmover_resselector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/smallmover_resselector/command.sh
Finished rna_farfar_syn_chi_res in 15 seconds [~ 497 test (60.90686274509804%) started, 319 in queue, 32 running]
Running Test sequence_recovery
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/sequence_recovery/command.sh
Finished res_lipo_ref2015_memb in 15 seconds [~ 498 test (61.029411764705884%) started, 318 in queue, 32 running]
Finished repeat_propagate_v2 in 15 seconds [~ 498 test (61.029411764705884%) started, 318 in queue, 31 running]
Running Test selected_residue_count_metric
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/selected_residue_count_metric/command.sh
Running Test rna_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_design/command.sh
Finished resource_database_locator in 16 seconds [~ 500 test (61.27450980392157%) started, 316 in queue, 32 running]
Running Test rna_assemble
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_assemble/command.sh
Finished pna_base_pairs in 15 seconds [~ 501 test (61.39705882352941%) started, 315 in queue, 32 running]
Running Test genkic_bin_perturbing
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/genkic_bin_perturbing/command.sh
Finished mp_quick_relax_ref2015_memb in 15 seconds [~ 502 test (61.51960784313726%) started, 314 in queue, 32 running]
Running Test fold_cst_new
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fold_cst_new/command.sh
Finished rama_mutation_selector in 16 seconds [~ 503 test (61.6421568627451%) started, 313 in queue, 32 running]
Finished mp_span_ang_ref2015_memb in 16 seconds [~ 503 test (61.6421568627451%) started, 313 in queue, 31 running]
Running Test enzscore_filter_ligand
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/enzscore_filter_ligand/command.sh
Running Test dihedral_constraint_generator
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/dihedral_constraint_generator/command.sh
Finished real_virt_mover in 16 seconds [~ 505 test (61.88725490196079%) started, 311 in queue, 32 running]
Finished readin_dna_rna_protein in 16 seconds [~ 505 test (61.88725490196079%) started, 311 in queue, 31 running]
Finished rdkit_metrics in 16 seconds [~ 505 test (61.88725490196079%) started, 311 in queue, 30 running]
Finished mf_flexbb_sc in 16 seconds [~ 505 test (61.88725490196079%) started, 311 in queue, 29 running]
Finished make_rot_lib in 16 seconds [~ 505 test (61.88725490196079%) started, 311 in queue, 28 running]
Running Test cluster_alns
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cluster_alns/command.sh
Running Test add_job_pair_data
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/add_job_pair_data/command.sh
Running Test StrandHelixGeometryFilter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/StrandHelixGeometryFilter/command.sh
Running Test StrandCurvatureByLevels
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/StrandCurvatureByLevels/command.sh
Running Test SecondaryStructureFilter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/SecondaryStructureFilter/command.sh
Finished database_session_resource in 16 seconds [~ 510 test (62.5%) started, 306 in queue, 32 running]
Running Test PeptideStubMover_prependRepeat
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/PeptideStubMover_prependRepeat/command.sh
Finished loop_creation in 16 seconds [~ 511 test (62.622549019607845%) started, 305 in queue, 32 running]
Finished genkic_ramaprepro_sampling in 16 seconds [~ 511 test (62.622549019607845%) started, 305 in queue, 31 running]
Finished bin_perturbation in 16 seconds [~ 511 test (62.622549019607845%) started, 305 in queue, 30 running]
Finished RBOut in 16 seconds [~ 511 test (62.622549019607845%) started, 305 in queue, 29 running]
Running Test OversaturatedHbondAcceptorFilter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/OversaturatedHbondAcceptorFilter/command.sh
Running Test MutateResidue_selector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/MutateResidue_selector/command.sh
Running Test LoopLengthChange
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/LoopLengthChange/command.sh
Running Test HelixBendFilter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/HelixBendFilter/command.sh
Finished features_pdb in 16 seconds [~ 515 test (63.11274509803921%) started, 301 in queue, 32 running]
Finished cst_info in 16 seconds [~ 515 test (63.11274509803921%) started, 301 in queue, 31 running]
Finished autosetup_metals_centroid in 16 seconds [~ 515 test (63.11274509803921%) started, 301 in queue, 30 running]
Finished PDB_diagnostic in 16 seconds [~ 515 test (63.11274509803921%) started, 301 in queue, 29 running]
Running Test FilterReportAsPoseExtraScoresMover
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/FilterReportAsPoseExtraScoresMover/command.sh
Running Test FavorSequenceProfileMover
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/FavorSequenceProfileMover/command.sh
Running Test DumpTrajectoryEnergy
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/DumpTrajectoryEnergy/command.sh
Running Test AddConstraintsToCurrentConformationMover
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/AddConstraintsToCurrentConformationMover/command.sh
Finished crosslinkermover_tetrahedral_metal in 16 seconds [~ 519 test (63.60294117647059%) started, 297 in queue, 32 running]
Running Test swm_rna_protonated_adenosine
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_rna_protonated_adenosine/command.sh
Finished InterfaceDdG in 16 seconds [~ 520 test (63.72549019607843%) started, 296 in queue, 32 running]
Running Test swa_rna_gagu_23_append_and_kic_close
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_23_append_and_kic_close/command.sh
Finished DumpTrajectoryEnergy_packing in 16 seconds [~ 521 test (63.84803921568628%) started, 295 in queue, 32 running]
Running Test swa_rna_gagu_22_prepend_and_kic_close
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_22_prepend_and_kic_close/command.sh
Finished swm_rna_fourwayjunction in 14 seconds [~ 522 test (63.970588235294116%) started, 294 in queue, 32 running]
Running Test swa_rna_gagu_16_prepend_dinucleotide_on_dinucleotide
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_16_prepend_dinucleotide_on_dinucleotide/command.sh
Finished ConsensusLoopDesign in 16 seconds [~ 523 test (64.09313725490196%) started, 293 in queue, 32 running]
Running Test swa_rna_gagu_13_chunk_combination_and_closure
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_13_chunk_combination_and_closure/command.sh
Finished swm_protein_move_inside_coiledcoil_by_bond in 15 seconds [~ 524 test (64.2156862745098%) started, 292 in queue, 32 running]
Running Test swa_rna_gagu_10_prepend_and_ccd_close
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_10_prepend_and_ccd_close/command.sh
Finished BFactorSelector in 16 seconds [~ 525 test (64.33823529411765%) started, 291 in queue, 32 running]
Running Test stored_residue_subset
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/stored_residue_subset/command.sh
Finished swm_protein_CCDmove in 15 seconds [~ 526 test (64.46078431372548%) started, 290 in queue, 32 running]
Running Test simple_cycpep_predict_terminal_disulfide_internal_permutations
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_terminal_disulfide_internal_permutations/command.sh
Finished swa_rna_gagu_15_combine_long_loop_sampling in 15 seconds [~ 527 test (64.58333333333333%) started, 289 in queue, 32 running]
Running Test simple_cycpep_predict_sidechain_isopeptide
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_sidechain_isopeptide/command.sh
Finished smallmover_resselector in 15 seconds [~ 528 test (64.70588235294117%) started, 288 in queue, 32 running]
Running Test oop_dock_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/oop_dock_design/command.sh
Finished sequence_recovery in 15 seconds [~ 529 test (64.82843137254902%) started, 287 in queue, 32 running]
Running Test mp_symmetry_load
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_symmetry_load/command.sh
Finished rna_assemble in 15 seconds [~ 530 test (64.95098039215686%) started, 286 in queue, 32 running]
Running Test mf_fixbb_sc
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mf_fixbb_sc/command.sh
Finished genkic_bin_perturbing in 15 seconds [~ 531 test (65.07352941176471%) started, 285 in queue, 32 running]
Finished fold_cst_new in 14 seconds [~ 531 test (65.07352941176471%) started, 285 in queue, 31 running]
Running Test genkic_dihedral_copying
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/genkic_dihedral_copying/command.sh
Running Test design_w_custom_palette-RNA
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/design_w_custom_palette-RNA/command.sh
Finished selected_residue_count_metric in 15 seconds [~ 533 test (65.31862745098039%) started, 283 in queue, 32 running]
Running Test density_refine_symm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/density_refine_symm/command.sh
Finished rna_design in 16 seconds [~ 534 test (65.44117647058823%) started, 282 in queue, 32 running]
Running Test dehydro_aa_patch
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/dehydro_aa_patch/command.sh
Finished cluster_alns in 15 seconds [~ 535 test (65.56372549019608%) started, 281 in queue, 32 running]
Running Test buried_area_filter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/buried_area_filter/command.sh
Finished add_job_pair_data in 15 seconds [~ 536 test (65.68627450980392%) started, 280 in queue, 32 running]
Running Test ambiguous_nmr_distance_constraint
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ambiguous_nmr_distance_constraint/command.sh
Finished enzscore_filter_ligand in 16 seconds [~ 537 test (65.80882352941177%) started, 279 in queue, 32 running]
Finished swa_rna_gagu_23_append_and_kic_close in 14 seconds [~ 537 test (65.80882352941177%) started, 279 in queue, 31 running]
Running Test SSElementSelector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/SSElementSelector/command.sh
Running Test symmetrical_residue_selector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/symmetrical_residue_selector/command.sh
Finished dihedral_constraint_generator in 16 seconds [~ 539 test (66.05392156862744%) started, 277 in queue, 32 running]
Running Test swm_build_full_model
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_build_full_model/command.sh
Finished StrandHelixGeometryFilter in 16 seconds [~ 540 test (66.17647058823529%) started, 276 in queue, 32 running]
Finished StrandCurvatureByLevels in 16 seconds [~ 540 test (66.17647058823529%) started, 276 in queue, 31 running]
Finished SecondaryStructureFilter in 16 seconds [~ 540 test (66.17647058823529%) started, 276 in queue, 30 running]
Finished PeptideStubMover_prependRepeat in 16 seconds [~ 540 test (66.17647058823529%) started, 276 in queue, 29 running]
Finished LoopLengthChange in 15 seconds [~ 540 test (66.17647058823529%) started, 276 in queue, 28 running]
Running Test swm_add_rosettascripts
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_add_rosettascripts/command.sh
Running Test swa_rna_gagu_18_rebuild_bulge
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_18_rebuild_bulge/command.sh
Running Test swa_rna_gagu_11_append_and_ccd_close
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_11_append_and_ccd_close/command.sh
Running Test set_torsion
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/set_torsion/command.sh
Running Test referencepose_mutateresidue
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/referencepose_mutateresidue/command.sh
Finished FilterReportAsPoseExtraScoresMover in 15 seconds [~ 545 test (66.78921568627452%) started, 271 in queue, 32 running]
Finished AddConstraintsToCurrentConformationMover in 15 seconds [~ 545 test (66.78921568627452%) started, 271 in queue, 31 running]
Finished swm_rna_protonated_adenosine in 15 seconds [~ 545 test (66.78921568627452%) started, 271 in queue, 30 running]
Running Test pocket_measure
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pocket_measure/command.sh
Running Test phiselector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/phiselector/command.sh
Running Test mp_dock
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_dock/command.sh
Finished OversaturatedHbondAcceptorFilter in 16 seconds [~ 548 test (67.15686274509804%) started, 268 in queue, 32 running]
Running Test metal_setup
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/metal_setup/command.sh
Finished MutateResidue_selector in 16 seconds [~ 549 test (67.27941176470588%) started, 267 in queue, 32 running]
Finished HelixBendFilter in 16 seconds [~ 549 test (67.27941176470588%) started, 267 in queue, 31 running]
Finished swa_rna_gagu_22_prepend_and_kic_close in 14 seconds [~ 549 test (67.27941176470588%) started, 267 in queue, 30 running]
Running Test make_and_perturb_bundle_multirepeat
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/make_and_perturb_bundle_multirepeat/command.sh
Running Test longest_continuous_polar_segment_filter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/longest_continuous_polar_segment_filter/command.sh
Running Test hbondstoresidue_selector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hbondstoresidue_selector/command.sh
Finished DumpTrajectoryEnergy in 16 seconds [~ 552 test (67.6470588235294%) started, 264 in queue, 32 running]
Running Test genkic_bin_setting
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/genkic_bin_setting/command.sh
Finished FavorSequenceProfileMover in 16 seconds [~ 553 test (67.76960784313725%) started, 263 in queue, 32 running]
Running Test create_clash-based_repack_shell
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/create_clash-based_repack_shell/command.sh
Finished swa_rna_gagu_16_prepend_dinucleotide_on_dinucleotide in 15 seconds [~ 554 test (67.8921568627451%) started, 262 in queue, 32 running]
Running Test copy_rotamer_mover
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/copy_rotamer_mover/command.sh
Finished swa_rna_gagu_10_prepend_and_ccd_close in 14 seconds [~ 555 test (68.01470588235294%) started, 261 in queue, 32 running]
Running Test binselector_probins
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/binselector_probins/command.sh
Finished swa_rna_gagu_13_chunk_combination_and_closure in 15 seconds [~ 556 test (68.13725490196079%) started, 260 in queue, 32 running]
Running Test binselector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/binselector/command.sh
Finished stored_residue_subset in 14 seconds [~ 557 test (68.25980392156863%) started, 259 in queue, 32 running]
Running Test backbonegridsampler
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/backbonegridsampler/command.sh
Finished simple_cycpep_predict_terminal_disulfide_internal_permutations in 14 seconds [~ 558 test (68.38235294117646%) started, 258 in queue, 32 running]
Running Test ModifyVariantTypeMover
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ModifyVariantTypeMover/command.sh
Finished oop_dock_design in 14 seconds [~ 559 test (68.50490196078431%) started, 257 in queue, 32 running]
Running Test tna_base_pairs
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/tna_base_pairs/command.sh
Finished simple_cycpep_predict_sidechain_isopeptide in 15 seconds [~ 560 test (68.62745098039215%) started, 256 in queue, 32 running]
Running Test swm_rna_move_inside_helix_by_bond
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_rna_move_inside_helix_by_bond/command.sh
Finished mp_symmetry_load in 14 seconds [~ 561 test (68.75%) started, 255 in queue, 32 running]
Running Test surface_docking
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/surface_docking/command.sh
Finished mf_fixbb_sc in 14 seconds [~ 562 test (68.87254901960785%) started, 254 in queue, 32 running]
Running Test rnp_ddg_relax_command_1
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rnp_ddg_relax_command_1/command.sh
Finished density_refine_symm in 15 seconds [~ 563 test (68.99509803921569%) started, 253 in queue, 32 running]
Running Test rna_puzzle6_j67_into_p6p7rigidbody_thread1
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_puzzle6_j67_into_p6p7rigidbody_thread1/command.sh
Finished genkic_dihedral_copying in 15 seconds [~ 564 test (69.11764705882354%) started, 252 in queue, 32 running]
Finished symmetrical_residue_selector in 13 seconds [~ 564 test (69.11764705882354%) started, 252 in queue, 31 running]
Finished swa_rna_gagu_18_rebuild_bulge in 13 seconds [~ 564 test (69.11764705882354%) started, 252 in queue, 30 running]
Running Test rna_denovo
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo/command.sh
Running Test helix_from_sequence
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/helix_from_sequence/command.sh
Running Test helical_bundle
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/helical_bundle/command.sh
Finished mp_dock in 13 seconds [~ 567 test (69.48529411764706%) started, 249 in queue, 32 running]
Running Test genkic_bin_sampling
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/genkic_bin_sampling/command.sh
Finished design_w_custom_palette-RNA in 15 seconds [~ 568 test (69.6078431372549%) started, 248 in queue, 32 running]
Finished buried_area_filter in 15 seconds [~ 568 test (69.6078431372549%) started, 248 in queue, 31 running]
Finished swm_build_full_model in 14 seconds [~ 568 test (69.6078431372549%) started, 248 in queue, 30 running]
Finished swa_rna_gagu_11_append_and_ccd_close in 13 seconds [~ 568 test (69.6078431372549%) started, 248 in queue, 29 running]
Running Test zinc_homodimer_setup
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/zinc_homodimer_setup/command.sh
Running Test target_clash
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/target_clash/command.sh
Running Test swa_rna_gagu_12_helix_addition
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_12_helix_addition/command.sh
Finished set_torsion in 13 seconds [~ 572 test (70.09803921568627%) started, 244 in queue, 32 running]
Running Test simple_cycpep_predict_terminal_disulfide_tails
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_terminal_disulfide_tails/command.sh
Running Test simple_cycpep_predict_symmetric_sampling
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_symmetric_sampling/command.sh
Finished dehydro_aa_patch in 15 seconds [~ 573 test (70.22058823529412%) started, 243 in queue, 32 running]
Finished referencepose_mutateresidue in 14 seconds [~ 573 test (70.22058823529412%) started, 243 in queue, 31 running]
Finished pocket_measure in 13 seconds [~ 573 test (70.22058823529412%) started, 243 in queue, 30 running]
Finished metal_setup in 13 seconds [~ 573 test (70.22058823529412%) started, 243 in queue, 29 running]
Running Test simple_cycpep_predict_nterm_isopeptide_lariat_tailless
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_nterm_isopeptide_lariat_tailless/command.sh
Running Test simple_cycpep_predict_nterm_isopeptide_lariat
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_nterm_isopeptide_lariat/command.sh
Running Test rna_denovo_new_FT_5P_j12_leadzyme
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_new_FT_5P_j12_leadzyme/command.sh
Running Test recces_turner
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/recces_turner/command.sh
Finished phiselector in 14 seconds [~ 577 test (70.71078431372548%) started, 239 in queue, 32 running]
Running Test mp_mutate_relax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_mutate_relax/command.sh
Finished hbondstoresidue_selector in 13 seconds [~ 578 test (70.83333333333333%) started, 238 in queue, 32 running]
Running Test mmtfIO_score_test
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mmtfIO_score_test/command.sh
Finished make_and_perturb_bundle_multirepeat in 14 seconds [~ 579 test (70.95588235294117%) started, 237 in queue, 32 running]
Finished longest_continuous_polar_segment_filter in 14 seconds [~ 579 test (70.95588235294117%) started, 237 in queue, 31 running]
Finished genkic_bin_setting in 13 seconds [~ 579 test (70.95588235294117%) started, 237 in queue, 30 running]
Running Test database_jd2_io
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/database_jd2_io/command.sh
Running Test database_jd2_compact_io
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/database_jd2_compact_io/command.sh
Running Test abinitio
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/abinitio/command.sh
Finished ambiguous_nmr_distance_constraint in 15 seconds [~ 582 test (71.32352941176471%) started, 234 in queue, 32 running]
Finished create_clash-based_repack_shell in 14 seconds [~ 582 test (71.32352941176471%) started, 234 in queue, 31 running]
Running Test swm_rna_nickedhelix
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_rna_nickedhelix/command.sh
Running Test simple_cycpep_predict_sidechain_isopeptide_reverse
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_sidechain_isopeptide_reverse/command.sh
Finished SSElementSelector in 15 seconds [~ 584 test (71.56862745098039%) started, 232 in queue, 32 running]
Running Test score_jd2
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/score_jd2/command.sh
Finished swm_add_rosettascripts in 17 seconds [~ 585 test (71.69117647058823%) started, 231 in queue, 32 running]
Running Test mp_range_relax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_range_relax/command.sh
Finished copy_rotamer_mover in 13 seconds [~ 586 test (71.81372549019608%) started, 230 in queue, 32 running]
Running Test molfile_to_params
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/molfile_to_params/command.sh
Finished binselector_probins in 14 seconds [~ 587 test (71.93627450980392%) started, 229 in queue, 32 running]
Running Test hshash_utils
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hshash_utils/command.sh
Finished binselector in 14 seconds [~ 588 test (72.05882352941177%) started, 228 in queue, 32 running]
Finished backbonegridsampler in 13 seconds [~ 588 test (72.05882352941177%) started, 228 in queue, 31 running]
Running Test glycosylation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/glycosylation/command.sh
Running Test InterfaceAnalyzer_resfile
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/InterfaceAnalyzer_resfile/command.sh
Finished ModifyVariantTypeMover in 13 seconds [~ 590 test (72.30392156862744%) started, 226 in queue, 32 running]
Running Test InterfaceAnalyzer_bothpack
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/InterfaceAnalyzer_bothpack/command.sh
Finished swm_rna_move_inside_helix_by_bond in 12 seconds [~ 591 test (72.42647058823529%) started, 225 in queue, 32 running]
Running Test unfolded_state_energy_calc
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/unfolded_state_energy_calc/command.sh
Finished simple_cycpep_predict_terminal_disulfide_tails in 8 seconds [~ 592 test (72.54901960784314%) started, 224 in queue, 32 running]
Running Test stepwise_lores
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/stepwise_lores/command.sh
Finished rnp_ddg_relax_command_1 in 10 seconds [~ 593 test (72.67156862745098%) started, 223 in queue, 32 running]
Running Test simple_cycpep_predict_cterm_isopeptide_lariat_tailless
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_cterm_isopeptide_lariat_tailless/command.sh
Finished tna_base_pairs in 15 seconds [~ 594 test (72.79411764705883%) started, 222 in queue, 32 running]
Finished surface_docking in 12 seconds [~ 594 test (72.79411764705883%) started, 222 in queue, 31 running]
Running Test rna_predict_chem_map
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_predict_chem_map/command.sh
Running Test rb_recces
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rb_recces/command.sh
Finished rna_puzzle6_j67_into_p6p7rigidbody_thread1 in 12 seconds [~ 596 test (73.03921568627452%) started, 220 in queue, 32 running]
Finished zinc_homodimer_setup in 11 seconds [~ 596 test (73.03921568627452%) started, 220 in queue, 31 running]
Finished rna_denovo_new_FT_5P_j12_leadzyme in 11 seconds [~ 596 test (73.03921568627452%) started, 220 in queue, 30 running]
Running Test mpi_multistate_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mpi_multistate_design/command.sh
Running Test mp_mutate_repack
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_mutate_repack/command.sh
Running Test gen_apo_grids
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/gen_apo_grids/command.sh
Finished helix_from_sequence in 12 seconds [~ 599 test (73.40686274509804%) started, 217 in queue, 32 running]
Running Test fold_and_dock
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fold_and_dock/command.sh
Finished rna_denovo in 12 seconds [~ 600 test (73.52941176470588%) started, 216 in queue, 32 running]
Finished simple_cycpep_predict_nterm_isopeptide_lariat in 12 seconds [~ 600 test (73.52941176470588%) started, 216 in queue, 31 running]
Finished mp_mutate_relax in 11 seconds [~ 600 test (73.52941176470588%) started, 216 in queue, 30 running]
Finished simple_cycpep_predict_sidechain_isopeptide_reverse in 11 seconds [~ 600 test (73.52941176470588%) started, 216 in queue, 29 running]
Running Test energy_based_clustering_alpha_aa_scorefile
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/energy_based_clustering_alpha_aa_scorefile/command.sh
Running Test docking_prepack
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/docking_prepack/command.sh
Running Test broker_membrane
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/broker_membrane/command.sh
Running Test blob_finder
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/blob_finder/command.sh
Finished swa_rna_gagu_12_helix_addition in 12 seconds [~ 604 test (74.01960784313725%) started, 212 in queue, 32 running]
Running Test trRosetta_test_predict_ubiquitin_cst_file_write_only
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/trRosetta_test_predict_ubiquitin_cst_file_write_only/command.sh
Finished simple_cycpep_predict_nterm_isopeptide_lariat_tailless in 12 seconds [~ 605 test (74.1421568627451%) started, 211 in queue, 32 running]
Finished recces_turner in 12 seconds [~ 605 test (74.1421568627451%) started, 211 in queue, 31 running]
Finished abinitio in 11 seconds [~ 605 test (74.1421568627451%) started, 211 in queue, 30 running]
Running Test trRosetta_test_predict_ubiquitin_cst_file_write
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/trRosetta_test_predict_ubiquitin_cst_file_write/command.sh
No correct command.sh file found for tensorflow_manager. Skipping.
Running Test trRosetta_test_predict_ubiquitin
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/trRosetta_test_predict_ubiquitin/command.sh
Running Test swm_rna_loop_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_rna_loop_design/command.sh
Finished helical_bundle in 13 seconds [~ 609 test (74.63235294117646%) started, 207 in queue, 32 running]
Finished simple_cycpep_predict_symmetric_sampling in 13 seconds [~ 609 test (74.63235294117646%) started, 207 in queue, 31 running]
Finished mmtfIO_score_test in 12 seconds [~ 609 test (74.63235294117646%) started, 207 in queue, 30 running]
Finished score_jd2 in 11 seconds [~ 609 test (74.63235294117646%) started, 207 in queue, 29 running]
Running Test swm_protein_from_scratch
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_protein_from_scratch/command.sh
Running Test simple_cycpep_predict_cterm_isopeptide_lariat
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_cterm_isopeptide_lariat/command.sh
Running Test rna_puzzle6_U75G76A77_on_thread1
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_puzzle6_U75G76A77_on_thread1/command.sh
Running Test mp_transform_optimize
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_transform_optimize/command.sh
Finished database_jd2_io in 12 seconds [~ 613 test (75.12254901960785%) started, 203 in queue, 32 running]
Finished database_jd2_compact_io in 12 seconds [~ 613 test (75.12254901960785%) started, 203 in queue, 31 running]
Running Test assemble_domains_jd2
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/assemble_domains_jd2/command.sh
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 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/InterfaceAnalyzer_prepack/command.sh
Finished genkic_bin_sampling in 13 seconds [~ 617 test (75.61274509803921%) started, 199 in queue, 32 running]
Finished swm_rna_nickedhelix in 12 seconds [~ 617 test (75.61274509803921%) started, 199 in queue, 31 running]
Finished glycosylation in 7 seconds [~ 617 test (75.61274509803921%) started, 199 in queue, 30 running]
Running Test swa_rna_gagu_17_append_floating_base
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_17_append_floating_base/command.sh
Running Test swa_rna_gagu_03_append_to_silent
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_03_append_to_silent/command.sh
Running Test simple_cycpep_predict_nmethyl
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_nmethyl/command.sh
Finished mp_range_relax in 11 seconds [~ 620 test (75.98039215686275%) started, 196 in queue, 32 running]
Running Test rna_motif
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_motif/command.sh
Finished target_clash in 15 seconds [~ 621 test (76.1029411764706%) started, 195 in queue, 32 running]
Running Test restype_converter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/restype_converter/command.sh
Finished hshash_utils in 11 seconds [~ 622 test (76.22549019607843%) started, 194 in queue, 32 running]
Running Test phosphorylation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/phosphorylation/command.sh
Finished InterfaceAnalyzer_resfile in 11 seconds [~ 623 test (76.34803921568627%) started, 193 in queue, 32 running]
Running Test pepspec_anchor_dock
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pepspec_anchor_dock/command.sh
Finished InterfaceAnalyzer_bothpack in 11 seconds [~ 624 test (76.47058823529412%) started, 192 in queue, 32 running]
Running Test mp_dock_setup
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_dock_setup/command.sh
Finished unfolded_state_energy_calc in 10 seconds [~ 625 test (76.59313725490196%) started, 191 in queue, 32 running]
Running Test ligand_motif_discovery
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ligand_motif_discovery/command.sh
Finished molfile_to_params in 14 seconds [~ 626 test (76.7156862745098%) started, 190 in queue, 32 running]
Finished stepwise_lores in 10 seconds [~ 626 test (76.7156862745098%) started, 190 in queue, 31 running]
Running Test docking_low_res
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/docking_low_res/command.sh
Running Test InterfaceAnalyzer_tracer
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/InterfaceAnalyzer_tracer/command.sh
Finished simple_cycpep_predict_cterm_isopeptide_lariat_tailless in 10 seconds [~ 628 test (76.96078431372548%) started, 188 in queue, 32 running]
Running Test InterfaceAnalyzer_allscores
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/InterfaceAnalyzer_allscores/command.sh
Finished rna_predict_chem_map in 9 seconds [~ 629 test (77.08333333333333%) started, 187 in queue, 32 running]
Running Test swa_rna_gagu_21_prepend_dinucleotide_on_dinucleotide_by_jump
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_21_prepend_dinucleotide_on_dinucleotide_by_jump/command.sh
Finished rb_recces in 10 seconds [~ 630 test (77.20588235294117%) started, 186 in queue, 32 running]
Running Test swa_rna_gagu_20_append_floating_base_by_jump
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_20_append_floating_base_by_jump/command.sh
Finished energy_based_clustering_alpha_aa_scorefile in 8 seconds [~ 631 test (77.32843137254902%) started, 185 in queue, 32 running]
Running Test swa_rna_gagu_08_append_dinucleotide
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_08_append_dinucleotide/command.sh
Finished swm_rna_loop_design in 8 seconds [~ 632 test (77.45098039215686%) started, 184 in queue, 32 running]
Running Test swa_rna_gagu_07_prepend_dinucleotide
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_07_prepend_dinucleotide/command.sh
Finished blob_finder in 9 seconds [~ 633 test (77.57352941176471%) started, 183 in queue, 32 running]
Finished swa_rna_gagu_17_append_floating_base in 8 seconds [~ 633 test (77.57352941176471%) started, 183 in queue, 31 running]
Running Test swa_rna_gagu_06_append_to_3primeterminus
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_06_append_to_3primeterminus/command.sh
Running Test swa_rna_gagu_05_prepend_to_5primeterminus
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_05_prepend_to_5primeterminus/command.sh
Finished rna_puzzle6_U75G76A77_on_thread1 in 9 seconds [~ 635 test (77.81862745098039%) started, 181 in queue, 32 running]
Finished simple_cycpep_predict_nmethyl in 8 seconds [~ 635 test (77.81862745098039%) started, 181 in queue, 31 running]
Running Test swa_rna_gagu_02_prepend
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_02_prepend/command.sh
Running Test swa_rna_gagu_01_append
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_01_append/command.sh
Finished mp_mutate_repack in 10 seconds [~ 637 test (78.06372549019608%) started, 179 in queue, 32 running]
Finished swm_protein_from_scratch in 9 seconds [~ 637 test (78.06372549019608%) started, 179 in queue, 31 running]
Finished mp_transform_optimize in 9 seconds [~ 637 test (78.06372549019608%) started, 179 in queue, 30 running]
Running Test simple_cycpep_predict_terminal_disulfide
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_terminal_disulfide/command.sh
Running Test simple_cycpep_predict_lanthionine
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_cycpep_predict_lanthionine/command.sh
Running Test rna_puzzle5_p2_GAAA_mini
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_puzzle5_p2_GAAA_mini/command.sh
Finished mpi_multistate_design in 10 seconds [~ 640 test (78.43137254901961%) started, 176 in queue, 32 running]
Finished gen_apo_grids in 10 seconds [~ 640 test (78.43137254901961%) started, 176 in queue, 31 running]
Finished docking_prepack in 10 seconds [~ 640 test (78.43137254901961%) started, 176 in queue, 30 running]
Finished simple_cycpep_predict_cterm_isopeptide_lariat in 9 seconds [~ 640 test (78.43137254901961%) started, 176 in queue, 29 running]
Running Test rna_denovo_grid_vdw
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_grid_vdw/command.sh
Running Test orbitals
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/orbitals/command.sh
Running Test metalloprotein_broker
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/metalloprotein_broker/command.sh
Running Test jscore
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/jscore/command.sh
Finished assemble_domains_jd2 in 9 seconds [~ 644 test (78.92156862745098%) started, 172 in queue, 32 running]
Finished swa_rna_gagu_03_append_to_silent in 9 seconds [~ 644 test (78.92156862745098%) started, 172 in queue, 31 running]
Running Test hotspot_stub_constraints
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hotspot_stub_constraints/command.sh
Finished broker_membrane in 10 seconds [~ 646 test (79.16666666666667%) started, 170 in queue, 32 running]
Running Test cmaes_minimizer
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cmaes_minimizer/command.sh
Running Test SID_rescore
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/SID_rescore/command.sh
Finished fold_and_dock in 10 seconds [~ 647 test (79.28921568627452%) started, 169 in queue, 32 running]
Finished rna_motif in 8 seconds [~ 647 test (79.28921568627452%) started, 169 in queue, 31 running]
Running Test InterfaceAnalyzer_ligand
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/InterfaceAnalyzer_ligand/command.sh
Running Test swm_rna_move_align_dock
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_rna_move_align_dock/command.sh
Finished InterfaceAnalyzer_prepack in 10 seconds [~ 649 test (79.5343137254902%) started, 167 in queue, 32 running]
Finished restype_converter in 8 seconds [~ 649 test (79.5343137254902%) started, 167 in queue, 31 running]
Running Test swa_rna_gagu_19_prepend_floating_base_by_jump
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_19_prepend_floating_base_by_jump/command.sh
Running Test struc_set_fragment_picker
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/struc_set_fragment_picker/command.sh
Finished trRosetta_test_predict_ubiquitin_cst_file_write_only in 11 seconds [~ 651 test (79.77941176470588%) started, 165 in queue, 32 running]
Running Test sequence_tolerance
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/sequence_tolerance/command.sh
Finished trRosetta_test_predict_ubiquitin_cst_file_write in 11 seconds [~ 652 test (79.90196078431373%) started, 164 in queue, 32 running]
Finished trRosetta_test_predict_ubiquitin in 11 seconds [~ 652 test (79.90196078431373%) started, 164 in queue, 31 running]
Running Test rna_minimize
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_minimize/command.sh
Running Test rna_helix
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_helix/command.sh
Finished phosphorylation in 8 seconds [~ 654 test (80.1470588235294%) started, 162 in queue, 32 running]
Running Test phosphonate
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/phosphonate/command.sh
Finished pepspec_anchor_dock in 8 seconds [~ 655 test (80.26960784313725%) started, 161 in queue, 32 running]
Running Test output_schema
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/output_schema/command.sh
Finished ligand_motif_discovery in 8 seconds [~ 656 test (80.3921568627451%) started, 160 in queue, 32 running]
Running Test ligand_motif_identification
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ligand_motif_identification/command.sh
Finished mp_dock_setup in 9 seconds [~ 657 test (80.51470588235294%) started, 159 in queue, 32 running]
Running Test identify_cdr_clusters
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/identify_cdr_clusters/command.sh
Finished docking_low_res in 8 seconds [~ 658 test (80.63725490196079%) started, 158 in queue, 32 running]
Running Test energy_based_clustering_alpha_aa_dihedral
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/energy_based_clustering_alpha_aa_dihedral/command.sh
Finished InterfaceAnalyzer_tracer in 8 seconds [~ 659 test (80.75980392156863%) started, 157 in queue, 32 running]
Running Test duplicate_header_guards
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/duplicate_header_guards/command.sh
Finished swa_rna_gagu_21_prepend_dinucleotide_on_dinucleotide_by_jump in 8 seconds [~ 660 test (80.88235294117646%) started, 156 in queue, 32 running]
Running Test cartesianddg
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cartesianddg/command.sh
Finished InterfaceAnalyzer_allscores in 8 seconds [~ 661 test (81.00490196078431%) started, 155 in queue, 32 running]
Finished swa_rna_gagu_20_append_floating_base_by_jump in 7 seconds [~ 661 test (81.00490196078431%) started, 155 in queue, 31 running]
Running Test antibody_numbering_converter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/antibody_numbering_converter/command.sh
Running Test ProQ
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ProQ/command.sh
Finished swa_rna_gagu_08_append_dinucleotide in 8 seconds [~ 663 test (81.25%) started, 153 in queue, 32 running]
Running Test swm_protein_preminimize
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_protein_preminimize/command.sh
Finished swa_rna_gagu_07_prepend_dinucleotide in 8 seconds [~ 664 test (81.37254901960785%) started, 152 in queue, 32 running]
Running Test swa_protein_cluster
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_protein_cluster/command.sh
Finished swa_rna_gagu_05_prepend_to_5primeterminus in 8 seconds [~ 665 test (81.49509803921569%) started, 151 in queue, 32 running]
Running Test rna_ribosome_tether
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_ribosome_tether/command.sh
Finished swa_rna_gagu_06_append_to_3primeterminus in 8 seconds [~ 666 test (81.61764705882354%) started, 150 in queue, 32 running]
Finished swa_rna_gagu_02_prepend in 8 seconds [~ 666 test (81.61764705882354%) started, 150 in queue, 31 running]
Running Test rna_denovo_bps
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_bps/command.sh
Running Test pymol_cif
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pymol_cif/command.sh
Finished swa_rna_gagu_01_append in 8 seconds [~ 668 test (81.86274509803921%) started, 148 in queue, 32 running]
Finished simple_cycpep_predict_terminal_disulfide in 8 seconds [~ 668 test (81.86274509803921%) started, 148 in queue, 31 running]
Finished swm_rna_move_align_dock in 7 seconds [~ 668 test (81.86274509803921%) started, 148 in queue, 30 running]
Running Test pwsho
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pwsho/command.sh
Running Test per_residue_energies
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/per_residue_energies/command.sh
Running Test mutate
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mutate/command.sh
Finished rna_puzzle5_p2_GAAA_mini in 8 seconds [~ 671 test (82.23039215686275%) started, 145 in queue, 32 running]
Finished struc_set_fragment_picker in 7 seconds [~ 671 test (82.23039215686275%) started, 145 in queue, 31 running]
Running Test mp_vis_emb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_vis_emb/command.sh
Running Test mp_interface_statistics
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_interface_statistics/command.sh
Finished rna_denovo_grid_vdw in 8 seconds [~ 673 test (82.47549019607843%) started, 143 in queue, 32 running]
Finished orbitals in 8 seconds [~ 673 test (82.47549019607843%) started, 143 in queue, 31 running]
Finished hotspot_stub_constraints in 8 seconds [~ 673 test (82.47549019607843%) started, 143 in queue, 30 running]
Running Test mg_modeler
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mg_modeler/command.sh
Running Test jrelax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/jrelax/command.sh
Running Test interface_energy
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/interface_energy/command.sh
Finished metalloprotein_broker in 8 seconds [~ 676 test (82.84313725490196%) started, 140 in queue, 32 running]
Finished jscore in 8 seconds [~ 676 test (82.84313725490196%) started, 140 in queue, 31 running]
Running Test ig_dump
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ig_dump/command.sh
Running Test glycan_clash_check
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/glycan_clash_check/command.sh
Finished simple_cycpep_predict_lanthionine in 8 seconds [~ 678 test (83.08823529411765%) started, 138 in queue, 32 running]
Finished cmaes_minimizer in 8 seconds [~ 678 test (83.08823529411765%) started, 138 in queue, 31 running]
Finished SID_rescore in 8 seconds [~ 678 test (83.08823529411765%) started, 138 in queue, 30 running]
Running Test geometric_solvation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/geometric_solvation/command.sh
Running Test gen_lig_grids
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/gen_lig_grids/command.sh
Running Test fragmentpicker_integration_demo
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fragmentpicker_integration_demo/command.sh
Finished InterfaceAnalyzer_ligand in 8 seconds [~ 681 test (83.45588235294117%) started, 135 in queue, 32 running]
Finished swa_rna_gagu_19_prepend_floating_base_by_jump in 8 seconds [~ 681 test (83.45588235294117%) started, 135 in queue, 31 running]
Finished sequence_tolerance in 7 seconds [~ 681 test (83.45588235294117%) started, 135 in queue, 30 running]
Finished rna_helix in 7 seconds [~ 681 test (83.45588235294117%) started, 135 in queue, 29 running]
Running Test extract_atomtree_diffs
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/extract_atomtree_diffs/command.sh
Running Test erraser_minimize
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/erraser_minimize/command.sh
Running Test energy_based_clustering_alpha_aa_bin_analysis
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/energy_based_clustering_alpha_aa_bin_analysis/command.sh
Running Test energy_based_clustering_alpha_aa
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/energy_based_clustering_alpha_aa/command.sh
Finished rna_minimize in 7 seconds [~ 685 test (83.94607843137256%) started, 131 in queue, 32 running]
Running Test docking_local_refine_min
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/docking_local_refine_min/command.sh
Finished phosphonate in 7 seconds [~ 686 test (84.06862745098039%) started, 130 in queue, 32 running]
Running Test distances
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/distances/command.sh
Finished output_schema in 7 seconds [~ 687 test (84.19117647058823%) started, 129 in queue, 32 running]
Running Test density_tools
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/density_tools/command.sh
Finished ligand_motif_identification in 7 seconds [~ 688 test (84.31372549019608%) started, 128 in queue, 32 running]
Running Test constel
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/constel/command.sh
Finished identify_cdr_clusters in 7 seconds [~ 689 test (84.43627450980392%) started, 127 in queue, 32 running]
Running Test coenzymes
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/coenzymes/command.sh
Finished energy_based_clustering_alpha_aa_dihedral in 7 seconds [~ 690 test (84.55882352941177%) started, 126 in queue, 32 running]
Running Test cl_complex_rescore
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cl_complex_rescore/command.sh
Finished swm_protein_preminimize in 6 seconds [~ 691 test (84.68137254901961%) started, 125 in queue, 32 running]
Running Test c-term_conjugation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/c-term_conjugation/command.sh
Finished cartesianddg in 7 seconds [~ 692 test (84.80392156862744%) started, 124 in queue, 32 running]
Running Test DARC_sampling_on_the_fly
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/DARC_sampling_on_the_fly/command.sh
Finished rna_ribosome_tether in 6 seconds [~ 693 test (84.92647058823529%) started, 123 in queue, 32 running]
Finished pymol_cif in 6 seconds [~ 693 test (84.92647058823529%) started, 123 in queue, 31 running]
Finished mutate in 5 seconds [~ 693 test (84.92647058823529%) started, 123 in queue, 30 running]
Running Test DARC_make_ray_files
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/DARC_make_ray_files/command.sh
Running Test swm_rna_move_two_strands
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_rna_move_two_strands/command.sh
Running Test sweep_respair_energies
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/sweep_respair_energies/command.sh
Finished ProQ in 7 seconds [~ 696 test (85.29411764705883%) started, 120 in queue, 32 running]
Finished swa_protein_cluster in 6 seconds [~ 696 test (85.29411764705883%) started, 120 in queue, 31 running]
Running Test swa_rna_loop_sampler
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_loop_sampler/command.sh
Running Test site_constraint
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/site_constraint/command.sh
Finished antibody_numbering_converter in 7 seconds [~ 698 test (85.53921568627452%) started, 118 in queue, 32 running]
Finished pwsho in 6 seconds [~ 698 test (85.53921568627452%) started, 118 in queue, 31 running]
Running Test shobuns
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/shobuns/command.sh
Finished duplicate_header_guards in 8 seconds [~ 700 test (85.7843137254902%) started, 116 in queue, 32 running]
Running Test rotamer_recovery_compare_two_structures
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rotamer_recovery_compare_two_structures/command.sh
Running Test rna_score
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_score/command.sh
Finished rna_denovo_bps in 6 seconds [~ 701 test (85.90686274509804%) started, 115 in queue, 32 running]
Finished per_residue_energies in 6 seconds [~ 701 test (85.90686274509804%) started, 115 in queue, 31 running]
Finished mp_vis_emb in 6 seconds [~ 701 test (85.90686274509804%) started, 115 in queue, 30 running]
Running Test rna_denovo_bps_helix_ends
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_bps_helix_ends/command.sh
Running Test rna_denovo_bps_fixed_ends
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_bps_fixed_ends/command.sh
Finished mp_interface_statistics in 6 seconds [~ 704 test (86.27450980392157%) started, 112 in queue, 32 running]
Running Test read_polymeric_components
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/read_polymeric_components/command.sh
Running Test pocket_suggest_targets
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pocket_suggest_targets/command.sh
Finished mg_modeler in 6 seconds [~ 705 test (86.3970588235294%) started, 111 in queue, 32 running]
Finished jrelax in 6 seconds [~ 705 test (86.3970588235294%) started, 111 in queue, 31 running]
Finished interface_energy in 6 seconds [~ 705 test (86.3970588235294%) started, 111 in queue, 30 running]
Finished geometric_solvation in 5 seconds [~ 705 test (86.3970588235294%) started, 111 in queue, 29 running]
Running Test noe_assignment
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/noe_assignment/command.sh
Running Test mp_transform
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_transform/command.sh
Running Test mp_score_jd2
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_score_jd2/command.sh
Running Test mp_dock_prepack
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_dock_prepack/command.sh
Finished glycan_clash_check in 6 seconds [~ 709 test (86.88725490196079%) started, 107 in queue, 32 running]
Finished fragmentpicker_integration_demo in 6 seconds [~ 709 test (86.88725490196079%) started, 107 in queue, 31 running]
Running Test measure_lcaa_radii
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/measure_lcaa_radii/command.sh
Running Test fragment_picker
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fragment_picker/command.sh
Finished ig_dump in 6 seconds [~ 711 test (87.13235294117646%) started, 105 in queue, 32 running]
Finished gen_lig_grids in 6 seconds [~ 711 test (87.13235294117646%) started, 105 in queue, 31 running]
Running Test fix_alignment_to_match_pdb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fix_alignment_to_match_pdb/command.sh
Running Test cs_rosetta_rna
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cs_rosetta_rna/command.sh
egrep: full_minimize_temp_1.out: No such file or directory
Finished extract_atomtree_diffs in 6 seconds [~ 713 test (87.37745098039215%) started, 103 in queue, 32 running]
Running Test cluster
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cluster/command.sh
Finished erraser_minimize in 6 seconds [~ 714 test (87.5%) started, 102 in queue, 32 running]
Running Test buried_unsat_kinemage
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/buried_unsat_kinemage/command.sh
Finished docking_local_refine_min in 6 seconds [~ 715 test (87.62254901960785%) started, 101 in queue, 32 running]
Running Test trRosettaProtocolMover_rosettascripts_diskwrite_only
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/trRosettaProtocolMover_rosettascripts_diskwrite_only/command.sh
Finished energy_based_clustering_alpha_aa_bin_analysis in 7 seconds [~ 716 test (87.74509803921569%) started, 100 in queue, 32 running]
Finished energy_based_clustering_alpha_aa in 7 seconds [~ 716 test (87.74509803921569%) started, 100 in queue, 31 running]
Running Test trRosettaProtocolMover_rosettascripts_diskwrite
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/trRosettaProtocolMover_rosettascripts_diskwrite/command.sh
Running Test trRosettaProtocolMover_rosettascripts
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/trRosettaProtocolMover_rosettascripts/command.sh
Finished distances in 6 seconds [~ 718 test (87.99019607843137%) started, 98 in queue, 32 running]
Running Test rna_denovo_new_FT_rna_two_chains
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_new_FT_rna_two_chains/command.sh
Finished density_tools in 7 seconds [~ 719 test (88.11274509803921%) started, 97 in queue, 32 running]
Finished constel in 6 seconds [~ 719 test (88.11274509803921%) started, 97 in queue, 31 running]
Running Test pH_mode
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pH_mode/command.sh
Running Test mpil_find_pore_bbarrel
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mpil_find_pore_bbarrel/command.sh
Finished coenzymes in 6 seconds [~ 721 test (88.3578431372549%) started, 95 in queue, 32 running]
Finished swm_rna_move_two_strands in 5 seconds [~ 721 test (88.3578431372549%) started, 95 in queue, 31 running]
Running Test mp_loadtime
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_loadtime/command.sh
Running Test mg_modeler_lores
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mg_modeler_lores/command.sh
Finished cl_complex_rescore in 6 seconds [~ 723 test (88.6029411764706%) started, 93 in queue, 32 running]
Finished c-term_conjugation in 6 seconds [~ 723 test (88.6029411764706%) started, 93 in queue, 31 running]
Running Test match_1c2t
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/match_1c2t/command.sh
Running Test make_mainchain_potential_symm_preproline
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/make_mainchain_potential_symm_preproline/command.sh
Finished sweep_respair_energies in 6 seconds [~ 725 test (88.84803921568627%) started, 91 in queue, 32 running]
Finished site_constraint in 5 seconds [~ 725 test (88.84803921568627%) started, 91 in queue, 31 running]
Finished read_polymeric_components in 5 seconds [~ 725 test (88.84803921568627%) started, 91 in queue, 30 running]
Running Test make_mainchain_potential_symm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/make_mainchain_potential_symm/command.sh
Running Test make_exemplar
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/make_exemplar/command.sh
Running Test features_database_schema
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/features_database_schema/command.sh
Finished shobuns in 5 seconds [~ 728 test (89.2156862745098%) started, 88 in queue, 32 running]
Finished rna_score in 5 seconds [~ 728 test (89.2156862745098%) started, 88 in queue, 31 running]
Running Test drrafter_setup_ribosome_test
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/drrafter_setup_ribosome_test/command.sh
Running Test drrafter_setup_real_test_H_no_init
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/drrafter_setup_real_test_H_no_init/command.sh
Finished DARC_sampling_on_the_fly in 6 seconds [~ 730 test (89.46078431372548%) started, 86 in queue, 32 running]
Finished swa_rna_loop_sampler in 6 seconds [~ 730 test (89.46078431372548%) started, 86 in queue, 31 running]
Finished mp_transform in 5 seconds [~ 730 test (89.46078431372548%) started, 86 in queue, 30 running]
Running Test drrafter_setup_real_test_H
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/drrafter_setup_real_test_H/command.sh
Running Test contactMap
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/contactMap/command.sh
Running Test cluster_filter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cluster_filter/command.sh
Finished rotamer_recovery_compare_two_structures in 6 seconds [~ 733 test (89.82843137254902%) started, 83 in queue, 32 running]
Finished rna_denovo_bps_helix_ends in 6 seconds [~ 733 test (89.82843137254902%) started, 83 in queue, 31 running]
Finished rna_denovo_bps_fixed_ends in 6 seconds [~ 733 test (89.82843137254902%) started, 83 in queue, 30 running]
Running Test ResidueDisorder
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ResidueDisorder/command.sh
Running Test RescorePDDF
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/RescorePDDF/command.sh
Running Test template_features
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/template_features/command.sh
Finished DARC_make_ray_files in 6 seconds [~ 736 test (90.19607843137256%) started, 80 in queue, 32 running]
Finished pocket_suggest_targets in 6 seconds [~ 736 test (90.19607843137256%) started, 80 in queue, 31 running]
Finished noe_assignment in 6 seconds [~ 736 test (90.19607843137256%) started, 80 in queue, 30 running]
Finished mp_dock_prepack in 6 seconds [~ 736 test (90.19607843137256%) started, 80 in queue, 29 running]
Running Test super_aln
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/super_aln/command.sh
Running Test silent2frag
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/silent2frag/command.sh
Running Test rna_screen_phosphates
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_screen_phosphates/command.sh
Running Test rings
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rings/command.sh
Finished mp_score_jd2 in 6 seconds [~ 740 test (90.68627450980392%) started, 76 in queue, 32 running]
Finished fragment_picker in 6 seconds [~ 740 test (90.68627450980392%) started, 76 in queue, 31 running]
Running Test nucleobase_sample_around
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/nucleobase_sample_around/command.sh
Running Test non-canonical_connectivities
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/non-canonical_connectivities/command.sh
Finished measure_lcaa_radii in 6 seconds [~ 742 test (90.93137254901961%) started, 74 in queue, 32 running]
Finished fix_alignment_to_match_pdb in 6 seconds [~ 742 test (90.93137254901961%) started, 74 in queue, 31 running]
Finished cs_rosetta_rna in 6 seconds [~ 742 test (90.93137254901961%) started, 74 in queue, 30 running]
Finished trRosettaProtocolMover_rosettascripts_diskwrite_only in 5 seconds [~ 742 test (90.93137254901961%) started, 74 in queue, 29 running]
Running Test motif_extraction
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/motif_extraction/command.sh
Running Test ld_converter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ld_converter/command.sh
Running Test code_template_tests_citations
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/code_template_tests_citations/command.sh
Running Test centroid_disulfide_scores
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/centroid_disulfide_scores/command.sh
Finished cluster in 6 seconds [~ 746 test (91.42156862745098%) started, 70 in queue, 32 running]
Finished trRosettaProtocolMover_rosettascripts_diskwrite in 5 seconds [~ 746 test (91.42156862745098%) started, 70 in queue, 31 running]
Finished trRosettaProtocolMover_rosettascripts in 5 seconds [~ 746 test (91.42156862745098%) started, 70 in queue, 30 running]
Running Test test_idealize
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/test_idealize/command.sh
Running Test test_d_l_readin
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/test_d_l_readin/command.sh
Running Test select_best_unique_ligand_poses
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/select_best_unique_ligand_poses/command.sh
Finished buried_unsat_kinemage in 6 seconds [~ 749 test (91.78921568627452%) started, 67 in queue, 32 running]
Running Test rosetta_scripts_info
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rosetta_scripts_info/command.sh
Finished rna_denovo_new_FT_rna_two_chains in 5 seconds [~ 750 test (91.91176470588235%) started, 66 in queue, 32 running]
Running Test rna_minimize_6D_loop_close
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_minimize_6D_loop_close/command.sh
Finished mpil_find_pore_bbarrel in 4 seconds [~ 751 test (92.0343137254902%) started, 65 in queue, 32 running]
Running Test r_pdb2top
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/r_pdb2top/command.sh
Finished pH_mode in 4 seconds [~ 752 test (92.15686274509804%) started, 64 in queue, 32 running]
Running Test per_residue_sc_sasa
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/per_residue_sc_sasa/command.sh
Finished template_features in 3 seconds [~ 753 test (92.27941176470588%) started, 63 in queue, 32 running]
Running Test oop_create
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/oop_create/command.sh
Finished super_aln in 3 seconds [~ 754 test (92.40196078431373%) started, 62 in queue, 32 running]
Finished test_d_l_readin in 2 seconds [~ 754 test (92.40196078431373%) started, 62 in queue, 31 running]
Running Test mpil_load_implicit_lipids
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mpil_load_implicit_lipids/command.sh
Running Test mpil_find_pore_ahelical
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mpil_find_pore_ahelical/command.sh
Finished mp_loadtime in 5 seconds [~ 756 test (92.6470588235294%) started, 60 in queue, 32 running]
Finished mg_modeler_lores in 5 seconds [~ 756 test (92.6470588235294%) started, 60 in queue, 31 running]
Finished make_mainchain_potential_symm_preproline in 5 seconds [~ 756 test (92.6470588235294%) started, 60 in queue, 30 running]
Finished silent2frag in 3 seconds [~ 756 test (92.6470588235294%) started, 60 in queue, 29 running]
Finished rings in 3 seconds [~ 756 test (92.6470588235294%) started, 60 in queue, 28 running]
Running Test minimize_6Dloopclose
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/minimize_6Dloopclose/command.sh
Running Test fit_helixparams_rms
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fit_helixparams_rms/command.sh
Running Test drrafter_error_estimation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/drrafter_error_estimation/command.sh
Running Test cstfile_to_theozyme_pdb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cstfile_to_theozyme_pdb/command.sh
Running Test code_template_tests_src
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/code_template_tests_src/command.sh
Finished make_mainchain_potential_symm in 5 seconds [~ 761 test (93.25980392156863%) started, 55 in queue, 32 running]
Finished rna_screen_phosphates in 4 seconds [~ 761 test (93.25980392156863%) started, 55 in queue, 31 running]
Running Test angle_recovery_stats
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/angle_recovery_stats/command.sh
Running Test N-terminal_acetylation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/N-terminal_acetylation/command.sh
Finished match_1c2t in 5 seconds [~ 763 test (93.50490196078431%) started, 53 in queue, 32 running]
Finished contactMap in 4 seconds [~ 763 test (93.50490196078431%) started, 53 in queue, 31 running]
Finished ResidueDisorder in 4 seconds [~ 763 test (93.50490196078431%) started, 53 in queue, 30 running]
Finished nucleobase_sample_around in 4 seconds [~ 763 test (93.50490196078431%) started, 53 in queue, 29 running]
Finished test_idealize in 3 seconds [~ 763 test (93.50490196078431%) started, 53 in queue, 28 running]
Running Test DNA_methylation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/DNA_methylation/command.sh
Running Test DARC_shapeonly
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/DARC_shapeonly/command.sh
Running Test DARC_electrostatics
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/DARC_electrostatics/command.sh
Running Test CCS_PARCS
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/CCS_PARCS/command.sh
Running Test CCD_loop_closure
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/CCD_loop_closure/command.sh
Finished drrafter_setup_real_test_H_no_init in 5 seconds [~ 768 test (94.11764705882354%) started, 48 in queue, 32 running]
Finished RescorePDDF in 4 seconds [~ 768 test (94.11764705882354%) started, 48 in queue, 31 running]
Finished ld_converter in 3 seconds [~ 768 test (94.11764705882354%) started, 48 in queue, 30 running]
Finished select_best_unique_ligand_poses in 3 seconds [~ 768 test (94.11764705882354%) started, 48 in queue, 29 running]
Running Test swa_rna_loop_clusterer
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_loop_clusterer/command.sh
Running Test swa_rna_gagu_14_combine_long_loop_filtering
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_14_combine_long_loop_filtering/command.sh
Running Test swa_rna_gagu_04_clustering
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swa_rna_gagu_04_clustering/command.sh
Running Test rna_suitename
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_suitename/command.sh
Finished drrafter_setup_ribosome_test in 5 seconds [~ 772 test (94.6078431372549%) started, 44 in queue, 32 running]
Finished drrafter_setup_real_test_H in 5 seconds [~ 772 test (94.6078431372549%) started, 44 in queue, 31 running]
Finished motif_extraction in 4 seconds [~ 772 test (94.6078431372549%) started, 44 in queue, 30 running]
Finished centroid_disulfide_scores in 4 seconds [~ 772 test (94.6078431372549%) started, 44 in queue, 29 running]
Running Test rna_cluster
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_cluster/command.sh
Running Test rna_add_WC_stats
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_add_WC_stats/command.sh
Running Test report_hbonds_for_plugin
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/report_hbonds_for_plugin/command.sh
Running Test ralford_dump_rotamers
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ralford_dump_rotamers/command.sh
Finished cluster_filter in 5 seconds [~ 776 test (95.09803921568627%) started, 40 in queue, 32 running]
Finished rna_minimize_6D_loop_close in 3 seconds [~ 777 test (95.22058823529412%) started, 39 in queue, 32 running]
Running Test r_rmsf
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/r_rmsf/command.sh
Running Test number_of_residuetypes
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/number_of_residuetypes/command.sh
Finished features_database_schema in 6 seconds [~ 778 test (95.34313725490196%) started, 38 in queue, 32 running]
Finished r_pdb2top in 3 seconds [~ 778 test (95.34313725490196%) started, 38 in queue, 31 running]
Running Test loop_hash
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/loop_hash/command.sh
Running Test include_cc_check
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/include_cc_check/command.sh
Finished per_residue_sc_sasa in 3 seconds [~ 780 test (95.58823529411765%) started, 36 in queue, 32 running]
Running Test fit_helixparams_a3b
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fit_helixparams_a3b/command.sh
database/citations/rosetta_citations.txt -> database/citations/rosetta_citations.original.txt
First script ran successfully.
Second script ran successfully.
Output matches expectation.
Finished non-canonical_connectivities in 6 seconds [~ 781 test (95.71078431372548%) started, 35 in queue, 32 running]
Finished code_template_tests_citations in 6 seconds [~ 781 test (95.71078431372548%) started, 35 in queue, 31 running]
Finished rosetta_scripts_info in 5 seconds [~ 781 test (95.71078431372548%) started, 35 in queue, 30 running]
Running Test calculate_sasa
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/calculate_sasa/command.sh
Running Test test_energy_method_options
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/test_energy_method_options/command.sh
Running Test per_residue_solvent_exposure
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/per_residue_solvent_exposure/command.sh
Finished N-terminal_acetylation in 2 seconds [~ 784 test (96.07843137254902%) started, 32 in queue, 32 running]
Running Test mp_span_from_pdb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_span_from_pdb/command.sh
Finished make_exemplar in 7 seconds [~ 785 test (96.20098039215686%) started, 31 in queue, 32 running]
Finished mpil_load_implicit_lipids in 3 seconds [~ 785 test (96.20098039215686%) started, 31 in queue, 31 running]
Finished mpil_find_pore_ahelical in 3 seconds [~ 785 test (96.20098039215686%) started, 31 in queue, 30 running]
Running Test hierarchical_clustering
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hierarchical_clustering/command.sh
Running Test fit_helixparams
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fit_helixparams/command.sh
Running Test discontinuous_sewing_hasher
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/discontinuous_sewing_hasher/command.sh
Finished oop_create in 3 seconds [~ 788 test (96.56862745098039%) started, 28 in queue, 32 running]
Finished minimize_6Dloopclose in 3 seconds [~ 788 test (96.56862745098039%) started, 28 in queue, 31 running]
Finished drrafter_error_estimation in 3 seconds [~ 788 test (96.56862745098039%) started, 28 in queue, 30 running]
Finished CCS_PARCS in 2 seconds [~ 788 test (96.56862745098039%) started, 28 in queue, 29 running]
Running Test combine_silent
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/combine_silent/command.sh
No correct command.sh file found for basic_gcn_tensorflow_test. Skipping.
Running Test burial_measure_centroid
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/burial_measure_centroid/command.sh
Running Test BuildPeptide
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/BuildPeptide/command.sh
Running Test trRosettaConstraintGenerator_rosettascripts
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/trRosettaConstraintGenerator_rosettascripts/command.sh
Finished DARC_electrostatics in 3 seconds [~ 793 test (97.18137254901961%) started, 23 in queue, 32 running]
Finished swa_rna_loop_clusterer in 2 seconds [~ 793 test (97.18137254901961%) started, 23 in queue, 31 running]
Finished swa_rna_gagu_04_clustering in 2 seconds [~ 793 test (97.18137254901961%) started, 23 in queue, 30 running]
Finished rna_suitename in 2 seconds [~ 793 test (97.18137254901961%) started, 23 in queue, 29 running]
Finished rna_cluster in 2 seconds [~ 793 test (97.18137254901961%) started, 23 in queue, 28 running]
Running Test score_aln
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/score_aln/command.sh
Running Test header_using_check
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/header_using_check/command.sh
Running Test extract_pdbs
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/extract_pdbs/command.sh
Running Test crossaln
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crossaln/command.sh
Finished rna_add_WC_stats in 2 seconds [~ 798 test (97.79411764705883%) started, 18 in queue, 32 running]
Running Test continuous_sewing_hasher
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/continuous_sewing_hasher/command.sh
Running Test rnp_ddg_relax_setup
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rnp_ddg_relax_setup/command.sh
PYTHON IS /Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python_virtual_environments/python-3.9/70fb5a411fc5470c895f6d4975b66fbe/bin/python
Finished cstfile_to_theozyme_pdb in 3 seconds [~ 799 test (97.91666666666667%) started, 17 in queue, 32 running]
Finished DARC_shapeonly in 3 seconds [~ 799 test (97.91666666666667%) started, 17 in queue, 31 running]
Finished swa_rna_gagu_14_combine_long_loop_filtering in 3 seconds [~ 799 test (97.91666666666667%) started, 17 in queue, 30 running]
Finished r_rmsf in 2 seconds [~ 799 test (97.91666666666667%) started, 17 in queue, 29 running]
Finished number_of_residuetypes in 2 seconds [~ 799 test (97.91666666666667%) started, 17 in queue, 28 running]
Finished rnp_ddg_relax_setup in 0 seconds [~ 799 test (97.91666666666667%) started, 17 in queue, 27 running]
Running Test rnp_ddg_relax_finalize
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rnp_ddg_relax_finalize/command.sh
Running Test rnp_ddg_finalize
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rnp_ddg_finalize/command.sh
Running Test rnp_ddg_calc_setup
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rnp_ddg_calc_setup/command.sh
Running Test mp_quick_relax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_quick_relax/command.sh
Running Test features_scientific_benchmark
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/features_scientific_benchmark/command.sh
Running Test features_postgres
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/features_postgres/command.sh
PYTHON IS /Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python_virtual_environments/python-3.9/70fb5a411fc5470c895f6d4975b66fbe/bin/python
PYTHON is /Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python_virtual_environments/python-3.9/70fb5a411fc5470c895f6d4975b66fbe/bin/python
PYTHON IS /Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python_virtual_environments/python-3.9/70fb5a411fc5470c895f6d4975b66fbe/bin/python
Finished fit_helixparams_rms in 4 seconds [~ 805 test (98.65196078431373%) started, 11 in queue, 32 running]
Finished angle_recovery_stats in 3 seconds [~ 805 test (98.65196078431373%) started, 11 in queue, 31 running]
Finished DNA_methylation in 3 seconds [~ 805 test (98.65196078431373%) started, 11 in queue, 30 running]
Finished report_hbonds_for_plugin in 3 seconds [~ 805 test (98.65196078431373%) started, 11 in queue, 29 running]
Finished ralford_dump_rotamers in 3 seconds [~ 805 test (98.65196078431373%) started, 11 in queue, 28 running]
Finished loop_hash in 2 seconds [~ 805 test (98.65196078431373%) started, 11 in queue, 27 running]
Finished rnp_ddg_relax_finalize in 0 seconds [~ 805 test (98.65196078431373%) started, 11 in queue, 26 running]
Finished mp_quick_relax in 0 seconds [~ 805 test (98.65196078431373%) started, 11 in queue, 25 running]
Finished features_scientific_benchmark in 0 seconds [~ 805 test (98.65196078431373%) started, 11 in queue, 24 running]
Finished features_postgres in 0 seconds [~ 805 test (98.65196078431373%) started, 11 in queue, 23 running]
Running Test drrafter_setup_simple
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/drrafter_setup_simple/command.sh
Running Test drrafter_setup_protein_dock
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/drrafter_setup_protein_dock/command.sh
Running Test drrafter_setup_build_missing
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/drrafter_setup_build_missing/command.sh
Running Test drrafter_setup
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/drrafter_setup/command.sh
Running Test code_template_tests_unit
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/code_template_tests_unit/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
Running Test code_template_tests_app
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/code_template_tests_app/command.sh
Running Test cluster_calibur
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cluster_calibur/command.sh
Running Test central_class_modification
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/central_class_modification/command.sh
Running Test case_sensitive_filenames
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/case_sensitive_filenames/command.sh
Finished test_energy_method_options in 1 seconds [~ 815 test (99.87745098039215%) started, 1 in queue, 32 running]
Finished rnp_ddg_calc_setup in 0 seconds [~ 815 test (99.87745098039215%) started, 1 in queue, 31 running]
Running Test Werror_check
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/Werror_check/command.sh
Running Test RescoreSAXS
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/RescoreSAXS/command.sh
Finished rnp_ddg_finalize in 0 seconds [~ 816 test (100.0%) started, 0 in queue, 31 running]
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.
Running Test HOW_TO_MAKE_TESTS
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/HOW_TO_MAKE_TESTS/command.sh
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 code_template_tests_src in 4 seconds [~ 816 test (100.0%) started, 0 in queue, 30 running]
Finished per_residue_solvent_exposure in 1 seconds [~ 816 test (100.0%) started, 0 in queue, 29 running]
Finished cluster_calibur in 0 seconds [~ 816 test (100.0%) started, 0 in queue, 28 running]
Finished central_class_modification in 0 seconds [~ 816 test (100.0%) started, 0 in queue, 27 running]
Finished Werror_check in 0 seconds [~ 816 test (100.0%) started, 0 in queue, 26 running]
Finished RescoreSAXS in 0 seconds [~ 816 test (100.0%) started, 0 in queue, 25 running]
Finished HOW_TO_MAKE_TESTS in 0 seconds [~ 816 test (100.0%) started, 0 in queue, 24 running]
>>> Illegal use of .cc file in an include statement detected!
sed: 1: "cc_includes.txt": command c expects \ followed by text
Encounter error while executing: ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/include_cc_check/command.sh
*** Test include_cc_check did not run! Check your --mode flag and paths. [2025-04-04 15:49:38.254735]
/usr/bin/git
1298fde858856152300a5d4b072b28448924a54c
Finished CCD_loop_closure in 4 seconds [~ 816 test (100.0%) started, 0 in queue, 23 running]
Finished include_cc_check in 2 seconds [~ 816 test (100.0%) started, 0 in queue, 22 running]
Finished drrafter_setup_simple in 0 seconds [~ 816 test (100.0%) started, 0 in queue, 21 running]
Finished drrafter_setup in 0 seconds [~ 816 test (100.0%) started, 0 in queue, 20 running]
Finished code_template_tests_unit in 0 seconds [~ 816 test (100.0%) started, 0 in queue, 19 running]
Finished fit_helixparams_a3b in 2 seconds [~ 816 test (100.0%) started, 0 in queue, 18 running]
Finished discontinuous_sewing_hasher in 1 seconds [~ 816 test (100.0%) started, 0 in queue, 17 running]
Finished trRosettaConstraintGenerator_rosettascripts in 1 seconds [~ 816 test (100.0%) started, 0 in queue, 16 running]
Finished drrafter_setup_protein_dock in 0 seconds [~ 816 test (100.0%) started, 0 in queue, 15 running]
Finished drrafter_setup_build_missing in 0 seconds [~ 816 test (100.0%) started, 0 in queue, 14 running]
Finished code_template_tests_app in 0 seconds [~ 816 test (100.0%) started, 0 in queue, 13 running]
Finished case_sensitive_filenames in 0 seconds [~ 816 test (100.0%) started, 0 in queue, 12 running]
Finished mp_span_from_pdb in 1 seconds [~ 816 test (100.0%) started, 0 in queue, 11 running]
Finished combine_silent in 1 seconds [~ 816 test (100.0%) started, 0 in queue, 10 running]
Finished burial_measure_centroid in 1 seconds [~ 816 test (100.0%) started, 0 in queue, 9 running]
Finished score_aln in 1 seconds [~ 816 test (100.0%) started, 0 in queue, 8 running]
Finished header_using_check in 1 seconds [~ 816 test (100.0%) started, 0 in queue, 7 running]
Finished extract_pdbs in 1 seconds [~ 816 test (100.0%) started, 0 in queue, 6 running]
Finished continuous_sewing_hasher in 1 seconds [~ 816 test (100.0%) started, 0 in queue, 5 running]
Finished calculate_sasa in 2 seconds [~ 816 test (100.0%) started, 0 in queue, 4 running]
Finished fit_helixparams in 1 seconds [~ 816 test (100.0%) started, 0 in queue, 3 running]
Finished crossaln in 1 seconds [~ 816 test (100.0%) started, 0 in queue, 2 running]
Finished hierarchical_clustering in 2 seconds [~ 816 test (100.0%) started, 0 in queue, 1 running]
Finished BuildPeptide in 2 seconds [~ 816 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
──────────────── 'takeshi' comparing commits:20732 mac.clang.python39.integration test_id=855736 vs. main:62149 previous_test_id=852256 ────────────────
{
"compared_with_test": {
"full_name": "mac.clang.python39.integration",
"name": "integration",
"platform": {
"compiler": "clang",
"extras": [],
"os": "mac",
"python": "3.9"
},
"platform_as_string": "mac.clang.python39",
"revision": {
"branch": "main",
"revision_id": 62149
},
"state": "failed",
"test_id": 852256
},
"summary": {
"failed": 5,
"failed_tests": [
"ligand_motif_identification",
"ligand_motif_discovery",
"remove_duplicate_motifs",
"real_motif_analysis",
"include_cc_check"
],
"total": 816
},
"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": "",
"state": "passed"
},
"antibody_designer": {
"log": "",
"state": "passed"
},
"antibody_designer_camelid": {
"log": "",
"state": "passed"
},
"antibody_designer_xml": {
"log": "",
"state": "passed"
},
"antibody_graft": {
"log": "",
"state": "passed"
},
"antibody_numbering_converter": {
"log": "",
"state": "passed"
},
"app_exception_handling": {
"log": "",
"state": "passed"
},
"assemble_domains_jd2": {
"log": "",
"state": "passed"
},
"auto-drrafter_final_results": {
"log": "",
"state": "passed"
},
"auto-drrafter_setup_run_R1": {
"log": "",
"state": "passed"
},
"auto-drrafter_setup_run_R2": {
"log": "",
"state": "passed"
},
"auto-drrafter_setup_run_R3": {
"log": "",
"state": "passed"
},
"autoNOE_rosetta": {
"log": "",
"state": "passed"
},
"autosetup_metals_centroid": {
"log": "",
"state": "passed"
},
"backbonegridsampler": {
"log": "",
"state": "passed"
},
"backbonegridsampler_multiresidue": {
"log": "",
"state": "passed"
},
"backbonegridsampler_nstruct_mode": {
"log": "",
"state": "passed"
},
"backrub": {
"log": "",
"state": "passed"
},
"backrub_interface_ddG": {
"log": "",
"state": "passed"
},
"backrub_pilot": {
"log": "",
"state": "passed"
},
"balancedKIC": {
"log": "",
"state": "passed"
},
"basic_gcn_tensorflow_test": {
"log": "",
"state": "passed"
},
"batch_relax": {
"log": "",
"state": "passed"
},
"bcl_fragment_mutate": {
"log": "",
"state": "passed"
},
"beta_strand_homodimer": {
"log": "",
"state": "passed"
},
"bin_initialization": {
"log": "",
"state": "passed"
},
"bin_perturbation": {
"log": "",
"state": "passed"
},
"binselector": {
"log": "",
"state": "passed"
},
"binselector_probins": {
"log": "",
"state": "passed"
},
"blob_finder": {
"log": "",
"state": "passed"
},
"bridge_chains": {
"log": "",
"state": "passed"
},
"broker": {
"log": "",
"state": "passed"
},
"broker_membrane": {
"log": "",
"state": "passed"
},
"bundlegridsampler": {
"log": "",
"state": "passed"
},
"bundlegridsampler_composition_energy": {
"log": "",
"state": "passed"
},
"bundlegridsampler_composition_energy_fract_range": {
"log": "",
"state": "passed"
},
"bundlegridsampler_copy_pitch": {
"log": "",
"state": "passed"
},
"bundlegridsampler_design": {
"log": "",
"state": "passed"
},
"bundlegridsampler_design_nstruct_mode": {
"log": "",
"state": "passed"
},
"bundlegridsampler_epsilon": {
"log": "",
"state": "passed"
},
"bundlegridsampler_multirepeat": {
"log": "",
"state": "passed"
},
"bundlegridsampler_z0_offset": {
"log": "",
"state": "passed"
},
"bundlegridsampler_z1_offset": {
"log": "",
"state": "passed"
},
"bundlereporter_filter": {
"log": "",
"state": "passed"
},
"burial_measure_centroid": {
"log": "",
"state": "passed"
},
"buried_area_filter": {
"log": "",
"state": "passed"
},
"buried_unsat_kinemage": {
"log": "",
"state": "passed"
},
"buried_unsat_voids_hbnet_design": {
"log": "",
"state": "passed"
},
"buried_unsat_voids_hbnet_design_symm": {
"log": "",
"state": "passed"
},
"c-term_conjugation": {
"log": "",
"state": "passed"
},
"calculate_sasa": {
"log": "",
"state": "passed"
},
"carbohydrates": {
"log": "",
"state": "passed"
},
"cart_min_glycans": {
"log": "",
"state": "passed"
},
"cartesianddg": {
"log": "",
"state": "passed"
},
"case_sensitive_filenames": {
"log": "",
"state": "passed"
},
"ccd_ends_graft_mover_rs": {
"log": "",
"state": "passed"
},
"central_class_modification": {
"log": "",
"state": "passed"
},
"centroid_disulfide_scores": {
"log": "",
"state": "passed"
},
"centroid_from_fullatom": {
"log": "",
"state": "passed"
},
"cl_complex_rescore": {
"log": "",
"state": "passed"
},
"classic_relax_1a19": {
"log": "",
"state": "passed"
},
"cleanAlignment": {
"log": "",
"state": "passed"
},
"cluster": {
"log": "",
"state": "passed"
},
"cluster_alns": {
"log": "",
"state": "passed"
},
"cluster_calibur": {
"log": "",
"state": "passed"
},
"cluster_filter": {
"log": "",
"state": "passed"
},
"cmaes_minimizer": {
"log": "",
"state": "passed"
},
"coarse_rna_scoring": {
"log": "",
"state": "passed"
},
"code_template_tests_app": {
"log": "",
"state": "passed"
},
"code_template_tests_citations": {
"log": "",
"state": "passed"
},
"code_template_tests_src": {
"log": "",
"state": "passed"
},
"code_template_tests_unit": {
"log": "",
"state": "passed"
},
"coenzymes": {
"log": "",
"state": "passed"
},
"combine_silent": {
"log": "",
"state": "passed"
},
"composition_energy_layers": {
"log": "",
"state": "passed"
},
"constel": {
"log": "",
"state": "passed"
},
"constraints_metric": {
"log": "",
"state": "passed"
},
"contactMap": {
"log": "",
"state": "passed"
},
"continuous_sewing_hasher": {
"log": "",
"state": "passed"
},
"control_flow_rs": {
"log": "",
"state": "passed"
},
"copy_rotamer_mover": {
"log": "",
"state": "passed"
},
"count_cycpep_sequences": {
"log": "",
"state": "passed"
},
"coupled_moves": {
"log": "",
"state": "passed"
},
"crankshaft_flip": {
"log": "",
"state": "passed"
},
"create_clash-based_repack_shell": {
"log": "",
"state": "passed"
},
"create_sequence_motif": {
"log": "",
"state": "passed"
},
"crossaln": {
"log": "",
"state": "passed"
},
"crosslinkermover_1_4_bbmb_asymm": {
"log": "",
"state": "passed"
},
"crosslinkermover_1_4_bbmb_c2_symmetry": {
"log": "",
"state": "passed"
},
"crosslinkermover_1_4_bbmb_s2_symm": {
"log": "",
"state": "passed"
},
"crosslinkermover_lanthionine": {
"log": "",
"state": "passed"
},
"crosslinkermover_methyllanthionine": {
"log": "",
"state": "passed"
},
"crosslinkermover_octahedral": {
"log": "",
"state": "passed"
},
"crosslinkermover_octahedral_s2_symm": {
"log": "",
"state": "passed"
},
"crosslinkermover_square_planar": {
"log": "",
"state": "passed"
},
"crosslinkermover_square_planar_d2_symm": {
"log": "",
"state": "passed"
},
"crosslinkermover_square_pyramidal": {
"log": "",
"state": "passed"
},
"crosslinkermover_tetrahedral_metal": {
"log": "",
"state": "passed"
},
"crosslinkermover_tetrahedral_metal_asp": {
"log": "",
"state": "passed"
},
"crosslinkermover_tetrahedral_metal_c2_symmetry": {
"log": "",
"state": "passed"
},
"crosslinkermover_tetrahedral_metal_d2_symmetry": {
"log": "",
"state": "passed"
},
"crosslinkermover_thioether": {
"log": "",
"state": "passed"
},
"crosslinkermover_tma": {
"log": "",
"state": "passed"
},
"crosslinkermover_tma_symm": {
"log": "",
"state": "passed"
},
"crosslinkermover_trigonal_planar": {
"log": "",
"state": "passed"
},
"crosslinkermover_trigonal_planar_c3_symm": {
"log": "",
"state": "passed"
},
"crosslinkermover_trigonal_pyramidal": {
"log": "",
"state": "passed"
},
"crosslinkermover_trigonal_pyramidal_c3_symm": {
"log": "",
"state": "passed"
},
"cs_rosetta_rna": {
"log": "",
"state": "passed"
},
"cst_info": {
"log": "",
"state": "passed"
},
"cstfile_to_theozyme_pdb": {
"log": "",
"state": "passed"
},
"custom_basetype_packer_palette": {
"log": "",
"state": "passed"
},
"cyclization": {
"log": "",
"state": "passed"
},
"cycpep_design_pipeline": {
"log": "",
"state": "passed"
},
"cycpep_rdkit_metric": {
"log": "",
"state": "passed"
},
"cycpep_rigid_body_permutation_mover": {
"log": "",
"state": "passed"
},
"cycpep_symmetry_filter": {
"log": "",
"state": "passed"
},
"d_workflow": {
"log": "",
"state": "passed"
},
"database_jd2_compact_io": {
"log": "",
"state": "passed"
},
"database_jd2_io": {
"log": "",
"state": "passed"
},
"database_md5": {
"log": "",
"state": "passed"
},
"database_session_resource": {
"log": "",
"state": "passed"
},
"ddG_ensemble": {
"log": "",
"state": "passed"
},
"ddG_of_mutation": {
"log": "",
"state": "passed"
},
"ddG_scan": {
"log": "",
"state": "passed"
},
"ddG_sym": {
"log": "",
"state": "passed"
},
"dehydro_aa_patch": {
"log": "",
"state": "passed"
},
"density_denovo": {
"log": "",
"state": "passed"
},
"density_refine": {
"log": "",
"state": "passed"
},
"density_refine_symm": {
"log": "",
"state": "passed"
},
"density_tools": {
"log": "",
"state": "passed"
},
"design_glycans": {
"log": "",
"state": "passed"
},
"design_w_custom_palette-CAAs": {
"log": "",
"state": "passed"
},
"design_w_custom_palette-NCAAs": {
"log": "",
"state": "passed"
},
"design_w_custom_palette-RNA": {
"log": "",
"state": "passed"
},
"dgdp_aio": {
"log": "",
"state": "passed"
},
"dgdp_script": {
"log": "",
"state": "passed"
},
"dihedral_constraint_generator": {
"log": "",
"state": "passed"
},
"discontinuous_sewing_hasher": {
"log": "",
"state": "passed"
},
"distances": {
"log": "",
"state": "passed"
},
"disulfidize_beta_cys": {
"log": "",
"state": "passed"
},
"dna_interface_design": {
"log": "",
"state": "passed"
},
"dock_glycans": {
"log": "",
"state": "passed"
},
"dock_with_hotspot_place_simultaneously": {
"log": "",
"state": "passed"
},
"docking_distance_constraints": {
"log": "",
"state": "passed"
},
"docking_ensemble": {
"log": "",
"state": "passed"
},
"docking_ensemble_prepack": {
"log": "",
"state": "passed"
},
"docking_full_protocol": {
"log": "",
"state": "passed"
},
"docking_local_refine": {
"log": "",
"state": "passed"
},
"docking_local_refine_min": {
"log": "",
"state": "passed"
},
"docking_low_res": {
"log": "",
"state": "passed"
},
"docking_prepack": {
"log": "",
"state": "passed"
},
"docking_site_constraints": {
"log": "",
"state": "passed"
},
"doug_dock_design_min_mod2_cal_cal": {
"log": "",
"state": "passed"
},
"drrafter_error_estimation": {
"log": "",
"state": "passed"
},
"drrafter_run": {
"log": "",
"state": "passed"
},
"drrafter_setup": {
"log": "",
"state": "passed"
},
"drrafter_setup_build_missing": {
"log": "",
"state": "passed"
},
"drrafter_setup_protein_dock": {
"log": "",
"state": "passed"
},
"drrafter_setup_real_test_H": {
"log": "",
"state": "passed"
},
"drrafter_setup_real_test_H_no_init": {
"log": "",
"state": "passed"
},
"drrafter_setup_ribosome_test": {
"log": "",
"state": "passed"
},
"drrafter_setup_simple": {
"log": "",
"state": "passed"
},
"duplicate_header_guards": {
"log": "",
"state": "passed"
},
"energy_based_clustering_alpha_aa": {
"log": "",
"state": "passed"
},
"energy_based_clustering_alpha_aa_bin_analysis": {
"log": "",
"state": "passed"
},
"energy_based_clustering_alpha_aa_dihedral": {
"log": "",
"state": "passed"
},
"energy_based_clustering_alpha_aa_scorefile": {
"log": "",
"state": "passed"
},
"entropy_correction": {
"log": "",
"state": "passed"
},
"enumerative_sampling": {
"log": "",
"state": "passed"
},
"enzdes": {
"log": "",
"state": "passed"
},
"enzscore_filter_dimetal": {
"log": "",
"state": "passed"
},
"enzscore_filter_dimetal_sym": {
"log": "",
"state": "passed"
},
"enzscore_filter_ligand": {
"log": "",
"state": "passed"
},
"enzscore_filter_metal": {
"log": "",
"state": "passed"
},
"enzscore_filter_metal_sym": {
"log": "",
"state": "passed"
},
"erraser_minimize": {
"log": "",
"state": "passed"
},
"esm_model_perplexity": {
"log": "",
"state": "passed"
},
"evolution": {
"log": "",
"state": "passed"
},
"exclusively_shared_jumps": {
"log": "",
"state": "passed"
},
"explicit_membrane": {
"log": "",
"state": "passed"
},
"extract_atomtree_diffs": {
"log": "",
"state": "passed"
},
"extract_pdbs": {
"log": "",
"state": "passed"
},
"farfar_mrna": {
"log": "",
"state": "passed"
},
"farnesyl": {
"log": "",
"state": "passed"
},
"fast_relax": {
"log": "",
"state": "passed"
},
"fast_relax_scripts": {
"log": "",
"state": "passed"
},
"favor_coupling_tensor": {
"log": "",
"state": "passed"
},
"favor_native_residue": {
"log": "",
"state": "passed"
},
"features": {
"log": "",
"state": "passed"
},
"features_database_schema": {
"log": "",
"state": "passed"
},
"features_parallel": {
"log": "",
"state": "passed"
},
"features_pdb": {
"log": "",
"state": "passed"
},
"features_pdb_mpi": {
"log": "",
"state": "passed"
},
"features_postgres": {
"log": "",
"state": "passed"
},
"features_scientific_benchmark": {
"log": "",
"state": "passed"
},
"fiber_diffraction": {
"log": "",
"state": "passed"
},
"fiber_diffraction_fad": {
"log": "",
"state": "passed"
},
"fit_helixparams": {
"log": "",
"state": "passed"
},
"fit_helixparams_a3b": {
"log": "",
"state": "passed"
},
"fit_helixparams_rms": {
"log": "",
"state": "passed"
},
"fix_alignment_to_match_pdb": {
"log": "",
"state": "passed"
},
"fixbb": {
"log": "",
"state": "passed"
},
"flexpepdock": {
"log": "",
"state": "passed"
},
"flexpepdock_abinitio": {
"log": "",
"state": "passed"
},
"fold_and_dock": {
"log": "",
"state": "passed"
},
"fold_cst_new": {
"log": "",
"state": "passed"
},
"fold_from_loops": {
"log": "",
"state": "passed"
},
"fragment_picker": {
"log": "",
"state": "passed"
},
"fragmentpicker_integration_demo": {
"log": "",
"state": "passed"
},
"fuzzy": {
"log": "",
"state": "passed"
},
"ga_ligand_dock": {
"log": "",
"state": "passed"
},
"ga_ligand_dock_amino_acid": {
"log": "",
"state": "passed"
},
"ga_ligand_dock_macrocycle": {
"log": "",
"state": "passed"
},
"gen_apo_grids": {
"log": "",
"state": "passed"
},
"gen_lig_grids": {
"log": "",
"state": "passed"
},
"generate_6Dloopclose": {
"log": "",
"state": "passed"
},
"genkic_bin_perturbing": {
"log": "",
"state": "passed"
},
"genkic_bin_sampling": {
"log": "",
"state": "passed"
},
"genkic_bin_setting": {
"log": "",
"state": "passed"
},
"genkic_dihedral_copying": {
"log": "",
"state": "passed"
},
"genkic_lowmemory_mode": {
"log": "",
"state": "passed"
},
"genkic_rama_filter": {
"log": "",
"state": "passed"
},
"genkic_ramaprepro_sampling": {
"log": "",
"state": "passed"
},
"genkic_sugars": {
"log": "",
"state": "passed"
},
"geometric_solvation": {
"log": "",
"state": "passed"
},
"glycan_anomers": {
"log": "",
"state": "passed"
},
"glycan_clash_check": {
"log": "",
"state": "passed"
},
"glycan_refinment": {
"log": "",
"state": "passed"
},
"glycan_relax": {
"log": "",
"state": "passed"
},
"glycan_sequon_scanner": {
"log": "",
"state": "passed"
},
"glycan_tree_relax": {
"log": "",
"state": "passed"
},
"glycomutagenesis": {
"log": "",
"state": "passed"
},
"glycopeptidedocking": {
"log": "",
"state": "passed"
},
"glycopeptidedocking_diglyco_long": {
"log": "",
"state": "passed"
},
"glycosylation": {
"log": "",
"state": "passed"
},
"grid_scores_features": {
"log": "",
"state": "passed"
},
"hbnet": {
"log": "",
"state": "passed"
},
"hbnet_asymm": {
"log": "",
"state": "passed"
},
"hbnet_energy": {
"log": "",
"state": "passed"
},
"hbnet_energy_rosettascripts_linear": {
"log": "",
"state": "passed"
},
"hbnet_energy_symm": {
"log": "",
"state": "passed"
},
"hbnet_use_input_rot": {
"log": "",
"state": "passed"
},
"hbonds": {
"log": "",
"state": "passed"
},
"hbonds_sp2": {
"log": "",
"state": "passed"
},
"hbondstoresidue_selector": {
"log": "",
"state": "passed"
},
"hbs_design": {
"log": "",
"state": "passed"
},
"header_using_check": {
"log": "",
"state": "passed"
},
"helical_bundle": {
"log": "",
"state": "passed"
},
"helical_bundle_nonideal": {
"log": "",
"state": "passed"
},
"helical_bundle_predict": {
"log": "",
"state": "passed"
},
"helical_bundle_predict_psipred": {
"log": "",
"state": "passed"
},
"helical_bundle_predict_psipred_with_helix_globals": {
"log": "",
"state": "passed"
},
"helical_bundle_predict_sequence": {
"log": "",
"state": "passed"
},
"helical_bundle_predict_skipping_residues": {
"log": "",
"state": "passed"
},
"helix_from_sequence": {
"log": "",
"state": "passed"
},
"hierarchical_clustering": {
"log": "",
"state": "passed"
},
"homodimer_fnd_ref2015_memb": {
"log": "",
"state": "passed"
},
"hotspot_graft": {
"log": "",
"state": "passed"
},
"hotspot_hashing": {
"log": "",
"state": "passed"
},
"hotspot_stub_constraints": {
"log": "",
"state": "passed"
},
"hshash_utils": {
"log": "",
"state": "passed"
},
"hts_io": {
"log": "",
"state": "passed"
},
"hybridization": {
"log": "",
"state": "passed"
},
"hydrate": {
"log": "",
"state": "passed"
},
"hydrate_relax": {
"log": "",
"state": "passed"
},
"identify_cdr_clusters": {
"log": "",
"state": "passed"
},
"ig_dump": {
"log": "",
"state": "passed"
},
"include_cc_check": {
"log": "Brief Diff:\nFiles /home/benchmark/working_dir/main:62149/include_cc_check/cc_includes.txt and /home/benchmark/working_dir/commits:20732/include_cc_check/cc_includes.txt differ\r\nOnly in /home/benchmark/working_dir/commits:20732/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:20732/include_cc_check/cc_includes.txt\r\n0a1\r\n> src/apps/public/motif_ligand_discovery/remove_duplicate_motifs.cc://#include <protocols/motifs/FindMotifPositionsOnLigandHelper.cc>\r\nOnly in /home/benchmark/working_dir/commits:20732/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"
},
"inverse_rotamer_remodel": {
"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:20732/ligand_motif_discovery: 4s0v_receptor_only_empty__WholeRatio_0.115602_SubRatio_0.416593.pdb\r\nOnly in /home/benchmark/working_dir/commits:20732/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_0.116585_SubRatio_0.521778.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:20732/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_0.116733_SubRatio_0.538074.pdb\r\nOnly in /home/benchmark/working_dir/commits:20732/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_0.116378_SubRatio_0.496296.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:20732/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_0.116824_SubRatio_0.543111.pdb\r\nOnly in /home/benchmark/working_dir/commits:20732/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_0.116609_SubRatio_0.524741.pdb\r\nOnly in /home/benchmark/working_dir/commits:20732/ligand_motif_discovery: 4s0v_receptor_only_suv_0.pdb\r\nOnly in /home/benchmark/working_dir/commits:20732/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\nFiles /home/benchmark/working_dir/main:62149/ligand_motif_discovery/flags and /home/benchmark/working_dir/commits:20732/ligand_motif_discovery/flags differ\r\nFiles /home/benchmark/working_dir/main:62149/ligand_motif_discovery/log and /home/benchmark/working_dir/commits:20732/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:20732/ligand_motif_discovery: 4s0v_receptor_only_empty__WholeRatio_0.115602_SubRatio_0.416593.pdb\r\nOnly in /home/benchmark/working_dir/commits:20732/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_0.116585_SubRatio_0.521778.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:20732/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_0.116733_SubRatio_0.538074.pdb\r\nOnly in /home/benchmark/working_dir/commits:20732/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_0.116378_SubRatio_0.496296.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:20732/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_0.116824_SubRatio_0.543111.pdb\r\nOnly in /home/benchmark/working_dir/commits:20732/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_0.116609_SubRatio_0.524741.pdb\r\nOnly in /home/benchmark/working_dir/commits:20732/ligand_motif_discovery: 4s0v_receptor_only_suv_0.pdb\r\nOnly in /home/benchmark/working_dir/commits:20732/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\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:20732/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_dimensions_sf 7,7,7\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 0.10\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:20732/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\n345a43,104\r\n> protocols.motifs.LigandDiscoverySearch: Current anchor residue position: 423\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> protocols.motifs.LigandDiscoverySearch: Starting to iterate through all ligands\r\n> protocols.motifs.LigandDiscoverySearch: On ligand suv\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n350,915c109,270\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.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\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> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> core.chemical.ResidueType: [ WARNING ] Residue PRO:NtermProteinFull claims it's a polymer, but it doesn't have the appropriate UPPER and LOWER connection points specified. Set MAINCHAIN_ATOMS in the topology file to remove this warning.\r\n> protocols.motifs.LigandDiscoverySearch: Done iterating all trios, moving to next ligand\r\n> protocols.motifs.LigandDiscoverySearch: Total passing attempts for ligand is 2\r\n> protocols.motifs.LigandDiscoverySearch: 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:20732/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:20732/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\n70a66\r\n> basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine\r\n72,922d67\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\n927,970c72\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\n975,1009c77\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\n1014,1064c82\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\n1069,1119c87\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\n1124,1177c92\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\n1182,1230c97\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\n1235,1274c102\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\n1279,1328c107\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\n1333,1385c112\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\n1390,1444c117\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\n1449,1865c122\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\n1870,1889c127\r\n< apps.pilot.ligand_motifs: 19: 18-19-20Writing ILE63A_Z2002_Ligatoms_18_19_20_A_4s0v.pdb\r\n< apps.pilot.ligand_motifs: Motif index contains: 1-4-5\r\n< apps.pilot.ligand_motifs: Motif index contains: 2-1-3\r\n< apps.pilot.ligand_motifs: Motif index contains: 2-1-4\r\n< apps.pilot.ligand_motifs: Motif index contains: 3-1-4\r\n< apps.pilot.ligand_motifs: Motif index contains: 4-5-6\r\n< apps.pilot.ligand_motifs: Motif index contains: 5-6-7\r\n< apps.pilot.ligand_motifs: Motif index contains: 6-7-8\r\n< apps.pilot.ligand_motifs: Motif index contains: 7-8-9\r\n< apps.pilot.ligand_motifs: Motif index contains: 8-9-10\r\n< apps.pilot.ligand_motifs: Motif index contains: 9-10-11\r\n< apps.pilot.ligand_motifs: Motif index contains: 10-11-12\r\n< apps.pilot.ligand_motifs: Motif index contains: 11-12-13\r\n< apps.pilot.ligand_motifs: Motif index contains: 12-13-14\r\n< apps.pilot.ligand_motifs: Motif index contains: 13-14-15\r\n< apps.pilot.ligand_motifs: Motif index contains: 14-15-16\r\n< apps.pilot.ligand_motifs: Motif index contains: 15-16-17\r\n< apps.pilot.ligand_motifs: Motif index contains: 16-17-18\r\n< apps.pilot.ligand_motifs: Motif index contains: 17-18-19\r\n< apps.pilot.ligand_motifs: Motif index contains: 18-19-20\r\n---\r\n> protocols.motifs.IdentifyLigandMotifs: Writing ILE63A_Z2002_Ligatoms_18_19_20_A_4s0v.pdb\r\n",
"state": "failed"
},
"ligand_water_docking": {
"log": "",
"state": "passed"
},
"longest_continuous_polar_segment_filter": {
"log": "",
"state": "passed"
},
"loop_creation": {
"log": "",
"state": "passed"
},
"loop_grower_N_term_symm": {
"log": "",
"state": "passed"
},
"loop_hash": {
"log": "",
"state": "passed"
},
"loop_modeling": {
"log": "",
"state": "passed"
},
"make_and_perturb_bundle_multirepeat": {
"log": "",
"state": "passed"
},
"make_exemplar": {
"log": "",
"state": "passed"
},
"make_mainchain_potential": {
"log": "",
"state": "passed"
},
"make_mainchain_potential_symm": {
"log": "",
"state": "passed"
},
"make_mainchain_potential_symm_preproline": {
"log": "",
"state": "passed"
},
"make_rot_lib": {
"log": "",
"state": "passed"
},
"make_symmdef_file": {
"log": "",
"state": "passed"
},
"match_1c2t": {
"log": "",
"state": "passed"
},
"match_1n9l": {
"log": "",
"state": "passed"
},
"match_6cpa": {
"log": "",
"state": "passed"
},
"match_xml": {
"log": "",
"state": "passed"
},
"measure_lcaa_radii": {
"log": "",
"state": "passed"
},
"membrane_abinitio": {
"log": "",
"state": "passed"
},
"membrane_relax": {
"log": "",
"state": "passed"
},
"membrane_relax_hbond": {
"log": "",
"state": "passed"
},
"metal_setup": {
"log": "",
"state": "passed"
},
"metalloprotein_abrelax": {
"log": "",
"state": "passed"
},
"metalloprotein_broker": {
"log": "",
"state": "passed"
},
"metropolis_hastings": {
"log": "",
"state": "passed"
},
"mf_fixbb_des": {
"log": "",
"state": "passed"
},
"mf_fixbb_sc": {
"log": "",
"state": "passed"
},
"mf_flexbb_sc": {
"log": "",
"state": "passed"
},
"mg_modeler": {
"log": "",
"state": "passed"
},
"mg_modeler_lores": {
"log": "",
"state": "passed"
},
"mhc_epitope": {
"log": "",
"state": "passed"
},
"mhc_epitope_nmer_preload": {
"log": "",
"state": "passed"
},
"min_pack_min": {
"log": "",
"state": "passed"
},
"minimize_6Dloopclose": {
"log": "",
"state": "passed"
},
"minimize_with_elec_dens": {
"log": "",
"state": "passed"
},
"mirror_symm": {
"log": "",
"state": "passed"
},
"mixed_monte_carlo": {
"log": "",
"state": "passed"
},
"mm_params": {
"log": "",
"state": "passed"
},
"mmtfIO_score_test": {
"log": "",
"state": "passed"
},
"molfile_to_params": {
"log": "",
"state": "passed"
},
"molfile_to_params_polymer": {
"log": "",
"state": "passed"
},
"motif_dna_packer_design": {
"log": "",
"state": "passed"
},
"motif_extraction": {
"log": "",
"state": "passed"
},
"motif_score_filter": {
"log": "",
"state": "passed"
},
"mp_dock": {
"log": "",
"state": "passed"
},
"mp_dock_ensemble": {
"log": "",
"state": "passed"
},
"mp_dock_prepack": {
"log": "",
"state": "passed"
},
"mp_dock_setup": {
"log": "",
"state": "passed"
},
"mp_domain_assembly": {
"log": "",
"state": "passed"
},
"mp_domain_assembly_FtsQ": {
"log": "",
"state": "passed"
},
"mp_f19_relax": {
"log": "",
"state": "passed"
},
"mp_find_interface": {
"log": "",
"state": "passed"
},
"mp_interface_statistics": {
"log": "",
"state": "passed"
},
"mp_ligand_interface": {
"log": "",
"state": "passed"
},
"mp_loadtime": {
"log": "",
"state": "passed"
},
"mp_mutate_relax": {
"log": "",
"state": "passed"
},
"mp_mutate_repack": {
"log": "",
"state": "passed"
},
"mp_quick_relax": {
"log": "",
"state": "passed"
},
"mp_quick_relax_ref2015_memb": {
"log": "",
"state": "passed"
},
"mp_range_relax": {
"log": "",
"state": "passed"
},
"mp_relax": {
"log": "",
"state": "passed"
},
"mp_relax_w_ligand": {
"log": "",
"state": "passed"
},
"mp_score_jd2": {
"log": "",
"state": "passed"
},
"mp_span_ang_ref2015_memb": {
"log": "",
"state": "passed"
},
"mp_span_from_pdb": {
"log": "",
"state": "passed"
},
"mp_symdock": {
"log": "",
"state": "passed"
},
"mp_symmetry_load": {
"log": "",
"state": "passed"
},
"mp_transform": {
"log": "",
"state": "passed"
},
"mp_transform_optimize": {
"log": "",
"state": "passed"
},
"mp_vis_emb": {
"log": "",
"state": "passed"
},
"mpi_multistate_design": {
"log": "",
"state": "passed"
},
"mpi_simple_cycpep_predict": {
"log": "",
"state": "passed"
},
"mpi_simple_cycpep_predict_4level": {
"log": "",
"state": "passed"
},
"mpi_simple_cycpep_predict_computing_pnear_to_all": {
"log": "",
"state": "passed"
},
"mpil_find_pore_ahelical": {
"log": "",
"state": "passed"
},
"mpil_find_pore_bbarrel": {
"log": "",
"state": "passed"
},
"mpil_load_implicit_lipids": {
"log": "",
"state": "passed"
},
"mr_protocols": {
"log": "",
"state": "passed"
},
"multistage_rosetta_scripts": {
"log": "",
"state": "passed"
},
"multistage_rosetta_scripts_clustering": {
"log": "",
"state": "passed"
},
"multithreaded_fastdesign": {
"log": "",
"state": "passed"
},
"multithreaded_fixbb": {
"log": "",
"state": "passed"
},
"multithreaded_interaction_graph_accuracy": {
"log": "",
"state": "passed"
},
"multithreaded_interaction_graph_accuracy_symm": {
"log": "",
"state": "passed"
},
"multithreaded_packrotamersmover": {
"log": "",
"state": "passed"
},
"mutate": {
"log": "",
"state": "passed"
},
"ncaa_fixbb": {
"log": "",
"state": "passed"
},
"ncbb_packer_palette": {
"log": "",
"state": "passed"
},
"netcharge_design": {
"log": "",
"state": "passed"
},
"netcharge_design_symm": {
"log": "",
"state": "passed"
},
"next_generation_KIC": {
"log": "",
"state": "passed"
},
"noe_assignment": {
"log": "",
"state": "passed"
},
"non-canonical_connectivities": {
"log": "",
"state": "passed"
},
"nonideal_rtmin": {
"log": "",
"state": "passed"
},
"nucleobase_sample_around": {
"log": "",
"state": "passed"
},
"number_of_residuetypes": {
"log": "",
"state": "passed"
},
"oligourea_design": {
"log": "",
"state": "passed"
},
"oligourea_predict": {
"log": "",
"state": "passed"
},
"oop_create": {
"log": "",
"state": "passed"
},
"oop_design": {
"log": "",
"state": "passed"
},
"oop_dock_design": {
"log": "",
"state": "passed"
},
"orbitals": {
"log": "",
"state": "passed"
},
"output_schema": {
"log": "",
"state": "passed"
},
"pH_mode": {
"log": "",
"state": "passed"
},
"pepspec": {
"log": "",
"state": "passed"
},
"pepspec_anchor_dock": {
"log": "",
"state": "passed"
},
"peptiderive": {
"log": "",
"state": "passed"
},
"per_residue_energies": {
"log": "",
"state": "passed"
},
"per_residue_sc_sasa": {
"log": "",
"state": "passed"
},
"per_residue_solvent_exposure": {
"log": "",
"state": "passed"
},
"pertmin": {
"log": "",
"state": "passed"
},
"perturb_helical_bundle": {
"log": "",
"state": "passed"
},
"perturb_helical_bundle_copying_pitch": {
"log": "",
"state": "passed"
},
"perturb_helical_bundle_epsilon": {
"log": "",
"state": "passed"
},
"perturb_helical_bundle_setting": {
"log": "",
"state": "passed"
},
"perturb_helical_bundle_z_offset": {
"log": "",
"state": "passed"
},
"phiselector": {
"log": "",
"state": "passed"
},
"phosphonate": {
"log": "",
"state": "passed"
},
"phosphorylation": {
"log": "",
"state": "passed"
},
"place_simultaneously": {
"log": "",
"state": "passed"
},
"pmut_scan": {
"log": "",
"state": "passed"
},
"pna": {
"log": "",
"state": "passed"
},
"pna_base_pairs": {
"log": "",
"state": "passed"
},
"pocket_measure": {
"log": "",
"state": "passed"
},
"pocket_relax": {
"log": "",
"state": "passed"
},
"pocket_suggest_targets": {
"log": "",
"state": "passed"
},
"polyaramid_test_trivial": {
"log": "",
"state": "passed"
},
"pose_sewing": {
"log": "",
"state": "passed"
},
"posttranslationalmod_io": {
"log": "",
"state": "passed"
},
"ppi_v3_suiteA": {
"log": "",
"state": "passed"
},
"ppi_v3_suiteB": {
"log": "",
"state": "passed"
},
"ppi_v3_suiteC": {
"log": "",
"state": "passed"
},
"ppi_v3_suiteD": {
"log": "",
"state": "passed"
},
"ppi_v3_suiteE": {
"log": "",
"state": "passed"
},
"ppi_v3_suiteF": {
"log": "",
"state": "passed"
},
"ppi_v3_suiteG": {
"log": "",
"state": "passed"
},
"ppk": {
"log": "",
"state": "passed"
},
"proteinMPNN_model_perplexity": {
"log": "",
"state": "passed"
},
"protocol_metric": {
"log": "",
"state": "passed"
},
"pwsho": {
"log": "",
"state": "passed"
},
"pymol_cif": {
"log": "",
"state": "passed"
},
"r_pdb2top": {
"log": "",
"state": "passed"
},
"r_rmsf": {
"log": "",
"state": "passed"
},
"ralford_dump_rotamers": {
"log": "",
"state": "passed"
},
"rama_mutation_selector": {
"log": "",
"state": "passed"
},
"range_relax_w_cst": {
"log": "",
"state": "passed"
},
"rb_recces": {
"log": "",
"state": "passed"
},
"rdkit_metrics": {
"log": "",
"state": "passed"
},
"read_polymeric_components": {
"log": "",
"state": "passed"
},
"readin_dna_rna_protein": {
"log": "",
"state": "passed"
},
"real_motif_analysis": {
"log": "Brief Diff:\ndiff: /home/benchmark/working_dir/main:62149/real_motif_analysis: No such file or directory\r\n",
"state": "failed"
},
"real_virt_mover": {
"log": "",
"state": "passed"
},
"recces_turner": {
"log": "",
"state": "passed"
},
"recon_design": {
"log": "",
"state": "passed"
},
"recon_design_mpi": {
"log": "",
"state": "passed"
},
"referencepose_mutateresidue": {
"log": "",
"state": "passed"
},
"relax_w_allatom_cst": {
"log": "",
"state": "passed"
},
"remodel": {
"log": "",
"state": "passed"
},
"remodel_disulfides": {
"log": "",
"state": "passed"
},
"remodel_disulfides_rosettascripts": {
"log": "",
"state": "passed"
},
"remodel_helical_repeat": {
"log": "",
"state": "passed"
},
"remove_duplicate_motifs": {
"log": "Brief Diff:\ndiff: /home/benchmark/working_dir/main:62149/remove_duplicate_motifs: No such file or directory\r\n",
"state": "failed"
},
"repack_with_elec_dens": {
"log": "",
"state": "passed"
},
"repeat_propagate": {
"log": "",
"state": "passed"
},
"repeat_propagate_v2": {
"log": "",
"state": "passed"
},
"repeat_propagate_v3": {
"log": "",
"state": "passed"
},
"repeat_relax": {
"log": "",
"state": "passed"
},
"replica_docking": {
"log": "",
"state": "passed"
},
"report_hbonds_for_plugin": {
"log": "",
"state": "passed"
},
"res_lipo_ref2015_memb": {
"log": "",
"state": "passed"
},
"residue_energy_breakdown": {
"log": "",
"state": "passed"
},
"resource_database_locator": {
"log": "",
"state": "passed"
},
"restype_converter": {
"log": "",
"state": "passed"
},
"rings": {
"log": "",
"state": "passed"
},
"rna_add_WC_stats": {
"log": "",
"state": "passed"
},
"rna_assemble": {
"log": "",
"state": "passed"
},
"rna_cluster": {
"log": "",
"state": "passed"
},
"rna_denovo": {
"log": "",
"state": "passed"
},
"rna_denovo_RNP_low_res": {
"log": "",
"state": "passed"
},
"rna_denovo_RNP_refine_native": {
"log": "",
"state": "passed"
},
"rna_denovo_base_pair_constraints": {
"log": "",
"state": "passed"
},
"rna_denovo_base_pair_setup": {
"log": "",
"state": "passed"
},
"rna_denovo_bps": {
"log": "",
"state": "passed"
},
"rna_denovo_bps_fixed_ends": {
"log": "",
"state": "passed"
},
"rna_denovo_bps_helix_ends": {
"log": "",
"state": "passed"
},
"rna_denovo_dna_bridge": {
"log": "",
"state": "passed"
},
"rna_denovo_fragment_homology_exclusion": {
"log": "",
"state": "passed"
},
"rna_denovo_grid_vdw": {
"log": "",
"state": "passed"
},
"rna_denovo_lariat": {
"log": "",
"state": "passed"
},
"rna_denovo_new_FT_2in_dens": {
"log": "",
"state": "passed"
},
"rna_denovo_new_FT_5P_j12_leadzyme": {
"log": "",
"state": "passed"
},
"rna_denovo_new_FT_RNP_2prot_dens": {
"log": "",
"state": "passed"
},
"rna_denovo_new_FT_rna_two_chains": {
"log": "",
"state": "passed"
},
"rna_denovo_new_libs": {
"log": "",
"state": "passed"
},
"rna_denovo_symm_hack": {
"log": "",
"state": "passed"
},
"rna_design": {
"log": "",
"state": "passed"
},
"rna_farfar_block_stack": {
"log": "",
"state": "passed"
},
"rna_farfar_noncanonical_hairpin": {
"log": "",
"state": "passed"
},
"rna_farfar_syn_chi_res": {
"log": "",
"state": "passed"
},
"rna_helix": {
"log": "",
"state": "passed"
},
"rna_minimize": {
"log": "",
"state": "passed"
},
"rna_minimize_6D_loop_close": {
"log": "",
"state": "passed"
},
"rna_motif": {
"log": "",
"state": "passed"
},
"rna_predict_chem_map": {
"log": "",
"state": "passed"
},
"rna_puzzle11_H2H3H4_run3_connectU40": {
"log": "",
"state": "passed"
},
"rna_puzzle12_P5P6P7_DMS": {
"log": "",
"state": "passed"
},
"rna_puzzle5_P15P3P8_noP4P6_4RB_G208phosphate_ligation": {
"log": "",
"state": "passed"
},
"rna_puzzle5_p2_GAAA_mini": {
"log": "",
"state": "passed"
},
"rna_puzzle6_U75G76A77_on_thread1": {
"log": "",
"state": "passed"
},
"rna_puzzle6_j67_into_p6p7rigidbody_thread1": {
"log": "",
"state": "passed"
},
"rna_ribosome_tether": {
"log": "",
"state": "passed"
},
"rna_score": {
"log": "",
"state": "passed"
},
"rna_screen_phosphates": {
"log": "",
"state": "passed"
},
"rna_suitename": {
"log": "",
"state": "passed"
},
"rnp_ddg_calc_mut": {
"log": "",
"state": "passed"
},
"rnp_ddg_calc_setup": {
"log": "",
"state": "passed"
},
"rnp_ddg_calc_wt": {
"log": "",
"state": "passed"
},
"rnp_ddg_finalize": {
"log": "",
"state": "passed"
},
"rnp_ddg_relax_command_1": {
"log": "",
"state": "passed"
},
"rnp_ddg_relax_command_2": {
"log": "",
"state": "passed"
},
"rnp_ddg_relax_finalize": {
"log": "",
"state": "passed"
},
"rnp_ddg_relax_setup": {
"log": "",
"state": "passed"
},
"rollmover": {
"log": "",
"state": "passed"
},
"rosetta_scripts_hbond_options": {
"log": "",
"state": "passed"
},
"rosetta_scripts_include": {
"log": "",
"state": "passed"
},
"rosetta_scripts_info": {
"log": "",
"state": "passed"
},
"rosetta_scripts_jd3": {
"log": "",
"state": "passed"
},
"rosetta_scripts_loops": {
"log": "",
"state": "passed"
},
"rosetta_scripts_setup": {
"log": "",
"state": "passed"
},
"rosie_ligand_docking": {
"log": "",
"state": "passed"
},
"rotamer_probability": {
"log": "",
"state": "passed"
},
"rotamer_recovery": {
"log": "",
"state": "passed"
},
"rotamer_recovery_compare_two_structures": {
"log": "",
"state": "passed"
},
"rs_flexbbmoves": {
"log": "",
"state": "passed"
},
"rs_loophash": {
"log": "",
"state": "passed"
},
"sample_seq_from_probs": {
"log": "",
"state": "passed"
},
"sasa_metric_options": {
"log": "",
"state": "passed"
},
"score12_docking": {
"log": "",
"state": "passed"
},
"score_aln": {
"log": "",
"state": "passed"
},
"score_jd2": {
"log": "",
"state": "passed"
},
"score_only_silence": {
"log": "",
"state": "passed"
},
"sdf_reader": {
"log": "",
"state": "passed"
},
"secondary_structure_output": {
"log": "",
"state": "passed"
},
"seed_ensemble_JD2_JI": {
"log": "",
"state": "passed"
},
"select_best_unique_ligand_poses": {
"log": "",
"state": "passed"
},
"selected_residue_count_metric": {
"log": "",
"state": "passed"
},
"sequence_profile_constraints": {
"log": "",
"state": "passed"
},
"sequence_recovery": {
"log": "",
"state": "passed"
},
"sequence_tolerance": {
"log": "",
"state": "passed"
},
"set_torsion": {
"log": "",
"state": "passed"
},
"shobuns": {
"log": "",
"state": "passed"
},
"silent2frag": {
"log": "",
"state": "passed"
},
"sim_cryo": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_1_4_bbmb": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_angle": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_anglelength": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_beta_thioether_lariat": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_bondangle_bondlength": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_cartesian": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_cispro": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_cterm_isopeptide_lariat": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_cterm_isopeptide_lariat_tailless": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_design": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_lanthionine": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_nmethyl": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_nterm_isopeptide_lariat": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_nterm_isopeptide_lariat_tailless": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_octahedral_metal": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_peptoid": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_setting": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_sidechain_isopeptide": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_sidechain_isopeptide_reverse": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_square_planar_metal": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_square_pyramidal_metal": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_symm_gly": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_symmetric_sampling": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_tbmb": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_terminal_disulfide": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_terminal_disulfide_internal_permutations": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_terminal_disulfide_tails": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_terminal_disulfide_tails_2": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_tetrahedral_metal": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_tetrahedral_metal_asp": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_thioether_cis_sampling": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_thioether_lariat": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_tma": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_trigonal_planar_metal": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_trigonal_pyramidal_metal": {
"log": "",
"state": "passed"
},
"simple_dna_test": {
"log": "",
"state": "passed"
},
"simple_glycosylation": {
"log": "",
"state": "passed"
},
"simple_glycosylation_alternate_AAs": {
"log": "",
"state": "passed"
},
"simple_grafting_movers": {
"log": "",
"state": "passed"
},
"simple_hbondstoatom": {
"log": "",
"state": "passed"
},
"simple_metric_cache": {
"log": "",
"state": "passed"
},
"simple_metric_features": {
"log": "",
"state": "passed"
},
"simple_metric_filter": {
"log": "",
"state": "passed"
},
"simple_metrics": {
"log": "",
"state": "passed"
},
"simple_metrics_b_factor": {
"log": "",
"state": "passed"
},
"simple_metrics_in_protocols": {
"log": "",
"state": "passed"
},
"simple_metrics_per_residue": {
"log": "",
"state": "passed"
},
"site_constraint": {
"log": "",
"state": "passed"
},
"small_molecule_lattice_dock": {
"log": "",
"state": "passed"
},
"smallmover_resselector": {
"log": "",
"state": "passed"
},
"smart_annealer": {
"log": "",
"state": "passed"
},
"splice_in_4loops_longer": {
"log": "",
"state": "passed"
},
"splice_in_4loops_shorter": {
"log": "",
"state": "passed"
},
"splice_out_H1_H2_longer": {
"log": "",
"state": "passed"
},
"splice_out_H1_H2_same": {
"log": "",
"state": "passed"
},
"splice_out_H1_H2_shorter": {
"log": "",
"state": "passed"
},
"splice_out_H3_longer": {
"log": "",
"state": "passed"
},
"splice_out_H3_same": {
"log": "",
"state": "passed"
},
"splice_out_H3_shorter": {
"log": "",
"state": "passed"
},
"splice_out_L1_L2_longer": {
"log": "",
"state": "passed"
},
"splice_out_L1_L2_same": {
"log": "",
"state": "passed"
},
"splice_out_L1_L2_shorter": {
"log": "",
"state": "passed"
},
"splice_out_L3_longer": {
"log": "",
"state": "passed"
},
"splice_out_L3_same": {
"log": "",
"state": "passed"
},
"splice_out_L3_shorter": {
"log": "",
"state": "passed"
},
"startfrom_file": {
"log": "",
"state": "passed"
},
"stepwise_lores": {
"log": "",
"state": "passed"
},
"stored_residue_subset": {
"log": "",
"state": "passed"
},
"struc_set_fragment_picker": {
"log": "",
"state": "passed"
},
"super_aln": {
"log": "",
"state": "passed"
},
"supercharge": {
"log": "",
"state": "passed"
},
"surface_docking": {
"log": "",
"state": "passed"
},
"swa_protein_CCDclose": {
"log": "",
"state": "passed"
},
"swa_protein_build_at_Cterminus": {
"log": "",
"state": "passed"
},
"swa_protein_build_at_Nterminus": {
"log": "",
"state": "passed"
},
"swa_protein_cluster": {
"log": "",
"state": "passed"
},
"swa_protein_combine_loops": {
"log": "",
"state": "passed"
},
"swa_protein_loop_sampler": {
"log": "",
"state": "passed"
},
"swa_protein_prepack": {
"log": "",
"state": "passed"
},
"swa_rna_erraser": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_01_append": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_02_prepend": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_03_append_to_silent": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_04_clustering": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_05_prepend_to_5primeterminus": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_06_append_to_3primeterminus": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_07_prepend_dinucleotide": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_08_append_dinucleotide": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_09_sample_virtual_ribose": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_10_prepend_and_ccd_close": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_11_append_and_ccd_close": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_12_helix_addition": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_13_chunk_combination_and_closure": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_14_combine_long_loop_filtering": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_15_combine_long_loop_sampling": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_16_prepend_dinucleotide_on_dinucleotide": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_17_append_floating_base": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_18_rebuild_bulge": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_19_prepend_floating_base_by_jump": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_20_append_floating_base_by_jump": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_21_prepend_dinucleotide_on_dinucleotide_by_jump": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_22_prepend_and_kic_close": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_23_append_and_kic_close": {
"log": "",
"state": "passed"
},
"swa_rna_loop_clusterer": {
"log": "",
"state": "passed"
},
"swa_rna_loop_sampler": {
"log": "",
"state": "passed"
},
"sweep_respair_energies": {
"log": "",
"state": "passed"
},
"swm_add_rosettascripts": {
"log": "",
"state": "passed"
},
"swm_beta_peptide_loop": {
"log": "",
"state": "passed"
},
"swm_build_full_model": {
"log": "",
"state": "passed"
},
"swm_dna_bridge": {
"log": "",
"state": "passed"
},
"swm_dna_loop": {
"log": "",
"state": "passed"
},
"swm_general_polymer_sampler": {
"log": "",
"state": "passed"
},
"swm_l_rna": {
"log": "",
"state": "passed"
},
"swm_protein_CCDmove": {
"log": "",
"state": "passed"
},
"swm_protein_from_scratch": {
"log": "",
"state": "passed"
},
"swm_protein_loop_sampler": {
"log": "",
"state": "passed"
},
"swm_protein_move_inside_coiledcoil_by_bond": {
"log": "",
"state": "passed"
},
"swm_protein_move_inside_helix_by_bond": {
"log": "",
"state": "passed"
},
"swm_protein_preminimize": {
"log": "",
"state": "passed"
},
"swm_rna_base_pair_constraints": {
"log": "",
"state": "passed"
},
"swm_rna_checkpoint_partition": {
"log": "",
"state": "passed"
},
"swm_rna_fourwayjunction": {
"log": "",
"state": "passed"
},
"swm_rna_loop_design": {
"log": "",
"state": "passed"
},
"swm_rna_move_align_dock": {
"log": "",
"state": "passed"
},
"swm_rna_move_inside_helix_by_bond": {
"log": "",
"state": "passed"
},
"swm_rna_move_inside_helix_by_jump": {
"log": "",
"state": "passed"
},
"swm_rna_move_two_strands": {
"log": "",
"state": "passed"
},
"swm_rna_nickedhelix": {
"log": "",
"state": "passed"
},
"swm_rna_protonated_adenosine": {
"log": "",
"state": "passed"
},
"swm_rna_singleloop": {
"log": "",
"state": "passed"
},
"swm_rna_srl_triplet": {
"log": "",
"state": "passed"
},
"symm_disulfidize": {
"log": "",
"state": "passed"
},
"symm_rotamer_boltzmann": {
"log": "",
"state": "passed"
},
"symmetric_cycpep_align_and_symmetrize": {
"log": "",
"state": "passed"
},
"symmetric_docking": {
"log": "",
"state": "passed"
},
"symmetrical_residue_selector": {
"log": "",
"state": "passed"
},
"symmetry_data_resource": {
"log": "",
"state": "passed"
},
"symmetry_multicomponent": {
"log": "",
"state": "passed"
},
"target_clash": {
"log": "",
"state": "passed"
},
"task_selector": {
"log": "",
"state": "passed"
},
"tcrmodel": {
"log": "",
"state": "passed"
},
"template_features": {
"log": "",
"state": "passed"
},
"tensorflow_connection_test": {
"log": "",
"state": "passed"
},
"tensorflow_manager": {
"log": "",
"state": "passed"
},
"tensorflow_simple_model_load_and_evaluate": {
"log": "",
"state": "passed"
},
"test1_benchmark": {
"log": "",
"state": "passed"
},
"test_computed_saxs_spectrum": {
"log": "",
"state": "passed"
},
"test_d_l_readin": {
"log": "",
"state": "passed"
},
"test_degreaser": {
"log": "",
"state": "passed"
},
"test_energy_method_options": {
"log": "",
"state": "passed"
},
"test_idealize": {
"log": "",
"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": "",
"state": "passed"
},
"threefold_symm_peptide_design": {
"log": "",
"state": "passed"
},
"threefoldlinkermover_tbmb": {
"log": "",
"state": "passed"
},
"threefoldlinkermover_tbmb_symmetric": {
"log": "",
"state": "passed"
},
"tna_base_pairs": {
"log": "",
"state": "passed"
},
"torsion_restricted_sampling": {
"log": "",
"state": "passed"
},
"trRosetta": {
"log": "",
"state": "passed"
},
"trRosettaConstraintGenerator": {
"log": "",
"state": "passed"
},
"trRosettaConstraintGenerator_rosettascripts": {
"log": "",
"state": "passed"
},
"trRosettaProtocolMover": {
"log": "",
"state": "passed"
},
"trRosettaProtocolMover_rosettascripts": {
"log": "",
"state": "passed"
},
"trRosettaProtocolMover_rosettascripts_diskwrite": {
"log": "",
"state": "passed"
},
"trRosettaProtocolMover_rosettascripts_diskwrite_only": {
"log": "",
"state": "passed"
},
"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"
}
}
}