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: 544bf3d3b3beb7543bdd5633b45112f36d341418
TOOLS: b0af2521cbed1f2bde597ef1c5406efa376a6f85
DEMOS: 48c9239db73b9a8c828954d9215c983b9f144c92
ERROR: Unable to find Python2 executable -- some integration tests may fail on that basis alone.
Verifying Python /Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python_virtual_environments/python-3.9/70fb5a411fc5470c895f6d4975b66fbe/bin/python to have version 3.*...
/Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python_virtual_environments/python-3.9/70fb5a411fc5470c895f6d4975b66fbe/bin/python -c 'import sys; sys.exit(sys.version_info[0] != 3)'
Python: `/Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python_virtual_environments/python-3.9/70fb5a411fc5470c895f6d4975b66fbe/bin/python`
Python2: `PYTHON2_NOT_FOUND`
Python3: `/Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python_virtual_environments/python-3.9/70fb5a411fc5470c895f6d4975b66fbe/bin/python`
Outdir: new
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
No correct command.sh file found for trRosetta_test_predict_ubiquitin_init_by_bins. Skipping.
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
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
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 trRosetta_test_predict. 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 trRosettaProtocolMover_rosettascripts_diskwrite_only
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/trRosettaProtocolMover_rosettascripts_diskwrite_only/command.sh
No correct command.sh file found for trRosettaProtocolMover. Skipping.
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
No correct command.sh file found for trRosettaConstraintGenerator. Skipping.
No correct command.sh file found for trRosetta. Skipping.
Running Test trRosettaConstraintGenerator_rosettascripts
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/trRosettaConstraintGenerator_rosettascripts/command.sh
Running Test tna_base_pairs
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/tna_base_pairs/command.sh
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 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 test_energy_method_options
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/test_energy_method_options/command.sh
No correct command.sh file found for tensorflow_simple_model_load_and_evaluate. Skipping.
No correct command.sh file found for tensorflow_manager. Skipping.
No correct command.sh file found for tensorflow_connection_test. Skipping.
Running Test test_degreaser
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/test_degreaser/command.sh
Running Test tcrmodel
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/tcrmodel/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 swm_rna_checkpoint_partition
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_rna_checkpoint_partition/command.sh
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
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
Running Test swm_dna_loop
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_dna_loop/command.sh
Running Test swm_dna_bridge
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_dna_bridge/command.sh
No correct command.sh file found for smart_annealer. Skipping.
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 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 simple_metrics_per_residue
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_metrics_per_residue/command.sh
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
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
Running Test simple_metrics
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_metrics/command.sh
Running Test simple_metric_filter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_metric_filter/command.sh
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_metric_cache
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/simple_metric_cache/command.sh
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 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_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 trRosettaConstraintGenerator_rosettascripts in 1 seconds [~ 44 test (5.41871921182266%) started, 768 in queue, 32 running]
Finished test_energy_method_options in 1 seconds [~ 44 test (5.41871921182266%) started, 768 in queue, 31 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
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 trRosettaProtocolMover_rosettascripts in 4 seconds [~ 46 test (5.665024630541872%) started, 766 in queue, 32 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
Finished trRosettaProtocolMover_rosettascripts_diskwrite_only in 5 seconds [~ 47 test (5.788177339901478%) started, 765 in queue, 32 running]
Finished trRosettaProtocolMover_rosettascripts_diskwrite in 5 seconds [~ 47 test (5.788177339901478%) started, 765 in queue, 31 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
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 trRosetta_test_predict_ubiquitin_cst_file_write_only in 11 seconds [~ 49 test (6.0344827586206895%) started, 763 in queue, 32 running]
Finished trRosetta_test_predict_ubiquitin_cst_file_write in 11 seconds [~ 49 test (6.0344827586206895%) started, 763 in queue, 31 running]
Finished trRosetta_test_predict_ubiquitin in 11 seconds [~ 49 test (6.0344827586206895%) started, 763 in queue, 30 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
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
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
Finished tna_base_pairs in 12 seconds [~ 52 test (6.403940886699507%) started, 760 in queue, 32 running]
Finished target_clash in 12 seconds [~ 52 test (6.403940886699507%) started, 760 in queue, 31 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
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
Finished swm_add_rosettascripts in 13 seconds [~ 54 test (6.650246305418719%) started, 758 in queue, 32 running]
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
Finished swm_rna_checkpoint_partition in 17 seconds [~ 55 test (6.773399014778325%) started, 757 in queue, 32 running]
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
Finished swm_general_polymer_sampler in 21 seconds [~ 56 test (6.896551724137931%) started, 756 in queue, 32 running]
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 simple_glycosylation_alternate_AAs in 28 seconds [~ 57 test (7.019704433497537%) started, 755 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
sed: 1: "threadlocal_tracers.txt": undefined label 'hreadlocal_tracers.txt'
Finished thread_local_tracers_check in 29 seconds [~ 58 test (7.142857142857143%) started, 754 in queue, 32 running]
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 simple_cycpep_predict_thioether_lariat in 28 seconds [~ 59 test (7.266009852216749%) started, 753 in queue, 32 running]
Finished simple_cycpep_predict_terminal_disulfide in 20 seconds [~ 59 test (7.266009852216749%) started, 753 in queue, 31 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
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
Finished tcrmodel in 34 seconds [~ 61 test (7.512315270935961%) started, 751 in queue, 32 running]
Finished simple_metrics_in_protocols in 34 seconds [~ 61 test (7.512315270935961%) started, 751 in queue, 31 running]
Finished simple_cycpep_predict_terminal_disulfide_tails in 22 seconds [~ 61 test (7.512315270935961%) started, 751 in queue, 30 running]
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 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 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 simple_metric_cache in 34 seconds [~ 64 test (7.8817733990147785%) started, 748 in queue, 32 running]
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
/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 34 seconds [~ 65 test (8.004926108374384%) started, 747 in queue, 32 running]
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
Finished simple_metric_filter in 36 seconds [~ 66 test (8.12807881773399%) started, 746 in queue, 32 running]
Finished simple_cycpep_predict_sidechain_isopeptide_reverse in 15 seconds [~ 66 test (8.12807881773399%) started, 746 in queue, 31 running]
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
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 simple_cycpep_predict_terminal_disulfide_internal_permutations in 26 seconds [~ 68 test (8.374384236453203%) started, 744 in queue, 32 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
Finished small_molecule_lattice_dock in 39 seconds [~ 69 test (8.497536945812808%) started, 743 in queue, 32 running]
Running Test sasa_metric_options
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/sasa_metric_options/command.sh
Finished simple_cycpep_predict_tetrahedral_metal_asp in 34 seconds [~ 70 test (8.620689655172415%) started, 742 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 simple_metrics_b_factor in 41 seconds [~ 71 test (8.74384236453202%) started, 741 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 simple_grafting_movers in 41 seconds [~ 72 test (8.866995073891626%) started, 740 in queue, 32 running]
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 rnp_ddg_relax_setup in 0 seconds [~ 73 test (8.990147783251231%) started, 739 in queue, 32 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
PYTHON IS /Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python_virtual_environments/python-3.9/70fb5a411fc5470c895f6d4975b66fbe/bin/python
Finished rnp_ddg_relax_finalize in 0 seconds [~ 74 test (9.113300492610838%) started, 738 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 simple_cycpep_predict_sidechain_isopeptide in 13 seconds [~ 75 test (9.236453201970443%) started, 737 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 simple_cycpep_predict_lanthionine in 8 seconds [~ 76 test (9.35960591133005%) started, 736 in queue, 32 running]
Running Test rnp_ddg_finalize
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rnp_ddg_finalize/command.sh
PYTHON IS /Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python_virtual_environments/python-3.9/70fb5a411fc5470c895f6d4975b66fbe/bin/python
Finished rnp_ddg_finalize in 0 seconds [~ 77 test (9.482758620689655%) started, 735 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 simple_cycpep_predict_thioether_cis_sampling in 38 seconds [~ 78 test (9.605911330049262%) started, 734 in queue, 32 running]
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
PYTHON is /Users/benchmark/scratch/w/prefix/mac/hikaru-2/mac/python_virtual_environments/python-3.9/70fb5a411fc5470c895f6d4975b66fbe/bin/python
Finished rnp_ddg_calc_setup in 0 seconds [~ 79 test (9.729064039408867%) started, 733 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 simple_cycpep_predict_cterm_isopeptide_lariat in 9 seconds [~ 80 test (9.852216748768473%) started, 732 in queue, 32 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
Finished simple_cycpep_predict_cterm_isopeptide_lariat_tailless in 10 seconds [~ 81 test (9.975369458128078%) started, 731 in queue, 32 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
Finished simple_cycpep_predict_square_planar_metal in 27 seconds [~ 82 test (10.098522167487685%) started, 730 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 simple_cycpep_predict_nterm_isopeptide_lariat_tailless in 12 seconds [~ 83 test (10.22167487684729%) started, 729 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 simple_cycpep_predict_nterm_isopeptide_lariat in 11 seconds [~ 84 test (10.344827586206897%) started, 728 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 simple_cycpep_predict_peptoid in 18 seconds [~ 85 test (10.467980295566502%) started, 727 in queue, 32 running]
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
Finished test_degreaser in 51 seconds [~ 86 test (10.591133004926109%) started, 726 in queue, 32 running]
Finished rna_denovo_new_FT_rna_two_chains in 5 seconds [~ 86 test (10.591133004926109%) started, 726 in queue, 31 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
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 selected_residue_count_metric in 15 seconds [~ 88 test (10.83743842364532%) started, 724 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 rna_predict_chem_map in 10 seconds [~ 89 test (10.960591133004925%) started, 723 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 sample_seq_from_probs in 15 seconds [~ 90 test (11.083743842364532%) started, 722 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 simple_cycpep_predict_terminal_disulfide_tails_2 in 44 seconds [~ 91 test (11.206896551724139%) started, 721 in queue, 32 running]
No correct command.sh file found for replica_docking. Skipping.
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 rnp_ddg_relax_command_1 in 15 seconds [~ 93 test (11.45320197044335%) started, 719 in queue, 32 running]
Running Test repeat_relax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/repeat_relax/command.sh
Finished rna_denovo_new_FT_5P_j12_leadzyme in 11 seconds [~ 94 test (11.576354679802956%) started, 718 in queue, 32 running]
Running Test repeat_propagate_v3
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/repeat_propagate_v3/command.sh
Finished simple_cycpep_predict_tma in 59 seconds [~ 95 test (11.699507389162562%) started, 717 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 sasa_metric_options in 21 seconds [~ 96 test (11.822660098522167%) started, 716 in queue, 32 running]
Running Test repeat_propagate
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/repeat_propagate/command.sh
Finished simple_cycpep_predict_trigonal_planar_metal in 62 seconds [~ 97 test (11.945812807881774%) started, 715 in queue, 32 running]
No correct command.sh file found for recon_design_mpi. 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
Finished simple_cycpep_predict_1_4_bbmb in 27 seconds [~ 99 test (12.192118226600986%) started, 713 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 restype_converter in 8 seconds [~ 100 test (12.31527093596059%) started, 712 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
Finished simple_cycpep_predict_beta_thioether_lariat in 32 seconds [~ 101 test (12.438423645320198%) started, 711 in queue, 32 running]
Finished remove_duplicate_motifs in 5 seconds [~ 101 test (12.438423645320198%) started, 711 in queue, 31 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 pymol_cif
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pymol_cif/command.sh
Finished read_polymeric_components in 5 seconds [~ 103 test (12.68472906403941%) started, 709 in queue, 32 running]
No correct command.sh file found for proteinMPNN_model_perplexity. Skipping.
Running Test protocol_metric
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/protocol_metric/command.sh
Finished simple_cycpep_predict_bondangle_bondlength in 37 seconds [~ 105 test (12.931034482758621%) started, 707 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 res_lipo_ref2015_memb in 16 seconds [~ 106 test (13.054187192118226%) started, 706 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 simple_cycpep_predict_tetrahedral_metal in 62 seconds [~ 107 test (13.177339901477833%) started, 705 in queue, 32 running]
Finished simple_cycpep_predict_octahedral_metal in 40 seconds [~ 107 test (13.177339901477833%) started, 705 in queue, 31 running]
Running Test pna_base_pairs
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pna_base_pairs/command.sh
Running Test phosphorylation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/phosphorylation/command.sh
Finished pymol_cif in 6 seconds [~ 109 test (13.423645320197044%) started, 703 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 repeat_propagate_v2 in 15 seconds [~ 110 test (13.54679802955665%) started, 702 in queue, 32 running]
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 repeat_propagate_v3 in 16 seconds [~ 111 test (13.669950738916256%) started, 701 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 repeat_propagate in 16 seconds [~ 112 test (13.793103448275861%) started, 700 in queue, 32 running]
Finished per_residue_solvent_exposure in 1 seconds [~ 112 test (13.793103448275861%) started, 700 in queue, 31 running]
Running Test oligourea_predict
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/oligourea_predict/command.sh
Running Test oligourea_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/oligourea_design/command.sh
Finished rna_denovo_new_libs in 34 seconds [~ 114 test (14.039408866995075%) started, 698 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 swm_dna_loop in 80 seconds [~ 115 test (14.16256157635468%) started, 697 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 phosphorylation in 9 seconds [~ 116 test (14.285714285714286%) started, 696 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 recon_design in 19 seconds [~ 117 test (14.408866995073891%) started, 695 in queue, 32 running]
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 mutate
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mutate/command.sh
Finished rna_denovo_new_FT_2in_dens in 33 seconds [~ 123 test (15.147783251231527%) started, 689 in queue, 32 running]
Finished output_schema in 7 seconds [~ 123 test (15.147783251231527%) started, 689 in queue, 31 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 multistage_rosetta_scripts
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/multistage_rosetta_scripts/command.sh
Finished rdkit_metrics in 16 seconds [~ 125 test (15.394088669950738%) started, 687 in queue, 32 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
Finished rna_denovo_new_FT_RNP_2prot_dens in 39 seconds [~ 126 test (15.517241379310345%) started, 686 in queue, 32 running]
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 simple_metrics in 86 seconds [~ 127 test (15.64039408866995%) started, 685 in queue, 32 running]
No correct command.sh file found for mpi_simple_cycpep_predict_computing_pnear_to_all. 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.
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 simple_metrics_per_residue in 86 seconds [~ 131 test (16.133004926108374%) started, 681 in queue, 32 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
Finished protocol_metric in 17 seconds [~ 132 test (16.25615763546798%) started, 680 in queue, 32 running]
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
Finished rna_denovo_symm_hack in 43 seconds [~ 133 test (16.379310344827587%) started, 679 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 mpil_load_implicit_lipids in 3 seconds [~ 134 test (16.502463054187192%) started, 678 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 pna_base_pairs in 15 seconds [~ 135 test (16.625615763546797%) started, 677 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 mpil_find_pore_ahelical in 3 seconds [~ 136 test (16.748768472906406%) started, 676 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 mpil_find_pore_bbarrel in 4 seconds [~ 137 test (16.87192118226601%) started, 675 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 mutate in 6 seconds [~ 138 test (16.995073891625616%) started, 674 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 perturb_helical_bundle_setting in 19 seconds [~ 139 test (17.11822660098522%) started, 673 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 voids_penalty_energy_design_symmetry in 95 seconds [~ 140 test (17.24137931034483%) started, 672 in queue, 32 running]
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
Finished rosetta_scripts_jd3 in 55 seconds [~ 141 test (17.364532019704434%) started, 671 in queue, 32 running]
Running Test mhc_epitope
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mhc_epitope/command.sh
Finished oligourea_design in 19 seconds [~ 142 test (17.48768472906404%) started, 670 in queue, 32 running]
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 swm_rna_base_pair_constraints in 97 seconds [~ 143 test (17.610837438423644%) started, 669 in queue, 32 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
Finished oligourea_predict in 23 seconds [~ 144 test (17.733990147783253%) started, 668 in queue, 32 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
Finished pose_sewing in 29 seconds [~ 145 test (17.857142857142858%) started, 667 in queue, 32 running]
Finished make_mainchain_potential_symm_preproline in 5 seconds [~ 145 test (17.857142857142858%) started, 667 in queue, 31 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
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_span_ang_ref2015_memb in 16 seconds [~ 147 test (18.103448275862068%) started, 665 in queue, 32 running]
Finished make_mainchain_potential_symm in 5 seconds [~ 147 test (18.103448275862068%) started, 665 in queue, 31 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
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 mmtfIO_score_test in 12 seconds [~ 149 test (18.34975369458128%) started, 663 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 mp_quick_relax_ref2015_memb in 16 seconds [~ 150 test (18.472906403940886%) started, 662 in queue, 32 running]
Running Test iphold
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/iphold/command.sh
Finished ncbb_packer_palette in 20 seconds [~ 151 test (18.59605911330049%) started, 661 in queue, 32 running]
Running Test interface_energy
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/interface_energy/command.sh
Finished repeat_relax in 47 seconds [~ 152 test (18.7192118226601%) started, 660 in queue, 32 running]
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 mp_ligand_interface in 17 seconds [~ 153 test (18.842364532019705%) started, 659 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 rna_denovo_fragment_homology_exclusion in 52 seconds [~ 154 test (18.96551724137931%) started, 658 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 multistage_rosetta_scripts_clustering in 23 seconds [~ 155 test (19.088669950738915%) started, 657 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 rnp_ddg_calc_wt in 64 seconds [~ 156 test (19.211822660098523%) started, 656 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 simple_cycpep_predict_trigonal_pyramidal_metal in 109 seconds [~ 157 test (19.334975369458128%) started, 655 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 ligand_motif_identification in 7 seconds [~ 158 test (19.458128078817733%) started, 654 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 interface_energy in 6 seconds [~ 159 test (19.58128078817734%) started, 653 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 multistage_rosetta_scripts in 26 seconds [~ 160 test (19.704433497536947%) started, 652 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 netcharge_design_symm in 32 seconds [~ 161 test (19.82758620689655%) started, 651 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 ligand_motif_discovery in 10 seconds [~ 162 test (19.950738916256157%) started, 650 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 mhc_epitope_nmer_preload in 23 seconds [~ 163 test (20.073891625615765%) started, 649 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 make_mainchain_potential in 23 seconds [~ 164 test (20.19704433497537%) started, 648 in queue, 32 running]
Running Test glycopeptidedocking_diglyco_long
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/glycopeptidedocking_diglyco_long/command.sh
Finished swm_dna_bridge in 126 seconds [~ 165 test (20.320197044334975%) started, 647 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 mixed_monte_carlo in 32 seconds [~ 166 test (20.44334975369458%) started, 646 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 loop_grower_N_term_symm in 24 seconds [~ 167 test (20.56650246305419%) started, 645 in queue, 32 running]
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 mp_domain_assembly in 39 seconds [~ 168 test (20.689655172413794%) started, 644 in queue, 32 running]
Running Test glycan_refinment
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/glycan_refinment/command.sh
Finished voids_penalty_energy_design in 130 seconds [~ 169 test (20.8128078817734%) started, 643 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 mhc_epitope in 38 seconds [~ 170 test (20.935960591133004%) started, 642 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 iphold in 32 seconds [~ 171 test (21.059113300492612%) started, 641 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 hydrate in 29 seconds [~ 172 test (21.182266009852217%) started, 640 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 netcharge_design in 57 seconds [~ 173 test (21.305418719211822%) started, 639 in queue, 32 running]
Running Test ga_ligand_dock
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ga_ligand_dock/command.sh
Finished ligand_dock_cholesterol in 35 seconds [~ 174 test (21.428571428571427%) started, 638 in queue, 32 running]
No correct command.sh file found for features_pdb_mpi. Skipping.
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 34 seconds [~ 176 test (21.67487684729064%) started, 636 in queue, 32 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
Finished rnp_ddg_calc_mut in 96 seconds [~ 177 test (21.798029556650246%) started, 635 in queue, 32 running]
Running Test fast_relax_scripts
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fast_relax_scripts/command.sh
Finished polyaramid_test_trivial in 68 seconds [~ 178 test (21.92118226600985%) started, 634 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 mp_dock_ensemble in 53 seconds [~ 179 test (22.04433497536946%) started, 633 in queue, 32 running]
Running Test farfar_mrna
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/farfar_mrna/command.sh
Finished homodimer_fnd_ref2015_memb in 36 seconds [~ 180 test (22.167487684729064%) started, 632 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 glycan_sequon_scanner in 19 seconds [~ 181 test (22.29064039408867%) started, 631 in queue, 32 running]
Running Test exclusively_shared_jumps
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/exclusively_shared_jumps/command.sh
Finished glycan_refinment in 18 seconds [~ 182 test (22.413793103448278%) started, 630 in queue, 32 running]
No correct command.sh file found for esm_model_perplexity. Skipping.
Running Test evolution
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/evolution/command.sh
Finished rnp_ddg_relax_command_2 in 107 seconds [~ 184 test (22.660098522167488%) started, 628 in queue, 32 running]
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
Finished hbnet_energy_symm in 37 seconds [~ 185 test (22.783251231527093%) started, 627 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 rna_denovo_dna_bridge in 96 seconds [~ 186 test (22.9064039408867%) started, 626 in queue, 32 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
Finished glycan_anomers in 22 seconds [~ 187 test (23.029556650246306%) started, 625 in queue, 32 running]
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 mp_domain_assembly_FtsQ in 65 seconds [~ 188 test (23.15270935960591%) started, 624 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 exclusively_shared_jumps in 17 seconds [~ 189 test (23.275862068965516%) started, 623 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 favor_coupling_tensor in 27 seconds [~ 190 test (23.399014778325125%) started, 622 in queue, 32 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
Finished enzscore_filter_ligand in 16 seconds [~ 191 test (23.52216748768473%) started, 621 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 fold_from_loops in 30 seconds [~ 192 test (23.645320197044335%) started, 620 in queue, 32 running]
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
Finished enzscore_filter_metal_sym in 19 seconds [~ 193 test (23.76847290640394%) started, 619 in queue, 32 running]
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 enzscore_filter_metal in 18 seconds [~ 194 test (23.891625615763548%) started, 618 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 genkic_sugars in 34 seconds [~ 195 test (24.014778325123153%) started, 617 in queue, 32 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
Finished drrafter_setup_simple in 1 seconds [~ 196 test (24.137931034482758%) started, 616 in queue, 32 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
Finished rna_denovo_lariat in 120 seconds [~ 197 test (24.261083743842363%) started, 615 in queue, 32 running]
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 enzscore_filter_dimetal_sym in 20 seconds [~ 198 test (24.38423645320197%) started, 614 in queue, 32 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
Finished enzscore_filter_dimetal in 19 seconds [~ 199 test (24.507389162561577%) started, 613 in queue, 32 running]
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
Finished drrafter_setup_protein_dock in 0 seconds [~ 200 test (24.63054187192118%) started, 612 in queue, 32 running]
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
Finished drrafter_setup_build_missing in 0 seconds [~ 201 test (24.753694581280786%) started, 611 in queue, 32 running]
Running Test drrafter_setup
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/drrafter_setup/command.sh
Finished drrafter_setup in 0 seconds [~ 202 test (24.876847290640395%) started, 610 in queue, 32 running]
Running Test drrafter_run
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/drrafter_run/command.sh
Finished energy_based_clustering_alpha_aa_dihedral in 7 seconds [~ 203 test (25.0%) started, 609 in queue, 32 running]
Running Test drrafter_error_estimation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/drrafter_error_estimation/command.sh
Finished energy_based_clustering_alpha_aa_bin_analysis in 7 seconds [~ 204 test (25.123152709359605%) started, 608 in queue, 32 running]
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 energy_based_clustering_alpha_aa in 7 seconds [~ 205 test (25.246305418719214%) started, 607 in queue, 32 running]
Running Test dgdp_script
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/dgdp_script/command.sh
Finished drrafter_setup_ribosome_test in 5 seconds [~ 206 test (25.36945812807882%) started, 606 in queue, 32 running]
Running Test dgdp_aio
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/dgdp_aio/command.sh
Finished energy_based_clustering_alpha_aa_scorefile in 10 seconds [~ 207 test (25.492610837438423%) started, 605 in queue, 32 running]
Finished drrafter_setup_real_test_H_no_init in 5 seconds [~ 207 test (25.492610837438423%) started, 605 in queue, 31 running]
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
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 molfile_to_params_polymer in 88 seconds [~ 209 test (25.738916256157637%) started, 603 in queue, 32 running]
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 farfar_mrna in 34 seconds [~ 210 test (25.862068965517242%) started, 602 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 drrafter_setup_real_test_H in 5 seconds [~ 211 test (25.985221674876847%) started, 601 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 drrafter_error_estimation in 3 seconds [~ 212 test (26.108374384236452%) started, 600 in queue, 32 running]
Running Test ddG_sym
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ddG_sym/command.sh
Finished duplicate_header_guards in 10 seconds [~ 213 test (26.23152709359606%) started, 599 in queue, 32 running]
Running Test database_md5
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/database_md5/command.sh
Finished ga_ligand_dock_amino_acid in 45 seconds [~ 214 test (26.354679802955665%) started, 598 in queue, 32 running]
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 helical_bundle_predict_sequence in 75 seconds [~ 215 test (26.47783251231527%) started, 597 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 explicit_membrane in 40 seconds [~ 216 test (26.600985221674875%) started, 596 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 helical_bundle_predict_skipping_residues in 77 seconds [~ 217 test (26.724137931034484%) started, 595 in queue, 32 running]
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 evolution in 37 seconds [~ 218 test (26.84729064039409%) started, 594 in queue, 32 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
Finished enumerative_sampling in 23 seconds [~ 219 test (26.970443349753694%) started, 593 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 helical_bundle_predict in 79 seconds [~ 220 test (27.0935960591133%) started, 592 in queue, 32 running]
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
Finished farnesyl in 50 seconds [~ 221 test (27.216748768472907%) started, 591 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 hbnet_energy_rosettascripts_linear in 79 seconds [~ 222 test (27.339901477832512%) started, 590 in queue, 32 running]
Finished dihedral_constraint_generator in 16 seconds [~ 222 test (27.339901477832512%) started, 590 in queue, 31 running]
Finished design_w_custom_palette-RNA in 15 seconds [~ 222 test (27.339901477832512%) started, 590 in queue, 30 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
Running Test crosslinkermover_tma
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_tma/command.sh
Running Test crosslinkermover_thioether
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_thioether/command.sh
Finished glycomutagenesis in 67 seconds [~ 225 test (27.70935960591133%) started, 587 in queue, 32 running]
Finished dehydro_aa_patch in 15 seconds [~ 225 test (27.70935960591133%) started, 587 in queue, 31 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
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 hydrate_relax in 88 seconds [~ 227 test (27.95566502463054%) started, 585 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 design_w_custom_palette-NCAAs in 25 seconds [~ 228 test (28.07881773399015%) started, 584 in queue, 32 running]
Finished design_w_custom_palette-CAAs in 23 seconds [~ 228 test (28.07881773399015%) started, 584 in queue, 31 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
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 helical_bundle_predict_psipred in 91 seconds [~ 230 test (28.32512315270936%) started, 582 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 custom_basetype_packer_palette in 17 seconds [~ 231 test (28.448275862068964%) started, 581 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 helical_bundle_predict_psipred_with_helix_globals in 94 seconds [~ 232 test (28.571428571428573%) started, 580 in queue, 32 running]
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 hbnet_energy in 87 seconds [~ 233 test (28.694581280788178%) started, 579 in queue, 32 running]
Running Test crosslinkermover_octahedral
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_octahedral/command.sh
Finished crosslinkermover_trigonal_pyramidal_c3_symm in 22 seconds [~ 234 test (28.817733990147783%) started, 578 in queue, 32 running]
Running Test crosslinkermover_methyllanthionine
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_methyllanthionine/command.sh
Finished crosslinkermover_thioether in 17 seconds [~ 235 test (28.940886699507388%) started, 577 in queue, 32 running]
Running Test crosslinkermover_lanthionine
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crosslinkermover_lanthionine/command.sh
Finished job_definition_script_vars in 108 seconds [~ 236 test (29.064039408866996%) started, 576 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 crosslinkermover_tetrahedral_metal_asp in 17 seconds [~ 237 test (29.1871921182266%) started, 575 in queue, 32 running]
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 crosslinkermover_trigonal_planar_c3_symm in 22 seconds [~ 238 test (29.310344827586206%) started, 574 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_trigonal_pyramidal in 25 seconds [~ 239 test (29.43349753694581%) started, 573 in queue, 32 running]
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 crosslinkermover_trigonal_planar in 24 seconds [~ 240 test (29.55665024630542%) started, 572 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 glycopeptidedocking in 92 seconds [~ 241 test (29.679802955665025%) started, 571 in queue, 32 running]
Finished crosslinkermover_tetrahedral_metal in 16 seconds [~ 241 test (29.679802955665025%) started, 571 in queue, 31 running]
Running Test crankshaft_flip
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/crankshaft_flip/command.sh
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 cycpep_rdkit_metric in 36 seconds [~ 243 test (29.926108374384235%) started, 569 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 cycpep_design_pipeline in 36 seconds [~ 244 test (30.049261083743843%) started, 568 in queue, 32 running]
Running Test constraints_metric
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/constraints_metric/command.sh
Finished crosslinkermover_lanthionine in 17 seconds [~ 245 test (30.17241379310345%) started, 567 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 cycpep_rigid_body_permutation_mover in 46 seconds [~ 246 test (30.295566502463053%) started, 566 in queue, 32 running]
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
Finished crosslinkermover_methyllanthionine in 20 seconds [~ 247 test (30.41871921182266%) started, 565 in queue, 32 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
Finished create_clash-based_repack_shell in 13 seconds [~ 248 test (30.541871921182267%) started, 564 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
Finished create_sequence_motif in 16 seconds [~ 249 test (30.665024630541872%) started, 563 in queue, 32 running]
Running Test cleanAlignment
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cleanAlignment/command.sh
Finished coenzymes in 6 seconds [~ 250 test (30.788177339901477%) started, 562 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
database/citations/rosetta_citations.txt -> database/citations/rosetta_citations.original.txt
First script ran successfully.
Second script ran successfully.
Output matches expectation.
Finished code_template_tests_citations in 6 seconds [~ 251 test (30.911330049261085%) started, 561 in queue, 32 running]
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
Finished cmaes_minimizer in 8 seconds [~ 252 test (31.03448275862069%) started, 560 in queue, 32 running]
Running Test case_sensitive_filenames
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/case_sensitive_filenames/command.sh
/usr/bin/git
544bf3d3b3beb7543bdd5633b45112f36d341418
Finished case_sensitive_filenames in 0 seconds [~ 253 test (31.157635467980295%) started, 559 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 simple_cycpep_predict_square_pyramidal_metal in 226 seconds [~ 254 test (31.2807881773399%) started, 558 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 cl_complex_rescore in 6 seconds [~ 255 test (31.40394088669951%) started, 557 in queue, 32 running]
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
Finished cartesianddg in 7 seconds [~ 256 test (31.527093596059114%) started, 556 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 coarse_rna_scoring in 18 seconds [~ 257 test (31.65024630541872%) started, 555 in queue, 32 running]
No correct command.sh file found for bcl_fragment_mutate. Skipping.
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
Finished ga_ligand_dock_macrocycle in 111 seconds [~ 260 test (32.01970443349754%) started, 552 in queue, 32 running]
Running Test balancedKIC
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/balancedKIC/command.sh
Finished burial_measure_centroid in 1 seconds [~ 261 test (32.142857142857146%) started, 551 in queue, 32 running]
Running Test autosetup_metals_centroid
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/autosetup_metals_centroid/command.sh
Finished crosslinkermover_1_4_bbmb_c2_symmetry in 37 seconds [~ 262 test (32.26600985221675%) started, 550 in queue, 32 running]
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 crosslinkermover_octahedral_s2_symm in 46 seconds [~ 263 test (32.389162561576356%) started, 549 in queue, 32 running]
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
Finished design_glycans in 73 seconds [~ 264 test (32.51231527093596%) started, 548 in queue, 32 running]
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
Finished constraints_metric in 31 seconds [~ 265 test (32.635467980295566%) started, 547 in queue, 32 running]
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 crosslinkermover_tetrahedral_metal_c2_symmetry in 61 seconds [~ 266 test (32.758620689655174%) started, 546 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 crosslinkermover_square_planar_d2_symm in 57 seconds [~ 267 test (32.881773399014776%) started, 545 in queue, 32 running]
No correct command.sh file found for antibody_cc. Skipping.
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 cleanAlignment in 30 seconds [~ 269 test (33.12807881773399%) started, 543 in queue, 32 running]
No correct command.sh file found for abinitio_with_trRosetta. Skipping.
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 crankshaft_flip in 45 seconds [~ 271 test (33.3743842364532%) started, 541 in queue, 32 running]
Running Test SSElementSelector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/SSElementSelector/command.sh
Finished autosetup_metals_centroid in 15 seconds [~ 272 test (33.49753694581281%) started, 540 in queue, 32 running]
Running Test SID_rescore
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/SID_rescore/command.sh
Finished cart_min_glycans in 24 seconds [~ 273 test (33.62068965517241%) started, 539 in queue, 32 running]
Running Test SID_ERMS_prediction
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/SID_ERMS_prediction/command.sh
Finished crosslinkermover_tma_symm in 73 seconds [~ 274 test (33.74384236453202%) started, 538 in queue, 32 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
Finished SID_rescore in 8 seconds [~ 275 test (33.86699507389162%) started, 537 in queue, 32 running]
Running Test ResidueDisorder
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ResidueDisorder/command.sh
Finished crosslinkermover_tetrahedral_metal_d2_symmetry in 80 seconds [~ 276 test (33.99014778325123%) started, 536 in queue, 32 running]
No correct command.sh file found for PTMPrediction. Skipping.
Running Test PolarDesign2019
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/PolarDesign2019/command.sh
Finished ambiguous_nmr_distance_constraint in 14 seconds [~ 278 test (34.23645320197044%) started, 534 in queue, 32 running]
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 ResidueDisorder in 4 seconds [~ 279 test (34.35960591133005%) started, 533 in queue, 32 running]
Running Test InterfaceAnalyzer_metrics
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/InterfaceAnalyzer_metrics/command.sh
Finished balancedKIC in 29 seconds [~ 280 test (34.48275862068966%) started, 532 in queue, 32 running]
Running Test InterfaceAnalyzer_ligand
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/InterfaceAnalyzer_ligand/command.sh
Finished SSElementSelector in 14 seconds [~ 281 test (34.60591133004926%) started, 531 in queue, 32 running]
Finished N-terminal_acetylation in 2 seconds [~ 281 test (34.60591133004926%) started, 531 in queue, 31 running]
Running Test HDXEnergy
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/HDXEnergy/command.sh
Running Test FavorSequenceProfileMover
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/FavorSequenceProfileMover/command.sh
Finished crosslinkermover_square_planar in 76 seconds [~ 283 test (34.85221674876847%) started, 529 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 crosslinkermover_1_4_bbmb_asymm in 66 seconds [~ 284 test (34.97536945812808%) started, 528 in queue, 32 running]
Running Test DumpTrajectoryEnergy
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/DumpTrajectoryEnergy/command.sh
Finished auto-drrafter_final_results in 26 seconds [~ 285 test (35.09852216748769%) started, 527 in queue, 32 running]
Running Test DNA_methylation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/DNA_methylation/command.sh
Finished ga_ligand_dock in 144 seconds [~ 286 test (35.22167487684729%) started, 526 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 crosslinkermover_square_pyramidal in 80 seconds [~ 287 test (35.3448275862069%) started, 525 in queue, 32 running]
Running Test CCS_PARCS
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/CCS_PARCS/command.sh
Finished DNA_methylation in 3 seconds [~ 288 test (35.467980295566505%) started, 524 in queue, 32 running]
Running Test BFactorSelector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/BFactorSelector/command.sh
Finished antibody_designer_camelid in 24 seconds [~ 289 test (35.59113300492611%) started, 523 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 CCS_PARCS in 2 seconds [~ 290 test (35.714285714285715%) started, 522 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 buried_unsat_voids_hbnet_design in 40 seconds [~ 291 test (35.83743842364532%) started, 521 in queue, 32 running]
Finished InterfaceAnalyzer_ligand in 8 seconds [~ 291 test (35.83743842364532%) started, 521 in queue, 31 running]
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 autoNOE_rosetta
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/autoNOE_rosetta/command.sh
Finished glycopeptidedocking_diglyco_long in 161 seconds [~ 293 test (36.083743842364534%) started, 519 in queue, 32 running]
Running Test bundlegridsampler_composition_energy
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bundlegridsampler_composition_energy/command.sh
Finished RunSimpleMetric_b_factor_test in 25 seconds [~ 294 test (36.206896551724135%) started, 518 in queue, 32 running]
Running Test ligand_dock_ensemble
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ligand_dock_ensemble/command.sh
Finished crosslinkermover_1_4_bbmb_s2_symm in 80 seconds [~ 295 test (36.330049261083744%) started, 517 in queue, 32 running]
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
Finished FavorSequenceProfileMover in 15 seconds [~ 296 test (36.45320197044335%) started, 516 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 drrafter_run in 119 seconds [~ 297 test (36.576354679802954%) started, 515 in queue, 32 running]
Running Test glycan_tree_relax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/glycan_tree_relax/command.sh
Finished DumpTrajectoryEnergy_packing in 16 seconds [~ 298 test (36.69950738916256%) started, 514 in queue, 32 running]
Finished DumpTrajectoryEnergy in 15 seconds [~ 298 test (36.69950738916256%) started, 514 in queue, 31 running]
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 ppi_v3_suiteC
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ppi_v3_suiteC/command.sh
Finished control_flow_rs in 76 seconds [~ 300 test (36.94581280788177%) started, 512 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 InterfaceAnalyzer_metrics in 20 seconds [~ 301 test (37.06896551724138%) started, 511 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 ContactMolecularSurface in 16 seconds [~ 302 test (37.19211822660098%) started, 510 in queue, 32 running]
Running Test remodel
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/remodel/command.sh
Finished BFactorSelector in 16 seconds [~ 303 test (37.31527093596059%) started, 509 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 SID_ERMS_prediction in 36 seconds [~ 304 test (37.4384236453202%) started, 508 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 HDXEnergy in 26 seconds [~ 305 test (37.5615763546798%) started, 507 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 mm_params in 21 seconds [~ 306 test (37.68472906403941%) started, 506 in queue, 32 running]
Running Test ddG_of_mutation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ddG_of_mutation/command.sh
Finished crosslinkermover_tma in 121 seconds [~ 307 test (37.80788177339902%) started, 505 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 count_cycpep_sequences in 96 seconds [~ 308 test (37.93103448275862%) started, 504 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_sym in 138 seconds [~ 309 test (38.05418719211823%) started, 503 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 fast_relax_scripts in 183 seconds [~ 310 test (38.17733990147783%) started, 502 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 AlignPDBInfoToSequences in 45 seconds [~ 311 test (38.30049261083744%) started, 501 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 antibody_designer_xml in 85 seconds [~ 312 test (38.423645320197046%) started, 500 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 auto-drrafter_setup_run_R3 in 97 seconds [~ 313 test (38.54679802955665%) started, 499 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 crosslinkermover_octahedral in 142 seconds [~ 314 test (38.669950738916256%) started, 498 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 autoNOE_rosetta in 64 seconds [~ 315 test (38.793103448275865%) started, 497 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 swa_rna_erraser in 53 seconds [~ 316 test (38.916256157635466%) started, 496 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 PolarDesign2019 in 78 seconds [~ 317 test (39.039408866995075%) started, 495 in queue, 32 running]
Running Test app_exception_handling
ulimit -t 960 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/app_exception_handling/command.sh
Finished buried_unsat_voids_hbnet_design_symm in 125 seconds [~ 318 test (39.16256157635468%) started, 494 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 swa_protein_loop_sampler in 56 seconds [~ 319 test (39.285714285714285%) started, 493 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
Finished auto-drrafter_setup_run_R1 in 124 seconds [~ 320 test (39.40886699507389%) started, 492 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 pertmin in 63 seconds [~ 321 test (39.532019704433495%) started, 491 in queue, 32 running]
Running Test nonideal_rtmin
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/nonideal_rtmin/command.sh
Finished dna_interface_design in 83 seconds [~ 322 test (39.6551724137931%) started, 490 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 dgdp_aio in 210 seconds [~ 323 test (39.77832512315271%) started, 489 in queue, 32 running]
Finished swa_protein_combine_loops in 40 seconds [~ 323 test (39.77832512315271%) started, 489 in queue, 31 running]
Running Test remodel_disulfides
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/remodel_disulfides/command.sh
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 ccd_ends_graft_mover_rs in 152 seconds [~ 325 test (40.02463054187192%) started, 487 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 antibody_designer in 95 seconds [~ 326 test (40.14778325123153%) started, 486 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 fiber_diffraction in 71 seconds [~ 327 test (40.27093596059113%) started, 485 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 bundlegridsampler_composition_energy_fract_range in 77 seconds [~ 328 test (40.39408866995074%) started, 484 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 ppi_v3_suiteF in 101 seconds [~ 329 test (40.51724137931034%) started, 483 in queue, 32 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
Finished simple_cycpep_predict in 62 seconds [~ 330 test (40.64039408866995%) started, 482 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 composition_energy_layers in 92 seconds [~ 331 test (40.76354679802956%) started, 481 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_rna_srl_triplet in 112 seconds [~ 332 test (40.88669950738916%) started, 480 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 ppi_v3_suiteC in 121 seconds [~ 333 test (41.00985221674877%) started, 479 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 motif_dna_packer_design in 48 seconds [~ 334 test (41.13300492610838%) started, 478 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 validate_database in 113 seconds [~ 335 test (41.25615763546798%) started, 477 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 add_helix_sequence_constraints_advanced_setup in 126 seconds [~ 336 test (41.37931034482759%) started, 476 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 hotspot_hashing in 73 seconds [~ 337 test (41.50246305418719%) started, 475 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 remodel_disulfides in 40 seconds [~ 338 test (41.6256157635468%) started, 474 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 stepwise_lores in 10 seconds [~ 339 test (41.748768472906406%) started, 473 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 mp_relax_w_ligand in 135 seconds [~ 340 test (41.87192118226601%) started, 472 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 bundlegridsampler_copy_pitch in 84 seconds [~ 341 test (41.995073891625616%) started, 471 in queue, 32 running]
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
sed: 1: "/Volumes/scratch/b3.w/r ...": bad flag in substitute command: 'o'
Finished database_md5 in 254 seconds [~ 342 test (42.118226600985224%) started, 470 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 simple_cycpep_predict_anglelength in 57 seconds [~ 343 test (42.241379310344826%) started, 469 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 glycan_tree_relax in 140 seconds [~ 344 test (42.364532019704434%) started, 468 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 rna_denovo_base_pair_constraints in 71 seconds [~ 345 test (42.48768472906404%) started, 467 in queue, 32 running]
Finished mirror_symm in 53 seconds [~ 345 test (42.48768472906404%) started, 467 in queue, 31 running]
Running Test d_workflow
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/d_workflow/command.sh
Running Test test1_benchmark
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/test1_benchmark/command.sh
Finished bundlegridsampler_composition_energy in 153 seconds [~ 347 test (42.73399014778325%) started, 465 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 ligand_dock_ensemble in 151 seconds [~ 348 test (42.857142857142854%) started, 464 in queue, 32 running]
Running Test match_6cpa
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/match_6cpa/command.sh
Finished simple_cycpep_predict_angle in 53 seconds [~ 349 test (42.98029556650246%) started, 463 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 add_helix_sequence_constraints in 156 seconds [~ 350 test (43.10344827586207%) started, 462 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 dgdp_script in 266 seconds [~ 351 test (43.22660098522167%) started, 461 in queue, 32 running]
Running Test antibody_H3
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/antibody_H3/command.sh
Finished rna_puzzle12_P5P6P7_DMS in 47 seconds [~ 352 test (43.34975369458128%) started, 460 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 membrane_relax in 67 seconds [~ 353 test (43.47290640394089%) started, 459 in queue, 32 running]
Running Test cyclization
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cyclization/command.sh
Finished membrane_relax_hbond in 68 seconds [~ 354 test (43.59605911330049%) started, 458 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 coupled_moves in 105 seconds [~ 355 test (43.7192118226601%) started, 457 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 remodel in 164 seconds [~ 356 test (43.8423645320197%) started, 456 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 simple_cycpep_predict_cartesian in 64 seconds [~ 357 test (43.96551724137931%) started, 455 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 match_6cpa in 25 seconds [~ 358 test (44.08866995073892%) started, 454 in queue, 32 running]
Running Test glycosylation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/glycosylation/command.sh
Finished rs_loophash in 59 seconds [~ 359 test (44.21182266009852%) started, 453 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 splice_in_4loops_shorter in 30 seconds [~ 360 test (44.33497536945813%) started, 452 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 glycosylation in 7 seconds [~ 361 test (44.45812807881774%) started, 451 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 simple_cycpep_predict_tbmb in 45 seconds [~ 362 test (44.58128078817734%) started, 450 in queue, 32 running]
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 auto-drrafter_setup_run_R2 in 225 seconds [~ 363 test (44.70443349753695%) started, 449 in queue, 32 running]
Running Test rna_denovo
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo/command.sh
Finished fiber_diffraction_fad in 78 seconds [~ 364 test (44.827586206896555%) started, 448 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 rna_puzzle5_p2_GAAA_mini in 8 seconds [~ 365 test (44.95073891625616%) started, 447 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 simple_cycpep_predict_setting in 51 seconds [~ 366 test (45.073891625615765%) started, 446 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 rna_denovo in 12 seconds [~ 367 test (45.19704433497537%) started, 445 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 SnugDock in 83 seconds [~ 368 test (45.320197044334975%) started, 444 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 ddG_of_mutation in 184 seconds [~ 369 test (45.443349753694584%) started, 443 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 perturb_helical_bundle_copying_pitch in 50 seconds [~ 370 test (45.566502463054185%) started, 442 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 AnchorFinder in 22 seconds [~ 371 test (45.689655172413794%) started, 441 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 hbnet_asymm in 82 seconds [~ 372 test (45.8128078817734%) started, 440 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 inverse_rotamer_remodel in 72 seconds [~ 373 test (45.935960591133004%) started, 439 in queue, 32 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
Finished simple_glycosylation in 73 seconds [~ 374 test (46.05911330049261%) started, 438 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 rosetta_scripts_loops in 83 seconds [~ 375 test (46.18226600985221%) started, 437 in queue, 32 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
Finished ddG_ensemble in 104 seconds [~ 376 test (46.30541871921182%) started, 436 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 d_workflow in 72 seconds [~ 377 test (46.42857142857143%) started, 435 in queue, 32 running]
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 swa_rna_gagu_09_sample_virtual_ribose in 80 seconds [~ 378 test (46.55172413793103%) started, 434 in queue, 32 running]
Finished vip in 78 seconds [~ 378 test (46.55172413793103%) started, 434 in queue, 31 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
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 hbnet in 51 seconds [~ 380 test (46.79802955665025%) started, 432 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 LoopAnalyzer in 74 seconds [~ 381 test (46.92118226600985%) started, 431 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 ligand_water_docking in 68 seconds [~ 382 test (47.04433497536946%) started, 430 in queue, 32 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
Finished swa_protein_CCDclose in 101 seconds [~ 383 test (47.16748768472906%) started, 429 in queue, 32 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
Finished bridge_chains in 50 seconds [~ 384 test (47.29064039408867%) started, 428 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 mr_protocols in 63 seconds [~ 385 test (47.41379310344828%) started, 427 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 swa_protein_cluster in 6 seconds [~ 386 test (47.53694581280788%) started, 426 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 nonideal_rtmin in 141 seconds [~ 387 test (47.66009852216749%) started, 425 in queue, 32 running]
Running Test PDB_diagnostic
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/PDB_diagnostic/command.sh
Finished hybridization in 55 seconds [~ 388 test (47.783251231527096%) started, 424 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 relax_w_allatom_cst in 71 seconds [~ 389 test (47.9064039408867%) started, 423 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 swm_build_full_model in 13 seconds [~ 390 test (48.029556650246306%) started, 422 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 splice_in_4loops_longer in 27 seconds [~ 391 test (48.152709359605915%) started, 421 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 secondary_structure_output in 39 seconds [~ 392 test (48.275862068965516%) started, 420 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 glycan_relax in 96 seconds [~ 393 test (48.399014778325125%) started, 419 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 splice_out_L1_L2_shorter in 20 seconds [~ 394 test (48.522167487684726%) started, 418 in queue, 32 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
Finished flexpepdock in 109 seconds [~ 395 test (48.645320197044335%) started, 417 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 test1_benchmark in 97 seconds [~ 396 test (48.76847290640394%) started, 416 in queue, 32 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
Finished mp_symdock in 44 seconds [~ 397 test (48.891625615763544%) started, 415 in queue, 32 running]
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 generate_6Dloopclose in 38 seconds [~ 398 test (49.01477832512315%) started, 414 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 PDB_diagnostic in 15 seconds [~ 399 test (49.13793103448276%) started, 413 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 supercharge in 76 seconds [~ 400 test (49.26108374384236%) started, 412 in queue, 32 running]
Finished rna_puzzle5_P15P3P8_noP4P6_4RB_G208phosphate_ligation in 52 seconds [~ 400 test (49.26108374384236%) started, 412 in queue, 31 running]
Running Test hshash_utils
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hshash_utils/command.sh
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 hts_io in 59 seconds [~ 402 test (49.50738916256157%) started, 410 in queue, 32 running]
Running Test thermal_sampler
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/thermal_sampler/command.sh
Finished range_relax_w_cst in 47 seconds [~ 403 test (49.63054187192118%) started, 409 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 match_1n9l in 27 seconds [~ 404 test (49.75369458128079%) started, 408 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 splice_out_H1_H2_longer in 31 seconds [~ 405 test (49.87684729064039%) started, 407 in queue, 32 running]
Finished splice_out_H1_H2_shorter in 22 seconds [~ 405 test (49.87684729064039%) started, 407 in queue, 31 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
Running Test docking_ensemble
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/docking_ensemble/command.sh
Finished swa_protein_prepack in 58 seconds [~ 407 test (50.12315270935961%) started, 405 in queue, 32 running]
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 ligand_dock_script in 50 seconds [~ 408 test (50.24630541871921%) started, 404 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 discontinuous_sewing_hasher in 1 seconds [~ 409 test (50.36945812807882%) started, 403 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 hshash_utils in 11 seconds [~ 410 test (50.49261083743843%) started, 402 in queue, 32 running]
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 splice_out_H1_H2_same in 27 seconds [~ 411 test (50.61576354679803%) started, 401 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 ppi_v3_suiteB in 42 seconds [~ 412 test (50.73891625615764%) started, 400 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 UBQ_E2_thioester_extra_bodies in 38 seconds [~ 413 test (50.86206896551724%) started, 399 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 jd2test_mmCIFin_PDBout in 79 seconds [~ 414 test (50.98522167487685%) started, 398 in queue, 32 running]
Running Test hotspot_graft
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hotspot_graft/command.sh
Finished ligand_database_io in 57 seconds [~ 415 test (51.108374384236456%) started, 397 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 kinemage_grid_output in 29 seconds [~ 416 test (51.23152709359606%) started, 396 in queue, 32 running]
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 threefold_symm_peptide_design in 26 seconds [~ 417 test (51.354679802955665%) started, 395 in queue, 32 running]
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 jd2test_mmCIFIO in 78 seconds [~ 418 test (51.477832512315274%) started, 394 in queue, 32 running]
Finished bundlegridsampler_epsilon in 41 seconds [~ 418 test (51.477832512315274%) started, 394 in queue, 31 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
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 remodel_disulfides_rosettascripts in 55 seconds [~ 420 test (51.724137931034484%) started, 392 in queue, 32 running]
Finished sdf_reader in 45 seconds [~ 420 test (51.724137931034484%) started, 392 in queue, 31 running]
Running Test TryDisulfPermutations
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/TryDisulfPermutations/command.sh
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 mp_relax in 43 seconds [~ 422 test (51.970443349753694%) started, 390 in queue, 32 running]
Finished splice_out_L1_L2_same in 25 seconds [~ 422 test (51.970443349753694%) started, 390 in queue, 31 running]
Running Test KIC_vicinity
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/KIC_vicinity/command.sh
Running Test task_selector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/task_selector/command.sh
Finished thermal_sampler in 19 seconds [~ 424 test (52.216748768472904%) started, 388 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 enzdes in 40 seconds [~ 425 test (52.33990147783251%) started, 387 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 rna_denovo_RNP_low_res in 36 seconds [~ 426 test (52.46305418719212%) started, 386 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 symm_disulfidize in 50 seconds [~ 427 test (52.58620689655172%) started, 385 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 dock_with_hotspot_place_simultaneously in 27 seconds [~ 428 test (52.70935960591133%) started, 384 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 rna_puzzle11_H2H3H4_run3_connectU40 in 22 seconds [~ 429 test (52.83251231527094%) started, 383 in queue, 32 running]
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 ppi_v3_suiteE in 36 seconds [~ 430 test (52.95566502463054%) started, 382 in queue, 32 running]
Running Test hbs_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hbs_design/command.sh
Finished genkic_rama_filter in 17 seconds [~ 431 test (53.07881773399015%) started, 381 in queue, 32 running]
Running Test bundlereporter_filter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bundlereporter_filter/command.sh
Finished remodel_helical_repeat in 47 seconds [~ 432 test (53.20197044334975%) started, 380 in queue, 32 running]
Running Test AnchoredDesign
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/AnchoredDesign/command.sh
Finished swm_rna_move_inside_helix_by_jump in 30 seconds [~ 433 test (53.32512315270936%) started, 379 in queue, 32 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
Finished batch_relax in 52 seconds [~ 434 test (53.44827586206897%) started, 378 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 fast_relax in 55 seconds [~ 435 test (53.57142857142857%) started, 377 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 ppi_v3_suiteA in 36 seconds [~ 436 test (53.69458128078818%) started, 376 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 KIC_with_fragments in 47 seconds [~ 437 test (53.81773399014779%) started, 375 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 swm_beta_peptide_loop in 24 seconds [~ 438 test (53.94088669950739%) started, 374 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 KIC_vicinity in 25 seconds [~ 439 test (54.064039408866996%) started, 373 in queue, 32 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
Finished simple_cycpep_predict_cispro in 26 seconds [~ 440 test (54.1871921182266%) started, 372 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 task_selector in 32 seconds [~ 441 test (54.310344827586206%) started, 371 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 disulfidize_beta_cys in 42 seconds [~ 442 test (54.433497536945815%) started, 370 in queue, 32 running]
Finished rna_denovo_RNP_refine_native in 36 seconds [~ 442 test (54.433497536945815%) started, 370 in queue, 31 running]
Running Test peptiderive
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/peptiderive/command.sh
Running Test oop_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/oop_design/command.sh
Finished mp_find_interface in 41 seconds [~ 444 test (54.679802955665025%) started, 368 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 [~ 445 test (54.80295566502463%) started, 367 in queue, 32 running]
Running Test dock_glycans
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/dock_glycans/command.sh
Finished splice_out_L1_L2_longer in 28 seconds [~ 446 test (54.926108374384235%) started, 366 in queue, 32 running]
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 TryDisulfPermutations in 41 seconds [~ 447 test (55.04926108374384%) started, 365 in queue, 32 running]
Running Test backrub_pilot
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/backrub_pilot/command.sh
Finished zinc_heterodimer in 45 seconds [~ 448 test (55.172413793103445%) started, 364 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 docking_site_constraints in 35 seconds [~ 449 test (55.29556650246305%) started, 363 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 swm_l_rna in 52 seconds [~ 450 test (55.41871921182266%) started, 362 in queue, 32 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
Finished ligand_dock_7cpa in 29 seconds [~ 451 test (55.54187192118226%) started, 361 in queue, 32 running]
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 pmut_scan in 55 seconds [~ 452 test (55.66502463054187%) started, 360 in queue, 32 running]
Finished docking_local_refine in 47 seconds [~ 452 test (55.66502463054187%) started, 360 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 rna_denovo_bps
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_denovo_bps/command.sh
Finished AlterSpecDisruption in 64 seconds [~ 454 test (55.91133004926108%) started, 358 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 rotamer_probability in 33 seconds [~ 455 test (56.03448275862069%) started, 357 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 simple_cycpep_predict_symm_gly in 27 seconds [~ 456 test (56.1576354679803%) started, 356 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 rna_farfar_block_stack in 33 seconds [~ 457 test (56.2807881773399%) started, 355 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 simple_cycpep_predict_design in 23 seconds [~ 458 test (56.40394088669951%) started, 354 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 swm_rna_singleloop in 29 seconds [~ 459 test (56.52709359605911%) started, 353 in queue, 32 running]
Running Test hbonds_sp2
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hbonds_sp2/command.sh
Finished ppi_v3_suiteG in 30 seconds [~ 460 test (56.65024630541872%) started, 352 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 swa_protein_build_at_Nterminus in 30 seconds [~ 461 test (56.77339901477833%) started, 351 in queue, 32 running]
Running Test fixbb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fixbb/command.sh
Finished ppi_v3_suiteD in 30 seconds [~ 462 test (56.89655172413793%) started, 350 in queue, 32 running]
Running Test entropy_correction
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/entropy_correction/command.sh
Finished rna_denovo_bps in 6 seconds [~ 463 test (57.01970443349754%) started, 349 in queue, 32 running]
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 AnchoredDesign in 34 seconds [~ 464 test (57.142857142857146%) started, 348 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
Finished rs_flexbbmoves in 29 seconds [~ 465 test (57.26600985221675%) started, 347 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 swm_protein_loop_sampler in 24 seconds [~ 466 test (57.389162561576356%) started, 346 in queue, 32 running]
Finished simple_cycpep_predict_symmetric_sampling in 12 seconds [~ 466 test (57.389162561576356%) started, 346 in queue, 31 running]
Running Test rna_assemble
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_assemble/command.sh
Running Test place_simultaneously
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/place_simultaneously/command.sh
Finished hbs_design in 42 seconds [~ 468 test (57.635467980295566%) started, 344 in queue, 32 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
Finished bundlereporter_filter in 41 seconds [~ 469 test (57.758620689655174%) started, 343 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 bundlegridsampler in 34 seconds [~ 470 test (57.881773399014776%) started, 342 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 beta_strand_homodimer in 61 seconds [~ 471 test (58.004926108374384%) started, 341 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 cyclization in 172 seconds [~ 472 test (58.12807881773399%) started, 340 in queue, 32 running]
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 antibody_H3 in 184 seconds [~ 473 test (58.251231527093594%) started, 339 in queue, 32 running]
Running Test membrane_abinitio
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/membrane_abinitio/command.sh
Finished docking_ensemble in 82 seconds [~ 474 test (58.3743842364532%) started, 338 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 bundlegridsampler_design_nstruct_mode in 31 seconds [~ 475 test (58.49753694581281%) started, 337 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 KIC_refine in 27 seconds [~ 476 test (58.62068965517241%) started, 336 in queue, 32 running]
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 rotamer_recovery in 14 seconds [~ 477 test (58.74384236453202%) started, 335 in queue, 32 running]
Running Test pepspec
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pepspec/command.sh
Finished hbonds_sp2 in 21 seconds [~ 478 test (58.86699507389162%) started, 334 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 oop_design in 37 seconds [~ 479 test (58.99014778325123%) started, 333 in queue, 32 running]
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 Enzrevert_xml in 29 seconds [~ 480 test (59.11330049261084%) started, 332 in queue, 32 running]
Running Test bin_initialization
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bin_initialization/command.sh
Finished rna_assemble in 14 seconds [~ 481 test (59.23645320197044%) started, 331 in queue, 32 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
Finished backrub_interface_ddG in 25 seconds [~ 482 test (59.35960591133005%) started, 330 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 dock_glycans in 35 seconds [~ 483 test (59.48275862068966%) started, 329 in queue, 32 running]
Finished inv_kin_lig_loop_design in 23 seconds [~ 483 test (59.48275862068966%) started, 329 in queue, 31 running]
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 rosetta_scripts_include
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rosetta_scripts_include/command.sh
Finished kinematic_looprelax in 36 seconds [~ 485 test (59.72906403940887%) started, 327 in queue, 32 running]
Finished backrub_pilot in 32 seconds [~ 485 test (59.72906403940887%) started, 327 in queue, 31 running]
Running Test rna_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_design/command.sh
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 hbonds in 23 seconds [~ 487 test (59.97536945812808%) started, 325 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 rosie_ligand_docking in 28 seconds [~ 488 test (60.09852216748769%) started, 324 in queue, 32 running]
Finished simple_hbondstoatom in 27 seconds [~ 488 test (60.09852216748769%) started, 324 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 mf_fixbb_des
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mf_fixbb_des/command.sh
Finished cycpep_symmetry_filter in 30 seconds [~ 490 test (60.3448275862069%) started, 322 in queue, 32 running]
Running Test match_xml
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/match_xml/command.sh
Finished features in 31 seconds [~ 491 test (60.467980295566505%) started, 321 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 bundlegridsampler_z1_offset in 25 seconds [~ 492 test (60.59113300492611%) started, 320 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 bundlegridsampler_z0_offset in 25 seconds [~ 493 test (60.714285714285715%) started, 319 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 place_simultaneously in 25 seconds [~ 494 test (60.83743842364532%) started, 318 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 splice_out_H3_same in 20 seconds [~ 495 test (60.960591133004925%) started, 317 in queue, 32 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
Finished swm_rna_protonated_adenosine in 14 seconds [~ 496 test (61.083743842364534%) started, 316 in queue, 32 running]
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 membrane_abinitio in 22 seconds [~ 497 test (61.206896551724135%) started, 315 in queue, 32 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
Finished doug_dock_design_min_mod2_cal_cal in 28 seconds [~ 498 test (61.330049261083744%) started, 314 in queue, 32 running]
Finished swm_rna_nickedhelix in 11 seconds [~ 498 test (61.330049261083744%) started, 314 in queue, 31 running]
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
Running Test fuzzy
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fuzzy/command.sh
Finished docking_full_protocol in 28 seconds [~ 500 test (61.576354679802954%) started, 312 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 rna_design in 15 seconds [~ 501 test (61.69950738916256%) started, 311 in queue, 32 running]
Running Test bundlegridsampler_multirepeat
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bundlegridsampler_multirepeat/command.sh
Finished swm_protein_move_inside_helix_by_bond in 17 seconds [~ 502 test (61.82266009852217%) started, 310 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 next_generation_KIC in 47 seconds [~ 503 test (61.94581280788177%) started, 309 in queue, 32 running]
Running Test score12_docking
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/score12_docking/command.sh
Finished entropy_correction in 41 seconds [~ 504 test (62.06896551724138%) started, 308 in queue, 32 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
Finished pepspec in 23 seconds [~ 505 test (62.19211822660098%) started, 307 in queue, 32 running]
Running Test pocket_relax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pocket_relax/command.sh
Finished symm_rotamer_boltzmann in 33 seconds [~ 506 test (62.31527093596059%) started, 306 in queue, 32 running]
Finished loop_modeling in 23 seconds [~ 506 test (62.31527093596059%) started, 306 in queue, 31 running]
Running Test mp_dock
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_dock/command.sh
Running Test bundlegridsampler_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bundlegridsampler_design/command.sh
Finished fixbb in 43 seconds [~ 508 test (62.5615763546798%) started, 304 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 bin_initialization in 24 seconds [~ 509 test (62.68472906403941%) started, 303 in queue, 32 running]
Running Test LayerDesign
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/LayerDesign/command.sh
Finished UBQ_E2_thioester in 36 seconds [~ 510 test (62.80788177339902%) started, 302 in queue, 32 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
Finished ligand_motif_design in 25 seconds [~ 511 test (62.93103448275862%) started, 301 in queue, 32 running]
Finished mf_fixbb_des in 21 seconds [~ 511 test (62.93103448275862%) started, 301 in queue, 31 running]
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 jd2test_PDBin_mmCIFout
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/jd2test_PDBin_mmCIFout/command.sh
Finished splice_out_L3_same in 27 seconds [~ 513 test (63.17733990147783%) started, 299 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 torsion_restricted_sampling in 25 seconds [~ 514 test (63.30049261083744%) started, 298 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 match_xml in 20 seconds [~ 515 test (63.423645320197046%) started, 297 in queue, 32 running]
Finished swa_rna_gagu_15_combine_long_loop_sampling in 15 seconds [~ 515 test (63.423645320197046%) started, 297 in queue, 31 running]
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 LayerSelector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/LayerSelector/command.sh
Finished sequence_profile_constraints in 25 seconds [~ 517 test (63.669950738916256%) started, 295 in queue, 32 running]
Running Test FloppyTail
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/FloppyTail/command.sh
Finished rosetta_scripts_include in 27 seconds [~ 518 test (63.793103448275865%) started, 294 in queue, 32 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
Finished perturb_helical_bundle in 27 seconds [~ 519 test (63.916256157635466%) started, 293 in queue, 32 running]
Finished helical_bundle_nonideal in 26 seconds [~ 519 test (63.916256157635466%) started, 293 in queue, 31 running]
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
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 splice_out_H3_shorter in 18 seconds [~ 521 test (64.16256157635468%) started, 291 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 readin_dna_rna_protein in 16 seconds [~ 522 test (64.28571428571429%) started, 290 in queue, 32 running]
Running Test posttranslationalmod_io
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/posttranslationalmod_io/command.sh
Finished genkic_lowmemory_mode in 27 seconds [~ 523 test (64.4088669950739%) started, 289 in queue, 32 running]
Finished fuzzy in 18 seconds [~ 523 test (64.4088669950739%) started, 289 in queue, 31 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 cluster_alns
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cluster_alns/command.sh
Finished docking_distance_constraints in 37 seconds [~ 525 test (64.65517241379311%) started, 287 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 mp_dock in 13 seconds [~ 526 test (64.77832512315271%) started, 286 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 flexpepdock_abinitio in 30 seconds [~ 527 test (64.90147783251231%) started, 285 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 ThreadingInputter in 20 seconds [~ 528 test (65.02463054187191%) started, 284 in queue, 32 running]
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 residue_energy_breakdown in 24 seconds [~ 529 test (65.14778325123153%) started, 283 in queue, 32 running]
Running Test mf_flexbb_sc
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mf_flexbb_sc/command.sh
Finished bundlegridsampler_multirepeat in 21 seconds [~ 530 test (65.27093596059113%) started, 282 in queue, 32 running]
Finished swm_rna_loop_design in 9 seconds [~ 530 test (65.27093596059113%) started, 282 in queue, 31 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
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 rosetta_scripts_setup in 17 seconds [~ 532 test (65.51724137931035%) started, 280 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 features_parallel in 33 seconds [~ 533 test (65.64039408866995%) started, 279 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 rna_puzzle6_j67_into_p6p7rigidbody_thread1 in 12 seconds [~ 534 test (65.76354679802955%) started, 278 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
Finished LayerDesign in 19 seconds [~ 535 test (65.88669950738917%) started, 277 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 swa_protein_build_at_Cterminus in 19 seconds [~ 536 test (66.00985221674877%) started, 276 in queue, 32 running]
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 FloppyTail in 16 seconds [~ 537 test (66.13300492610837%) started, 275 in queue, 32 running]
Running Test AnchoredPDBCreator
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/AnchoredPDBCreator/command.sh
Finished swm_rna_fourwayjunction in 15 seconds [~ 538 test (66.25615763546799%) started, 274 in queue, 32 running]
Finished continuous_sewing_hasher in 1 seconds [~ 538 test (66.25615763546799%) started, 274 in queue, 31 running]
Running Test threefoldlinkermover_tbmb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/threefoldlinkermover_tbmb/command.sh
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 threefoldlinkermover_tbmb_symmetric in 16 seconds [~ 540 test (66.50246305418719%) started, 272 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 score12_docking in 25 seconds [~ 541 test (66.6256157635468%) started, 271 in queue, 32 running]
Finished bundlegridsampler_design in 23 seconds [~ 541 test (66.6256157635468%) started, 271 in queue, 31 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
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 add_constraints_to_current_conformation in 20 seconds [~ 543 test (66.87192118226601%) started, 269 in queue, 32 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 LayerSelector in 21 seconds [~ 544 test (66.99507389162562%) started, 268 in queue, 32 running]
Running Test ppk
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ppk/command.sh
Finished cluster_alns in 15 seconds [~ 545 test (67.11822660098522%) started, 267 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 jd2test_PDBin_mmCIFout_extra_data_separate in 23 seconds [~ 546 test (67.24137931034483%) started, 266 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 pocket_relax in 26 seconds [~ 547 test (67.36453201970443%) started, 265 in queue, 32 running]
Finished jd2test_PDBin_mmCIFout in 24 seconds [~ 547 test (67.36453201970443%) started, 265 in queue, 31 running]
Finished jd2test_PDBIO in 23 seconds [~ 547 test (67.36453201970443%) started, 265 in queue, 30 running]
Running Test rollmover
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rollmover/command.sh
Running Test oop_dock_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/oop_dock_design/command.sh
Running Test metalloprotein_abrelax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/metalloprotein_abrelax/command.sh
Finished UBQ_Gp_LYX-Cterm in 27 seconds [~ 550 test (67.73399014778325%) started, 262 in queue, 32 running]
Finished density_refine in 24 seconds [~ 550 test (67.73399014778325%) started, 262 in queue, 31 running]
Running Test backbonegridsampler_nstruct_mode
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/backbonegridsampler_nstruct_mode/command.sh
Running Test backbonegridsampler_multiresidue
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/backbonegridsampler_multiresidue/command.sh
Finished posttranslationalmod_io in 19 seconds [~ 552 test (67.98029556650246%) started, 260 in queue, 32 running]
Running Test LayerDesign_symm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/LayerDesign_symm/command.sh
Finished motif_score_filter in 21 seconds [~ 553 test (68.10344827586206%) started, 259 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 mf_flexbb_sc in 16 seconds [~ 554 test (68.22660098522168%) started, 258 in queue, 32 running]
Running Test startfrom_file
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/startfrom_file/command.sh
Finished molfile_to_params in 14 seconds [~ 555 test (68.34975369458128%) started, 257 in queue, 32 running]
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 antibody_graft in 19 seconds [~ 556 test (68.47290640394088%) started, 256 in queue, 32 running]
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
Finished simple_dna_test in 17 seconds [~ 557 test (68.5960591133005%) started, 255 in queue, 32 running]
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 swa_rna_gagu_13_chunk_combination_and_closure in 14 seconds [~ 558 test (68.7192118226601%) started, 254 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 splice_out_H3_longer in 46 seconds [~ 559 test (68.8423645320197%) started, 253 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 UBQ_Gp_CYD-CYD in 21 seconds [~ 560 test (68.96551724137932%) started, 252 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 sequence_recovery in 15 seconds [~ 561 test (69.08866995073892%) started, 251 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 score_only_silence in 22 seconds [~ 562 test (69.21182266009852%) started, 250 in queue, 32 running]
Finished threefoldlinkermover_tbmb in 16 seconds [~ 562 test (69.21182266009852%) started, 250 in queue, 31 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
Running Test broker
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/broker/command.sh
Finished genkic_bin_perturbing in 15 seconds [~ 564 test (69.45812807881774%) started, 248 in queue, 32 running]
Running Test bin_perturbation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/bin_perturbation/command.sh
Finished symmetric_cycpep_align_and_symmetrize in 16 seconds [~ 565 test (69.58128078817734%) started, 247 in queue, 32 running]
Running Test RBOut
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/RBOut/command.sh
Finished mp_symmetry_load in 14 seconds [~ 566 test (69.70443349753694%) started, 246 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 ReadResfile_with_selector in 19 seconds [~ 567 test (69.82758620689656%) started, 245 in queue, 32 running]
Finished oop_dock_design in 14 seconds [~ 567 test (69.82758620689656%) started, 245 in queue, 31 running]
Running Test symmetrical_residue_selector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/symmetrical_residue_selector/command.sh
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 AnchoredPDBCreator in 19 seconds [~ 569 test (70.07389162561576%) started, 243 in queue, 32 running]
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
Finished simple_cycpep_predict_nmethyl in 9 seconds [~ 570 test (70.19704433497537%) started, 242 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 centroid_from_fullatom in 22 seconds [~ 571 test (70.32019704433498%) started, 241 in queue, 32 running]
Finished ppk in 18 seconds [~ 571 test (70.32019704433498%) started, 241 in queue, 31 running]
Running Test smallmover_resselector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/smallmover_resselector/command.sh
Running Test rna_motif
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_motif/command.sh
Finished metalloprotein_abrelax in 17 seconds [~ 573 test (70.56650246305419%) started, 239 in queue, 32 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
Finished swm_rna_move_inside_helix_by_bond in 12 seconds [~ 574 test (70.6896551724138%) started, 238 in queue, 32 running]
Running Test rama_mutation_selector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rama_mutation_selector/command.sh
Finished backbonegridsampler_multiresidue in 18 seconds [~ 575 test (70.8128078817734%) started, 237 in queue, 32 running]
Finished LayerDesign_symm in 17 seconds [~ 575 test (70.8128078817734%) started, 237 in queue, 31 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
Running Test min_pack_min
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/min_pack_min/command.sh
Finished backbonegridsampler_nstruct_mode in 18 seconds [~ 577 test (71.05911330049261%) started, 235 in queue, 32 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
Finished rollmover in 19 seconds [~ 578 test (71.18226600985221%) started, 234 in queue, 32 running]
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 ligand_dock_grid in 20 seconds [~ 579 test (71.30541871921183%) started, 233 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 splice_out_L3_shorter in 23 seconds [~ 580 test (71.42857142857143%) started, 232 in queue, 32 running]
Running Test UnsatSelector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/UnsatSelector/command.sh
Finished splice_out_L3_longer in 32 seconds [~ 581 test (71.55172413793103%) started, 231 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 mp_mutate_relax in 12 seconds [~ 582 test (71.67487684729063%) started, 230 in queue, 32 running]
Running Test symmetric_docking
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/symmetric_docking/command.sh
Finished perturb_helical_bundle_z_offset in 17 seconds [~ 583 test (71.79802955665025%) started, 229 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 startfrom_file in 19 seconds [~ 584 test (71.92118226600985%) started, 228 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 perturb_helical_bundle_epsilon in 17 seconds [~ 585 test (72.04433497536945%) started, 227 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 rna_motif in 9 seconds [~ 586 test (72.16748768472907%) started, 226 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 fold_cst_new in 14 seconds [~ 587 test (72.29064039408867%) started, 225 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 symmetrical_residue_selector in 13 seconds [~ 588 test (72.41379310344827%) started, 224 in queue, 32 running]
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 bin_perturbation in 16 seconds [~ 589 test (72.53694581280789%) started, 223 in queue, 32 running]
Running Test grid_scores_features
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/grid_scores_features/command.sh
Finished swa_rna_gagu_18_rebuild_bulge in 13 seconds [~ 590 test (72.66009852216749%) started, 222 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 RBOut in 16 seconds [~ 591 test (72.78325123152709%) started, 221 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 swm_protein_move_inside_coiledcoil_by_bond in 15 seconds [~ 592 test (72.9064039408867%) started, 220 in queue, 32 running]
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
Finished swa_rna_gagu_10_prepend_and_ccd_close in 14 seconds [~ 593 test (73.0295566502463%) started, 219 in queue, 32 running]
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
Finished mp_range_relax in 11 seconds [~ 594 test (73.15270935960591%) started, 218 in queue, 32 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
Finished metropolis_hastings in 20 seconds [~ 595 test (73.27586206896552%) started, 217 in queue, 32 running]
Running Test mp_score_jd2
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_score_jd2/command.sh
Finished broker in 20 seconds [~ 596 test (73.39901477832512%) started, 216 in queue, 32 running]
Running Test mp_mutate_repack
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_mutate_repack/command.sh
Finished smallmover_resselector in 15 seconds [~ 597 test (73.52216748768473%) started, 215 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 peptiderive in 120 seconds [~ 598 test (73.64532019704434%) started, 214 in queue, 32 running]
Finished minimize_with_elec_dens in 23 seconds [~ 598 test (73.64532019704434%) started, 214 in queue, 31 running]
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 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 rama_mutation_selector in 16 seconds [~ 600 test (73.89162561576354%) started, 212 in queue, 32 running]
Running Test classic_relax_1a19
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/classic_relax_1a19/command.sh
Finished repack_with_elec_dens in 18 seconds [~ 601 test (74.01477832512315%) started, 211 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 genkic_ramaprepro_sampling in 16 seconds [~ 602 test (74.13793103448276%) started, 210 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 mp_vis_emb in 6 seconds [~ 603 test (74.26108374384236%) started, 209 in queue, 32 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
Finished mp_score_jd2 in 6 seconds [~ 604 test (74.38423645320196%) started, 208 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 ddG_scan in 18 seconds [~ 605 test (74.50738916256158%) started, 207 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 min_pack_min in 19 seconds [~ 606 test (74.63054187192118%) started, 206 in queue, 32 running]
Finished UnsatSelector in 17 seconds [~ 606 test (74.63054187192118%) started, 206 in queue, 31 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
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 symmetry_multicomponent in 25 seconds [~ 608 test (74.8768472906404%) started, 204 in queue, 32 running]
Finished swm_protein_CCDmove in 14 seconds [~ 608 test (74.8768472906404%) started, 204 in queue, 31 running]
Running Test surface_docking
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/surface_docking/command.sh
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 swa_rna_gagu_23_append_and_kic_close in 14 seconds [~ 610 test (75.1231527093596%) started, 202 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 PeptideCyclizeMover in 18 seconds [~ 611 test (75.24630541871922%) started, 201 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
Finished symmetric_docking in 18 seconds [~ 612 test (75.36945812807882%) started, 200 in queue, 32 running]
Running Test loop_creation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/loop_creation/command.sh
Finished mf_fixbb_sc in 14 seconds [~ 613 test (75.49261083743842%) started, 199 in queue, 32 running]
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
Finished rna_farfar_syn_chi_res in 15 seconds [~ 614 test (75.61576354679804%) started, 198 in queue, 32 running]
Running Test jscore
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/jscore/command.sh
Finished favor_native_residue in 31 seconds [~ 615 test (75.73891625615764%) started, 197 in queue, 32 running]
Finished mp_mutate_repack in 11 seconds [~ 615 test (75.73891625615764%) started, 197 in queue, 31 running]
Finished DARC_sampling_on_the_fly in 6 seconds [~ 615 test (75.73891625615764%) started, 197 in queue, 30 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 density_refine_symm
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/density_refine_symm/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
Finished swa_rna_gagu_11_append_and_ccd_close in 13 seconds [~ 618 test (76.10837438423646%) started, 194 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 DARC_make_ray_files in 6 seconds [~ 619 test (76.23152709359606%) started, 193 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 make_rot_lib in 16 seconds [~ 620 test (76.35467980295566%) started, 192 in queue, 32 running]
Running Test broker_membrane
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/broker_membrane/command.sh
Finished grid_scores_features in 16 seconds [~ 621 test (76.47783251231527%) started, 191 in queue, 32 running]
Running Test InterfaceDdG
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/InterfaceDdG/command.sh
Finished helix_from_sequence in 12 seconds [~ 622 test (76.60098522167488%) started, 190 in queue, 32 running]
Running Test zinc_homodimer_design
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/zinc_homodimer_design/command.sh
Finished metal_setup in 13 seconds [~ 623 test (76.72413793103448%) started, 189 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 rna_denovo_base_pair_setup in 17 seconds [~ 624 test (76.84729064039409%) started, 188 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 density_denovo in 20 seconds [~ 625 test (76.9704433497537%) started, 187 in queue, 32 running]
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 cluster in 6 seconds [~ 626 test (77.0935960591133%) started, 186 in queue, 32 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
Finished jscore in 8 seconds [~ 627 test (77.21674876847291%) started, 185 in queue, 32 running]
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 backrub in 64 seconds [~ 628 test (77.33990147783251%) started, 184 in queue, 32 running]
Running Test cluster_filter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cluster_filter/command.sh
Finished buried_area_filter in 14 seconds [~ 629 test (77.46305418719211%) started, 183 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 surface_docking in 12 seconds [~ 630 test (77.58620689655173%) started, 182 in queue, 32 running]
Running Test abinitio
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/abinitio/command.sh
Finished carbohydrates in 23 seconds [~ 631 test (77.70935960591133%) started, 181 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_H3_camelid in 64 seconds [~ 632 test (77.83251231527093%) started, 180 in queue, 32 running]
Running Test StrandHelixGeometryFilter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/StrandHelixGeometryFilter/command.sh
Finished swa_rna_gagu_22_prepend_and_kic_close in 14 seconds [~ 633 test (77.95566502463055%) started, 179 in queue, 32 running]
Running Test StrandCurvatureByLevels
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/StrandCurvatureByLevels/command.sh
Finished classic_relax_1a19 in 18 seconds [~ 634 test (78.07881773399015%) started, 178 in queue, 32 running]
Finished stored_residue_subset in 14 seconds [~ 634 test (78.07881773399015%) started, 178 in queue, 31 running]
Running Test HelixBendFilter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/HelixBendFilter/command.sh
Running Test zinc_homodimer_setup
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/zinc_homodimer_setup/command.sh
Finished swa_rna_gagu_16_prepend_dinucleotide_on_dinucleotide in 15 seconds [~ 636 test (78.32512315270937%) started, 176 in queue, 32 running]
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
Finished write_mol_file in 16 seconds [~ 637 test (78.44827586206897%) started, 175 in queue, 32 running]
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 ConsensusLoopDesign in 16 seconds [~ 638 test (78.57142857142857%) started, 174 in queue, 32 running]
Running Test set_torsion
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/set_torsion/command.sh
Finished longest_continuous_polar_segment_filter in 13 seconds [~ 639 test (78.69458128078817%) started, 173 in queue, 32 running]
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
Finished broker_membrane in 11 seconds [~ 640 test (78.81773399014779%) started, 172 in queue, 32 running]
Running Test referencepose_mutateresidue
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/referencepose_mutateresidue/command.sh
Finished cluster_filter in 5 seconds [~ 641 test (78.94088669950739%) started, 171 in queue, 32 running]
Running Test recces_turner
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/recces_turner/command.sh
Finished resource_database_locator in 16 seconds [~ 642 test (79.06403940886699%) started, 170 in queue, 32 running]
Finished swa_rna_gagu_14_combine_long_loop_filtering in 3 seconds [~ 642 test (79.06403940886699%) started, 170 in queue, 31 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
Finished copy_rotamer_mover in 13 seconds [~ 644 test (79.3103448275862%) started, 168 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 loop_creation in 16 seconds [~ 645 test (79.43349753694581%) started, 167 in queue, 32 running]
Finished rosetta_scripts_hbond_options in 18 seconds [~ 646 test (79.55665024630542%) started, 166 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 make_symmdef_file in 37 seconds [~ 647 test (79.67980295566502%) started, 165 in queue, 32 running]
Running Test helical_bundle
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/helical_bundle/command.sh
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 density_refine_symm in 14 seconds [~ 648 test (79.80295566502463%) started, 164 in queue, 32 running]
Running Test features_pdb
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/features_pdb/command.sh
Finished genkic_dihedral_copying in 15 seconds [~ 649 test (79.92610837438424%) started, 163 in queue, 32 running]
Running Test cst_info
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cst_info/command.sh
Finished mp_transform_optimize in 9 seconds [~ 650 test (80.04926108374384%) started, 162 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 database_session_resource in 16 seconds [~ 651 test (80.17241379310344%) started, 161 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 gen_apo_grids in 10 seconds [~ 652 test (80.29556650246306%) started, 160 in queue, 32 running]
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
Finished InterfaceDdG in 16 seconds [~ 653 test (80.41871921182266%) started, 159 in queue, 32 running]
Running Test SecondaryStructureFilter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/SecondaryStructureFilter/command.sh
Finished hbnet_use_input_rot in 29 seconds [~ 654 test (80.54187192118226%) started, 158 in queue, 32 running]
Running Test OversaturatedHbondAcceptorFilter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/OversaturatedHbondAcceptorFilter/command.sh
Finished symmetry_data_resource in 16 seconds [~ 655 test (80.66502463054188%) started, 157 in queue, 32 running]
Running Test MutateResidue_selector
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/MutateResidue_selector/command.sh
Finished abinitio in 11 seconds [~ 656 test (80.78817733990148%) started, 156 in queue, 32 running]
Running Test LoopLengthChange
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/LoopLengthChange/command.sh
Finished make_and_perturb_bundle_multirepeat in 13 seconds [~ 657 test (80.91133004926108%) started, 155 in queue, 32 running]
Running Test InterfaceAnalyzer_resfile
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/InterfaceAnalyzer_resfile/command.sh
Finished zinc_homodimer_design in 18 seconds [~ 658 test (81.03448275862068%) started, 154 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 test_computed_saxs_spectrum in 18 seconds [~ 659 test (81.1576354679803%) started, 153 in queue, 32 running]
Finished docking_ensemble_prepack in 98 seconds [~ 660 test (81.2807881773399%) started, 152 in queue, 32 running]
Running Test FilterReportAsPoseExtraScoresMover
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/FilterReportAsPoseExtraScoresMover/command.sh
Finished rna_puzzle6_U75G76A77_on_thread1 in 9 seconds [~ 661 test (81.4039408866995%) started, 151 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
Running Test real_virt_mover
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/real_virt_mover/command.sh
Finished binselector in 14 seconds [~ 662 test (81.52709359605912%) started, 150 in queue, 32 running]
Running Test pwsho
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pwsho/command.sh
Finished zinc_homodimer_setup in 11 seconds [~ 663 test (81.65024630541872%) started, 149 in queue, 32 running]
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 swa_rna_gagu_12_helix_addition in 12 seconds [~ 664 test (81.77339901477832%) started, 148 in queue, 32 running]
Finished mp_dock_setup in 9 seconds [~ 664 test (81.77339901477832%) started, 148 in queue, 31 running]
Running Test mp_dock_prepack
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_dock_prepack/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 set_torsion in 13 seconds [~ 666 test (82.01970443349754%) started, 146 in queue, 32 running]
Finished recces_turner in 12 seconds [~ 666 test (82.01970443349754%) started, 146 in queue, 31 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
Running Test PeptideStubMover_prependRepeat
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/PeptideStubMover_prependRepeat/command.sh
Finished StrandHelixGeometryFilter in 16 seconds [~ 668 test (82.26600985221675%) started, 144 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 StrandCurvatureByLevels in 15 seconds [~ 669 test (82.38916256157636%) started, 143 in queue, 32 running]
Running Test InterfaceAnalyzer_prepack
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/InterfaceAnalyzer_prepack/command.sh
Finished HelixBendFilter in 15 seconds [~ 670 test (82.51231527093596%) started, 142 in queue, 32 running]
Running Test FlipChirality
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/FlipChirality/command.sh
Finished referencepose_mutateresidue in 13 seconds [~ 671 test (82.63546798029557%) started, 141 in queue, 32 running]
Running Test AddConstraintsToCurrentConformationMover
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/AddConstraintsToCurrentConformationMover/command.sh
Finished pocket_measure in 13 seconds [~ 672 test (82.75862068965517%) started, 140 in queue, 32 running]
Finished phiselector in 13 seconds [~ 672 test (82.75862068965517%) started, 140 in queue, 31 running]
Running Test vancomycin
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/vancomycin/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
Finished helical_bundle in 13 seconds [~ 674 test (83.00492610837438%) started, 138 in queue, 32 running]
Running Test silent2frag
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/silent2frag/command.sh
Finished genkic_bin_setting in 13 seconds [~ 675 test (83.12807881773399%) started, 137 in queue, 32 running]
Running Test rb_recces
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rb_recces/command.sh
Finished pwsho in 6 seconds [~ 676 test (83.2512315270936%) started, 136 in queue, 32 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
Finished mp_interface_statistics in 6 seconds [~ 677 test (83.3743842364532%) started, 135 in queue, 32 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
Finished UBQ_E2_thioester_two_ubiquitins in 19 seconds [~ 678 test (83.49753694581281%) started, 134 in queue, 32 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
Finished binselector_probins in 13 seconds [~ 679 test (83.62068965517241%) started, 133 in queue, 32 running]
Finished mp_dock_prepack in 5 seconds [~ 679 test (83.62068965517241%) started, 133 in queue, 31 running]
Running Test site_constraint
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/site_constraint/command.sh
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 backbonegridsampler in 13 seconds [~ 681 test (83.86699507389163%) started, 131 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 features_pdb in 16 seconds [~ 682 test (83.99014778325123%) started, 130 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 silent2frag in 3 seconds [~ 683 test (84.11330049261083%) started, 129 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 cst_info in 16 seconds [~ 684 test (84.23645320197045%) started, 128 in queue, 32 running]
Running Test fragment_picker
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fragment_picker/command.sh
Finished InterfaceAnalyzer_resfile in 11 seconds [~ 685 test (84.35960591133005%) started, 127 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 unfolded_state_energy_calc in 10 seconds [~ 686 test (84.48275862068965%) started, 126 in queue, 32 running]
Running Test metalloprotein_broker
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/metalloprotein_broker/command.sh
Finished InterfaceAnalyzer_bothpack in 11 seconds [~ 687 test (84.60591133004927%) started, 125 in queue, 32 running]
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 r_pdb2top in 3 seconds [~ 688 test (84.72906403940887%) started, 124 in queue, 32 running]
Running Test docking_prepack
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/docking_prepack/command.sh
Finished add_job_pair_data in 15 seconds [~ 689 test (84.85221674876847%) started, 123 in queue, 32 running]
Running Test InterfaceAnalyzer_tracer
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/InterfaceAnalyzer_tracer/command.sh
Finished seed_ensemble_JD2_JI in 51 seconds [~ 690 test (84.97536945812809%) started, 122 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 SecondaryStructureFilter in 15 seconds [~ 691 test (85.09852216748769%) started, 121 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 site_constraint in 5 seconds [~ 692 test (85.22167487684729%) started, 120 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 OversaturatedHbondAcceptorFilter in 15 seconds [~ 693 test (85.34482758620689%) started, 119 in queue, 32 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
Finished LoopLengthChange in 15 seconds [~ 694 test (85.4679802955665%) started, 118 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
>>> 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. [2024-05-14 16:34:45.415916]
Finished MutateResidue_selector in 15 seconds [~ 695 test (85.5911330049261%) started, 117 in queue, 32 running]
Finished include_cc_check in 3 seconds [~ 695 test (85.5911330049261%) started, 117 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 InterfaceAnalyzer_prepack in 10 seconds [~ 697 test (85.83743842364532%) started, 115 in queue, 32 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
Finished FilterReportAsPoseExtraScoresMover in 15 seconds [~ 698 test (85.96059113300493%) started, 114 in queue, 32 running]
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 swa_rna_gagu_03_append_to_silent in 9 seconds [~ 699 test (86.08374384236453%) started, 113 in queue, 32 running]
Finished antibody_numbering_converter in 7 seconds [~ 699 test (86.08374384236453%) started, 113 in queue, 31 running]
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
Running Test rna_helix
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_helix/command.sh
Finished hbondstoresidue_selector in 13 seconds [~ 701 test (86.33004926108374%) started, 111 in queue, 32 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
Finished fragment_picker in 5 seconds [~ 702 test (86.45320197044335%) started, 110 in queue, 32 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 real_virt_mover in 16 seconds [~ 703 test (86.57635467980296%) started, 109 in queue, 32 running]
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 assemble_domains_jd2 in 9 seconds [~ 704 test (86.69950738916256%) started, 108 in queue, 32 running]
Running Test geometric_solvation
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/geometric_solvation/command.sh
Finished rb_recces in 10 seconds [~ 705 test (86.82266009852216%) started, 107 in queue, 32 running]
Running Test ProQ
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ProQ/command.sh
Finished genkic_bin_sampling in 13 seconds [~ 706 test (86.94581280788178%) started, 106 in queue, 32 running]
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 ModifyVariantTypeMover in 13 seconds [~ 707 test (87.06896551724138%) started, 105 in queue, 32 running]
Finished mpi_multistate_design in 10 seconds [~ 707 test (87.06896551724138%) started, 105 in queue, 31 running]
Finished identify_cdr_clusters in 7 seconds [~ 707 test (87.06896551724138%) started, 105 in queue, 30 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
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 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 phosphonate in 7 seconds [~ 710 test (87.4384236453202%) started, 102 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 pepspec_anchor_dock in 9 seconds [~ 711 test (87.5615763546798%) started, 101 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 PeptideStubMover_prependRepeat in 15 seconds [~ 712 test (87.6847290640394%) started, 100 in queue, 32 running]
Running Test orbitals
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/orbitals/command.sh
Finished metalloprotein_broker in 8 seconds [~ 713 test (87.80788177339902%) started, 99 in queue, 32 running]
Running Test mp_transform
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mp_transform/command.sh
Finished AddConstraintsToCurrentConformationMover in 15 seconds [~ 714 test (87.93103448275862%) started, 98 in queue, 32 running]
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_tracer in 9 seconds [~ 715 test (88.05418719211822%) started, 97 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 InterfaceAnalyzer_allscores in 9 seconds [~ 716 test (88.17733990147784%) started, 96 in queue, 32 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
Finished FlipChirality in 16 seconds [~ 717 test (88.30049261083744%) started, 95 in queue, 32 running]
Finished vancomycin in 15 seconds [~ 717 test (88.30049261083744%) started, 95 in queue, 31 running]
Finished swa_rna_gagu_21_prepend_dinucleotide_on_dinucleotide_by_jump in 8 seconds [~ 717 test (88.30049261083744%) started, 95 in queue, 30 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 swm_protein_preminimize
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/swm_protein_preminimize/command.sh
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
Finished swa_rna_gagu_08_append_dinucleotide in 8 seconds [~ 720 test (88.66995073891626%) started, 92 in queue, 32 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
Finished docking_prepack in 10 seconds [~ 721 test (88.79310344827586%) started, 91 in queue, 32 running]
Finished swa_rna_gagu_05_prepend_to_5primeterminus in 8 seconds [~ 721 test (88.79310344827586%) started, 91 in queue, 31 running]
Running Test shobuns
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/shobuns/command.sh
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 [~ 723 test (89.03940886699507%) started, 89 in queue, 32 running]
Finished rna_helix in 7 seconds [~ 723 test (89.03940886699507%) started, 89 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_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
Finished ncaa_fixbb in 30 seconds [~ 725 test (89.28571428571429%) started, 87 in queue, 32 running]
Finished swa_rna_gagu_17_append_floating_base in 8 seconds [~ 725 test (89.28571428571429%) started, 87 in queue, 31 running]
Finished struc_set_fragment_picker in 7 seconds [~ 725 test (89.28571428571429%) started, 87 in queue, 30 running]
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
Running Test pna
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/pna/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
Finished swa_rna_gagu_02_prepend in 8 seconds [~ 728 test (89.65517241379311%) started, 84 in queue, 32 running]
Finished glycan_clash_check in 6 seconds [~ 728 test (89.65517241379311%) started, 84 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 jrelax
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/jrelax/command.sh
Finished geometric_solvation in 6 seconds [~ 730 test (89.90147783251231%) started, 82 in queue, 32 running]
Running Test ig_dump
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ig_dump/command.sh
Finished swa_rna_gagu_01_append in 8 seconds [~ 731 test (90.02463054187191%) started, 81 in queue, 32 running]
Finished rna_denovo_grid_vdw in 8 seconds [~ 731 test (90.02463054187191%) started, 81 in queue, 31 running]
Running Test erraser_minimize
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/erraser_minimize/command.sh
Running Test density_tools
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/density_tools/command.sh
Finished hotspot_stub_constraints in 8 seconds [~ 733 test (90.27093596059113%) started, 79 in queue, 32 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
Finished ProQ in 7 seconds [~ 734 test (90.39408866995073%) started, 78 in queue, 32 running]
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
Finished swm_rna_move_align_dock in 7 seconds [~ 735 test (90.51724137931035%) started, 77 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 swa_rna_loop_clusterer in 2 seconds [~ 736 test (90.64039408866995%) started, 76 in queue, 32 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
Finished mp_transform in 5 seconds [~ 737 test (90.76354679802955%) started, 75 in queue, 32 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
Finished sequence_tolerance in 7 seconds [~ 738 test (90.88669950738917%) started, 74 in queue, 32 running]
Running Test mg_modeler
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/mg_modeler/command.sh
Finished swa_rna_gagu_19_prepend_floating_base_by_jump in 7 seconds [~ 739 test (91.00985221674877%) started, 73 in queue, 32 running]
Running Test gen_lig_grids
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/gen_lig_grids/command.sh
Finished swa_rna_gagu_20_append_floating_base_by_jump in 8 seconds [~ 740 test (91.13300492610837%) started, 72 in queue, 32 running]
Finished swa_rna_gagu_07_prepend_dinucleotide in 8 seconds [~ 740 test (91.13300492610837%) started, 72 in queue, 31 running]
Running Test distances
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/distances/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
Finished fragmentpicker_integration_demo in 6 seconds [~ 742 test (91.37931034482759%) started, 70 in queue, 32 running]
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
Finished orbitals in 8 seconds [~ 743 test (91.50246305418719%) started, 69 in queue, 32 running]
Finished extract_atomtree_diffs in 6 seconds [~ 743 test (91.50246305418719%) started, 69 in queue, 31 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 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
Finished swm_protein_preminimize in 6 seconds [~ 745 test (91.7487684729064%) started, 67 in queue, 32 running]
Finished shobuns in 5 seconds [~ 745 test (91.7487684729064%) started, 67 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 header_using_check
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/header_using_check/command.sh
Finished rna_denovo_bps_helix_ends in 5 seconds [~ 747 test (91.99507389162562%) started, 65 in queue, 32 running]
Finished match_1c2t in 5 seconds [~ 747 test (91.99507389162562%) started, 65 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 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 rna_ribosome_tether in 6 seconds [~ 749 test (92.24137931034483%) started, 63 in queue, 32 running]
Finished rna_denovo_bps_fixed_ends in 6 seconds [~ 749 test (92.24137931034483%) started, 63 in queue, 31 running]
Finished angle_recovery_stats in 3 seconds [~ 749 test (92.24137931034483%) started, 63 in queue, 30 running]
Running Test sweep_respair_energies
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/sweep_respair_energies/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 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 header_using_check in 1 seconds [~ 752 test (92.61083743842364%) started, 60 in queue, 32 running]
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 per_residue_energies in 6 seconds [~ 753 test (92.73399014778325%) started, 59 in queue, 32 running]
Finished jrelax in 6 seconds [~ 753 test (92.73399014778325%) started, 59 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 rna_minimize in 7 seconds [~ 755 test (92.98029556650246%) started, 57 in queue, 32 running]
Finished ig_dump in 6 seconds [~ 755 test (92.98029556650246%) started, 57 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 contactMap
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/contactMap/command.sh
egrep: full_minimize_temp_1.out: No such file or directory
Finished rna_farfar_noncanonical_hairpin in 22 seconds [~ 757 test (93.22660098522168%) started, 55 in queue, 32 running]
Finished score_jd2 in 11 seconds [~ 757 test (93.22660098522168%) started, 55 in queue, 31 running]
Finished docking_low_res in 8 seconds [~ 757 test (93.22660098522168%) started, 55 in queue, 30 running]
Finished erraser_minimize in 6 seconds [~ 757 test (93.22660098522168%) started, 55 in queue, 29 running]
Running Test constel
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/constel/command.sh
Running Test buried_unsat_kinemage
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/buried_unsat_kinemage/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 density_tools in 7 seconds [~ 761 test (93.7192118226601%) started, 51 in queue, 32 running]
Running Test noe_assignment
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/noe_assignment/command.sh
Finished c-term_conjugation in 6 seconds [~ 762 test (93.8423645320197%) started, 50 in queue, 32 running]
Running Test motif_extraction
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/motif_extraction/command.sh
Finished swa_rna_loop_sampler in 6 seconds [~ 763 test (93.96551724137932%) started, 49 in queue, 32 running]
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
Finished super_aln in 3 seconds [~ 764 test (94.08866995073892%) started, 48 in queue, 32 running]
Running Test rna_screen_phosphates
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_screen_phosphates/command.sh
Finished swm_protein_from_scratch in 9 seconds [~ 765 test (94.21182266009852%) started, 47 in queue, 32 running]
Finished swa_rna_gagu_04_clustering in 2 seconds [~ 765 test (94.21182266009852%) started, 47 in queue, 31 running]
Running Test rna_score
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_score/command.sh
Running Test nucleobase_sample_around
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/nucleobase_sample_around/command.sh
Finished mg_modeler in 6 seconds [~ 767 test (94.45812807881774%) started, 45 in queue, 32 running]
Finished swm_rna_move_two_strands in 5 seconds [~ 767 test (94.45812807881774%) started, 45 in queue, 31 running]
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 cluster_calibur
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/cluster_calibur/command.sh
Calibur clustering has been broken since its inception.
The external version was never successfully integration tested because
of typos in the integration test. The version ported to Rosetta has never
worked either.
Since now it causes hard-failures on release_debug, it needs to be
deactivated for now.
Finished fold_and_dock in 11 seconds [~ 769 test (94.70443349753694%) started, 43 in queue, 32 running]
Finished gen_lig_grids in 6 seconds [~ 769 test (94.70443349753694%) started, 43 in queue, 31 running]
Finished cs_rosetta_rna in 6 seconds [~ 769 test (94.70443349753694%) started, 43 in queue, 30 running]
Finished cluster_calibur in 0 seconds [~ 769 test (94.70443349753694%) started, 43 in queue, 29 running]
Running Test DARC_shapeonly
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/DARC_shapeonly/command.sh
Running Test test_idealize
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/test_idealize/command.sh
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 select_best_unique_ligand_poses in 3 seconds [~ 773 test (95.19704433497537%) started, 39 in queue, 32 running]
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 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 distances in 6 seconds [~ 774 test (95.32019704433498%) started, 38 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 pH_mode in 5 seconds [~ 775 test (95.44334975369458%) started, 37 in queue, 32 running]
Running Test minimize_6Dloopclose
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/minimize_6Dloopclose/command.sh
Finished rotamer_recovery_compare_two_structures in 6 seconds [~ 776 test (95.56650246305419%) started, 36 in queue, 32 running]
Running Test ld_converter
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ld_converter/command.sh
Finished template_features in 3 seconds [~ 777 test (95.6896551724138%) started, 35 in queue, 32 running]
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 fix_alignment_to_match_pdb in 6 seconds [~ 778 test (95.8128078817734%) started, 34 in queue, 32 running]
Finished sweep_respair_energies in 5 seconds [~ 778 test (95.8128078817734%) started, 34 in queue, 31 running]
Finished contactMap in 4 seconds [~ 778 test (95.8128078817734%) started, 34 in queue, 30 running]
Running Test centroid_disulfide_scores
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/centroid_disulfide_scores/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 rna_suitename
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_suitename/command.sh
Finished mp_loadtime in 5 seconds [~ 781 test (96.18226600985221%) started, 31 in queue, 32 running]
Finished mg_modeler_lores in 5 seconds [~ 781 test (96.18226600985221%) started, 31 in queue, 31 running]
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 rings
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rings/command.sh
Finished motif_extraction in 3 seconds [~ 783 test (96.42857142857143%) started, 29 in queue, 32 running]
Finished cstfile_to_theozyme_pdb in 3 seconds [~ 783 test (96.42857142857143%) started, 29 in queue, 31 running]
Running Test ralford_dump_rotamers
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/ralford_dump_rotamers/command.sh
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 docking_local_refine_min in 6 seconds [~ 785 test (96.67487684729063%) started, 27 in queue, 32 running]
Running Test make_exemplar
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/make_exemplar/command.sh
Finished pocket_suggest_targets in 6 seconds [~ 786 test (96.79802955665025%) started, 26 in queue, 32 running]
Finished RescorePDDF in 4 seconds [~ 786 test (96.79802955665025%) started, 26 in queue, 31 running]
Finished DARC_shapeonly in 3 seconds [~ 786 test (96.79802955665025%) started, 26 in queue, 30 running]
Finished report_hbonds_for_plugin in 3 seconds [~ 786 test (96.79802955665025%) started, 26 in queue, 29 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 fit_helixparams_a3b
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fit_helixparams_a3b/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
Running Test calculate_sasa
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/calculate_sasa/command.sh
Finished rna_screen_phosphates in 4 seconds [~ 790 test (97.29064039408867%) started, 22 in queue, 32 running]
Finished test_idealize in 3 seconds [~ 790 test (97.29064039408867%) started, 22 in queue, 31 running]
Finished rna_minimize_6D_loop_close in 3 seconds [~ 790 test (97.29064039408867%) started, 22 in queue, 30 running]
Finished per_residue_sc_sasa in 3 seconds [~ 790 test (97.29064039408867%) started, 22 in queue, 29 running]
Running Test CCD_loop_closure
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/CCD_loop_closure/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 rna_cluster
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/rna_cluster/command.sh
Running Test r_rmsf
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/r_rmsf/command.sh
Finished measure_lcaa_radii in 6 seconds [~ 794 test (97.78325123152709%) started, 18 in queue, 32 running]
Finished nucleobase_sample_around in 4 seconds [~ 794 test (97.78325123152709%) started, 18 in queue, 31 running]
Running Test number_of_residuetypes
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/number_of_residuetypes/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 fit_helixparams_rms in 4 seconds [~ 796 test (98.0295566502463%) started, 16 in queue, 32 running]
Running Test fit_helixparams
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/fit_helixparams/command.sh
Finished minimize_6Dloopclose in 3 seconds [~ 797 test (98.15270935960591%) started, 15 in queue, 32 running]
Running Test combine_silent
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/combine_silent/command.sh
Finished database_jd2_io in 12 seconds [~ 798 test (98.27586206896552%) started, 14 in queue, 32 running]
Finished oop_create in 3 seconds [~ 798 test (98.27586206896552%) started, 14 in queue, 31 running]
Running Test BuildPeptide
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/BuildPeptide/command.sh
Running Test score_aln
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/score_aln/command.sh
Finished database_jd2_compact_io in 12 seconds [~ 800 test (98.52216748768473%) started, 12 in queue, 32 running]
Finished buried_unsat_kinemage in 6 seconds [~ 800 test (98.52216748768473%) started, 12 in queue, 31 running]
Finished noe_assignment in 5 seconds [~ 800 test (98.52216748768473%) started, 12 in queue, 30 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
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 hierarchical_clustering
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/hierarchical_clustering/command.sh
Finished constel in 6 seconds [~ 803 test (98.89162561576354%) started, 9 in queue, 32 running]
Finished mp_quick_relax in 0 seconds [~ 803 test (98.89162561576354%) started, 9 in queue, 31 running]
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
Finished mp_span_from_pdb in 2 seconds [~ 805 test (99.13793103448276%) started, 7 in queue, 32 running]
Finished features_scientific_benchmark in 0 seconds [~ 805 test (99.13793103448276%) started, 7 in queue, 31 running]
Finished features_postgres in 0 seconds [~ 805 test (99.13793103448276%) started, 7 in queue, 30 running]
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
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
Finished rna_score in 5 seconds [~ 808 test (99.50738916256158%) started, 4 in queue, 32 running]
Finished rna_suitename in 2 seconds [~ 808 test (99.50738916256158%) started, 4 in queue, 31 running]
Finished code_template_tests_unit in 0 seconds [~ 808 test (99.50738916256158%) started, 4 in queue, 30 running]
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 central_class_modification
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/central_class_modification/command.sh
Running Test Werror_check
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/Werror_check/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 ld_converter in 3 seconds [~ 811 test (99.8768472906404%) started, 1 in queue, 32 running]
Finished DARC_electrostatics in 2 seconds [~ 811 test (99.8768472906404%) started, 1 in queue, 31 running]
Finished rna_add_WC_stats in 2 seconds [~ 811 test (99.8768472906404%) started, 1 in queue, 30 running]
Finished central_class_modification in 0 seconds [~ 811 test (99.8768472906404%) started, 1 in queue, 29 running]
Finished Werror_check in 0 seconds [~ 811 test (99.8768472906404%) started, 1 in queue, 28 running]
Running Test RescoreSAXS
ulimit -t 480 && bash /Volumes/scratch/b3.w/rosetta/commits/rosetta/tests/integration/new/RescoreSAXS/command.sh
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
Finished loop_hash in 2 seconds [~ 812 test (100.0%) started, 0 in queue, 28 running]
Finished RescoreSAXS in 0 seconds [~ 812 test (100.0%) started, 0 in queue, 27 running]
Finished HOW_TO_MAKE_TESTS in 0 seconds [~ 812 test (100.0%) started, 0 in queue, 26 running]
Finished ralford_dump_rotamers in 2 seconds [~ 812 test (100.0%) started, 0 in queue, 25 running]
Finished fit_helixparams_a3b in 2 seconds [~ 812 test (100.0%) started, 0 in queue, 24 running]
Finished calculate_sasa in 2 seconds [~ 812 test (100.0%) started, 0 in queue, 23 running]
Finished combine_silent in 1 seconds [~ 812 test (100.0%) started, 0 in queue, 22 running]
Finished score_aln in 1 seconds [~ 812 test (100.0%) started, 0 in queue, 21 running]
Finished code_template_tests_app in 0 seconds [~ 812 test (100.0%) started, 0 in queue, 20 running]
Finished rna_cluster in 2 seconds [~ 812 test (100.0%) started, 0 in queue, 19 running]
Finished r_rmsf in 2 seconds [~ 812 test (100.0%) started, 0 in queue, 18 running]
Finished fit_helixparams in 2 seconds [~ 812 test (100.0%) started, 0 in queue, 17 running]
Finished rings in 3 seconds [~ 812 test (100.0%) started, 0 in queue, 16 running]
Finished test_d_l_readin in 2 seconds [~ 812 test (100.0%) started, 0 in queue, 15 running]
Finished number_of_residuetypes in 2 seconds [~ 812 test (100.0%) started, 0 in queue, 14 running]
Finished extract_pdbs in 1 seconds [~ 812 test (100.0%) started, 0 in queue, 13 running]
Finished centroid_disulfide_scores in 4 seconds [~ 812 test (100.0%) started, 0 in queue, 12 running]
Finished BuildPeptide in 2 seconds [~ 812 test (100.0%) started, 0 in queue, 11 running]
Finished crossaln in 1 seconds [~ 812 test (100.0%) started, 0 in queue, 10 running]
Finished hierarchical_clustering in 2 seconds [~ 812 test (100.0%) started, 0 in queue, 9 running]
test_general
test_abstract
test_mover
test_ws_energy_method
test_1b_energy_method
test_2b_energy_method
test_task_operation
test_features_reporter
test_residue_selector
test_residue_selector_in_core
test_crosslinker_mover_helper
test_util
Finished code_template_tests_src in 3 seconds [~ 812 test (100.0%) started, 0 in queue, 8 running]
Finished CCD_loop_closure in 3 seconds [~ 812 test (100.0%) started, 0 in queue, 7 running]
Finished features_database_schema in 5 seconds [~ 812 test (100.0%) started, 0 in queue, 6 running]
Finished InterfaceAnalyzer in 26 seconds [~ 812 test (100.0%) started, 0 in queue, 5 running]
Finished non-canonical_connectivities in 4 seconds [~ 812 test (100.0%) started, 0 in queue, 4 running]
Finished rosetta_scripts_info in 3 seconds [~ 812 test (100.0%) started, 0 in queue, 3 running]
Finished make_exemplar in 5 seconds [~ 812 test (100.0%) started, 0 in queue, 2 running]
Finished pna in 18 seconds [~ 812 test (100.0%) started, 0 in queue, 1 running]
Finished app_exception_handling in 446 seconds [~ 812 test (100.0%) started, 0 in queue, 0 running]
Skipping comparison/analysis phase because command line option "--skip-comparison" was specified...
Missing new/runtimes.yaml
──────────────── 'hojo-4' comparing commits:20420 mac.clang.python39.integration test_id=828507 vs. main:62109 previous_test_id=827795 ────────────────
{
"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": 62109
},
"state": "failed",
"test_id": 827795
},
"summary": {
"failed": 3,
"failed_tests": [
"include_cc_check",
"remove_duplicate_motifs",
"ligand_motif_discovery"
],
"total": 812
},
"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"
},
"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:62109/include_cc_check/cc_includes.txt and /home/benchmark/working_dir/commits:20420/include_cc_check/cc_includes.txt differ\r\nOnly in /home/benchmark/working_dir/commits:20420/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:62109/include_cc_check/cc_includes.txt /home/benchmark/working_dir/commits:20420/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:20420/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/commits:20420/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio16_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120970_SubRatio_0.803259.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio22_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120911_SubRatio_0.793778.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/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_delta_-24.612108_motifs_11_sigmotifs_7.pdb\r\nOnly in /home/benchmark/working_dir/main:62109/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:20420/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000_WholeRatio_0.120947_SubRatio_0.802667.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio46_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120951_SubRatio_0.776593.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/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_delta_-25.058549_motifs_11_sigmotifs_7.pdb\r\nOnly in /home/benchmark/working_dir/main:62109/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:20420/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000_WholeRatio_0.120987_SubRatio_0.801185.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio97_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120951_SubRatio_0.802667.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: ASN423A_Z0_Ligatoms_4_3_16_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: ASN423A_Z0_Ligatoms_4_3_16_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: empty_WholeRatio_0.119936_SubRatio_0.645037.pdb\r\nFiles /home/benchmark/working_dir/main:62109/ligand_motif_discovery/flags and /home/benchmark/working_dir/commits:20420/ligand_motif_discovery/flags differ\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: GLN134A_Z0_Ligatoms_19_20_21_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: GLN134A_Z0_Ligatoms_19_20_21_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: GLN85A_Z0_Ligatoms_11_12_13_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: GLN85A_Z0_Ligatoms_24_25_30_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: HIS447A_Z0_Ligatoms_14_13_15_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: HIS447A_Z0_Ligatoms_14_13_15_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: ILE419A_Z0_Ligatoms_8_9_10_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: ILE419A_Z0_Ligatoms_8_9_10_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nFiles /home/benchmark/working_dir/main:62109/ligand_motif_discovery/log and /home/benchmark/working_dir/commits:20420/ligand_motif_discovery/log differ\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: PHE169A_Z0_Ligatoms_8_9_10_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: PHE169A_Z0_Ligatoms_8_9_10_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: PRO82A_Z0_Ligatoms_24_25_30_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: PRO82A_Z0_Ligatoms_24_25_30_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: THR62A_Z0_Ligatoms_27_28_32_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: THR62A_Z0_Ligatoms_27_28_32_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: THR86A_Z0_Ligatoms_22_21_23_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: THR86A_Z0_Ligatoms_22_21_23_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: TYR451A_Z0_Ligatoms_14_13_15_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: TYR451A_Z0_Ligatoms_27_28_32_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: VAL450A_Z0_Ligatoms_11_12_13_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: VAL450A_Z0_Ligatoms_11_12_13_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\n\n\nFull Diff:\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio16_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120970_SubRatio_0.803259.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio22_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120911_SubRatio_0.793778.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/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_delta_-24.612108_motifs_11_sigmotifs_7.pdb\r\nOnly in /home/benchmark/working_dir/main:62109/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:20420/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000_WholeRatio_0.120947_SubRatio_0.802667.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio46_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120951_SubRatio_0.776593.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/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_delta_-25.058549_motifs_11_sigmotifs_7.pdb\r\nOnly in /home/benchmark/working_dir/main:62109/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:20420/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000_WholeRatio_0.120987_SubRatio_0.801185.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio97_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120951_SubRatio_0.802667.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: ASN423A_Z0_Ligatoms_4_3_16_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: ASN423A_Z0_Ligatoms_4_3_16_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: empty_WholeRatio_0.119936_SubRatio_0.645037.pdb\r\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62109/ligand_motif_discovery/flags /home/benchmark/working_dir/commits:20420/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\n7a19,39\r\n> \r\n> #optional flags for demonstrative purposes of extra features of app: \r\n> \r\n> #collecting motifs from good-placed ligands\r\n> -collect_motifs_from_placed_ligand true\r\n> #define important residues in the binding pocket that we want to see motifs collected against\r\n> #protocol notes which residues get motifs found against them\r\n> -significant_residues_for_motifs 447,450,419,134,86,423,451,85,62\r\n> \r\n> #space fill method\r\n> #define cube-shaped binding pocket about coordinate (coordinate corresponds to within 4s0v.pdb, shifts with script)\r\n> -binding_pocket_center_sf 54,6,53\r\n> -binding_pocket_radius_sf 7\r\n> #define cutoff of how much of binding pocket volume must be filled compared to empty pocket (>15% more filled than empty when ligand is placed)\r\n> -space_fill_cutoff_differential_score_sub 0.15\r\n> \r\n> #optional export of space fill matrices to PDB (only recommended for debugging and tuning cutoffs for binding pocket)\r\n> -output_space_fill_matrix_pdbs true\r\n> \r\n> #verbosity; using second-least verbose level\r\n> -motifs:verbose 2\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: GLN134A_Z0_Ligatoms_19_20_21_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: GLN134A_Z0_Ligatoms_19_20_21_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: GLN85A_Z0_Ligatoms_11_12_13_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: GLN85A_Z0_Ligatoms_24_25_30_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: HIS447A_Z0_Ligatoms_14_13_15_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: HIS447A_Z0_Ligatoms_14_13_15_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: ILE419A_Z0_Ligatoms_8_9_10_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: ILE419A_Z0_Ligatoms_8_9_10_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62109/ligand_motif_discovery/log /home/benchmark/working_dir/commits:20420/ligand_motif_discovery/log\r\n19d18\r\n< LigandDiscoverySearch_get_motif_sublibrary_by_aa: Created motif sub-library for residue ASN with 24 motifs in it.\r\n20a20,25\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> LigandDiscoverySearch_out: Current anchor residue position: 423\r\n> LigandDiscoverySearch_get_motif_sublibrary_by_aa: Created motif sub-library for residue ASN with 24 motifs in it.\r\n41,42d45\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\n43a47,60\r\n> LigandDiscoverySearch_create_protein_matrix_space_fill: Creating space fill matrix. Dimensions of matrix are 88,53,113\r\n> LigandDiscoverySearch_create_protein_matrix_space_fill: Total: 527032\r\n> LigandDiscoverySearch_create_protein_matrix_space_fill: Occupied: 63210\r\n> LigandDiscoverySearch_create_protein_matrix_space_fill: Unoccupied: 463822\r\n> LigandDiscoverySearch_create_protein_matrix_space_fill: Occupied-Total Ratio: 0.119936\r\n> LigandDiscoverySearch_create_protein_matrix_space_fill: binding_pocket_dimensions: 7,7,7\r\n> LigandDiscoverySearch_create_protein_matrix_space_fill: binding_pocket_dimensions: 7,7,7\r\n> LigandDiscoverySearch_create_protein_matrix_space_fill: Sub-region stats without placed region, bound by adjusted coordinates: x(47->61) y(19->33) z(74->88)\r\n> LigandDiscoverySearch_create_protein_matrix_space_fill: Total: 3375\r\n> LigandDiscoverySearch_create_protein_matrix_space_fill: Occupied: 2177\r\n> LigandDiscoverySearch_create_protein_matrix_space_fill: Unoccupied: 1198\r\n> LigandDiscoverySearch_create_protein_matrix_space_fill: Occupied-Total Ratio: 0.645037\r\n> LigandDiscoverySearch_export_space_fill_matrix_as_C_H_O_N_pdb: Preparing to make visualization pose for empty_WholeRatio_0.119936_SubRatio_0.645037.pdb\r\n> LigandDiscoverySearch_export_space_fill_matrix_as_C_H_O_N_pdb: Making viualization pdb empty_WholeRatio_0.119936_SubRatio_0.645037.pdb\r\n48,51c65,66\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---\r\n> LigandDiscoverySearch_out: Finding all atom trios for this ligand\r\n> LigandDiscoverySearch_out: Number of unique atom trios in this ligand are: 104\r\n53,55d67\r\n< LigandDiscoverySearch_out: Trio is C9 N3 C13\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n61,63d72\r\n< LigandDiscoverySearch_out: Trio is C9 N3 C10\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n69,71d77\r\n< LigandDiscoverySearch_out: Trio is C9 C8 N1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n77,79d82\r\n< LigandDiscoverySearch_out: Trio is N3 C9 C8 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n85,87d87\r\n< LigandDiscoverySearch_out: Trio is N3 C13 C14\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n93,95d92\r\n< LigandDiscoverySearch_out: Trio is N3 C13 O2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n101,103d97\r\n< LigandDiscoverySearch_out: Trio is N3 C10 C23\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n109,111d102\r\n< LigandDiscoverySearch_out: Trio is N3 C10 C11\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n117,119d107\r\n< LigandDiscoverySearch_out: Trio is C13 N3 C9 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n125,127d112\r\n< LigandDiscoverySearch_out: Trio is C13 N3 C10\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n133,135d117\r\n< LigandDiscoverySearch_out: Trio is C13 C14 C15\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n141,143d122\r\n< LigandDiscoverySearch_out: Trio is C13 C14 C19\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n149,151d127\r\n< LigandDiscoverySearch_out: Trio is C14 C13 N3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n157,159d132\r\n< LigandDiscoverySearch_out: Trio is C14 C13 O2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n165,167d137\r\n< LigandDiscoverySearch_out: Trio is C14 C15 N4 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n173,176c143,145\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---\r\n> LigandDiscoverySearch_export_space_fill_matrix_as_C_H_O_N_pdb: Preparing to make visualization pose for 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio16_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120970_SubRatio_0.803259.pdb\r\n> LigandDiscoverySearch_export_space_fill_matrix_as_C_H_O_N_pdb: Making viualization pdb 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio16_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120970_SubRatio_0.803259.pdb\r\n> LigandDiscoverySearch_out: Made minipose of size 56\r\n182,184d150\r\n< LigandDiscoverySearch_out: Trio is C14 C19 C18\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n190,192d155\r\n< LigandDiscoverySearch_out: Trio is C15 C14 C13\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n198,200d160\r\n< LigandDiscoverySearch_out: Trio is C15 C14 C19\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n206,208d165\r\n< LigandDiscoverySearch_out: Trio is C15 N4 N5 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n214,216d170\r\n< LigandDiscoverySearch_out: Trio is C15 N4 N6 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n222,224c176,177\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---\r\n> LigandDiscoverySearch_export_space_fill_matrix_as_C_H_O_N_pdb: Preparing to make visualization pose for 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio22_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120911_SubRatio_0.793778.pdb\r\n> LigandDiscoverySearch_export_space_fill_matrix_as_C_H_O_N_pdb: Making viualization pdb 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio22_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120911_SubRatio_0.793778.pdb\r\n226c179\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 1\r\n---\r\n> LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n228c181\r\n< LigandDiscoverySearch_out: Total cases for trio: 1\r\n---\r\n> LigandDiscoverySearch_out: Total cases for trio: 0\r\n230,232d182\r\n< LigandDiscoverySearch_out: Trio is N4 C15 C14\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n238,240d187\r\n< LigandDiscoverySearch_out: Trio is N4 C15 C16\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n246,248d192\r\n< LigandDiscoverySearch_out: Trio is N4 N5 C20\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n254,256d197\r\n< LigandDiscoverySearch_out: Trio is N4 N6 C21\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n262,264d202\r\n< LigandDiscoverySearch_out: Trio is N5 N4 C15\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n270,272d207\r\n< LigandDiscoverySearch_out: Trio is N5 N4 N6 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n278,280d212\r\n< LigandDiscoverySearch_out: Trio is N5 C20 C21\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n286,288d217\r\n< LigandDiscoverySearch_out: Trio is C20 N5 N4 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n294,296d222\r\n< LigandDiscoverySearch_out: Trio is C20 C21 N6 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n302,304d227\r\n< LigandDiscoverySearch_out: Trio is C21 C20 N5 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n310,312d232\r\n< LigandDiscoverySearch_out: Trio is C21 N6 N4 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n318,320d237\r\n< LigandDiscoverySearch_out: Trio is N6 N4 C15\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n326,328d242\r\n< LigandDiscoverySearch_out: Trio is N6 N4 N5 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n334,341c248,254\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> LigandDiscoverySearch_export_space_fill_matrix_as_C_H_O_N_pdb: Preparing to make visualization pose for 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000_WholeRatio_0.120947_SubRatio_0.802667.pdb\r\n> LigandDiscoverySearch_export_space_fill_matrix_as_C_H_O_N_pdb: Making viualization pdb 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000_WholeRatio_0.120947_SubRatio_0.802667.pdb\r\n> LigandDiscoverySearch_out: Pre-move delta score = 104.291, fa_atr = -16.0527, fa_rep = 163.157, fa_atr_rep before = 5707.93\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\n345a259,262\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\n350,352c267,1696\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---\r\n> protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -1195.52 -1195.52\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 C9 \r\n> apps.pilot.ligand_motifs: ATOM j: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: ATOM k: 1 Name: C9 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 1, type is CH2; 2, type is Npro; 1, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM k: 3 Name: C13\r\n> apps.pilot.ligand_motifs: Connected triplet is: 1, type is CH2; 2, type is Npro; 3, type is COO \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: 3\r\n> apps.pilot.ligand_motifs: ATOM k: 17 Name: C10\r\n> apps.pilot.ligand_motifs: Connected triplet is: 1, type is CH2; 2, type is Npro; 17, type is CH1 \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 j: 22 Name: C8 \r\n> apps.pilot.ligand_motifs: ATOM k: 1 Name: C9 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 1, type is CH2; 22, type is CH2; 1, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM k: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 1, type is CH2; 22, type is CH2; 21, type is Nhis \r\n> apps.pilot.ligand_motifs: atom_i: 1\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 22\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 21\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 2\r\n> apps.pilot.ligand_motifs: atom name is N3 \r\n> apps.pilot.ligand_motifs: ATOM j: 1 Name: C9 \r\n> apps.pilot.ligand_motifs: ATOM k: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 2, type is Npro; 1, type is CH2; 2, type is Npro \r\n> apps.pilot.ligand_motifs: ATOM k: 22 Name: C8 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 2, type is Npro; 1, type is CH2; 22, 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: 22\r\n> apps.pilot.ligand_motifs: ATOM j: 3 Name: C13\r\n> apps.pilot.ligand_motifs: ATOM k: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 2, type is Npro; 3, type is COO; 2, type is Npro \r\n> apps.pilot.ligand_motifs: ATOM k: 4 Name: C14\r\n> apps.pilot.ligand_motifs: Connected triplet is: 2, type is Npro; 3, type is COO; 4, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 2\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 3\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 4\r\n> apps.pilot.ligand_motifs: ATOM k: 16 Name: O2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 2, type is Npro; 3, type is COO; 16, type is ONH2 \r\n> apps.pilot.ligand_motifs: atom_i: 2\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: 17 Name: C10\r\n> apps.pilot.ligand_motifs: ATOM k: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 2, type is Npro; 17, type is CH1; 2, type is Npro \r\n> apps.pilot.ligand_motifs: ATOM k: 18 Name: C23\r\n> apps.pilot.ligand_motifs: Connected triplet is: 2, type is Npro; 17, type is CH1; 18, type is CH3 \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 k: 19 Name: C11\r\n> apps.pilot.ligand_motifs: Connected triplet is: 2, type is Npro; 17, type is CH1; 19, 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: 19\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 3\r\n> apps.pilot.ligand_motifs: atom name is C13\r\n> apps.pilot.ligand_motifs: ATOM j: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: ATOM k: 1 Name: C9 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 3, type is COO; 2, type is Npro; 1, type is CH2 \r\n> apps.pilot.ligand_motifs: atom_i: 3\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: 3 Name: C13\r\n> apps.pilot.ligand_motifs: Connected triplet is: 3, type is COO; 2, type is Npro; 3, type is COO \r\n> apps.pilot.ligand_motifs: ATOM k: 17 Name: C10\r\n> apps.pilot.ligand_motifs: Connected triplet is: 3, type is COO; 2, type is Npro; 17, type is CH1 \r\n> apps.pilot.ligand_motifs: atom_i: 3\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 j: 4 Name: C14\r\n> apps.pilot.ligand_motifs: ATOM k: 3 Name: C13\r\n> apps.pilot.ligand_motifs: Connected triplet is: 3, type is COO; 4, type is aroC; 3, type is COO \r\n> apps.pilot.ligand_motifs: ATOM k: 5 Name: C15\r\n> apps.pilot.ligand_motifs: Connected triplet is: 3, type is COO; 4, type is aroC; 5, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 3\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: ATOM k: 14 Name: C19\r\n> apps.pilot.ligand_motifs: Connected triplet is: 3, type is COO; 4, type is aroC; 14, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 3\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 4\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 14\r\n> apps.pilot.ligand_motifs: ATOM j: 16 Name: O2 \r\n> apps.pilot.ligand_motifs: ATOM k: 3 Name: C13\r\n> apps.pilot.ligand_motifs: Connected triplet is: 3, type is COO; 16, type is ONH2; 3, type is COO \r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 4\r\n> apps.pilot.ligand_motifs: atom name is C14\r\n> apps.pilot.ligand_motifs: ATOM j: 3 Name: C13\r\n> apps.pilot.ligand_motifs: ATOM k: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 4, type is aroC; 3, type is COO; 2, type is Npro \r\n> apps.pilot.ligand_motifs: atom_i: 4\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 3\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 2\r\n> apps.pilot.ligand_motifs: ATOM k: 4 Name: C14\r\n> apps.pilot.ligand_motifs: Connected triplet is: 4, type is aroC; 3, type is COO; 4, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 16 Name: O2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 4, type is aroC; 3, type is COO; 16, type is ONH2 \r\n> apps.pilot.ligand_motifs: atom_i: 4\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: C15\r\n> apps.pilot.ligand_motifs: ATOM k: 4 Name: C14\r\n> apps.pilot.ligand_motifs: Connected triplet is: 4, type is aroC; 5, type is aroC; 4, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 6 Name: N4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 4, type is aroC; 5, type is aroC; 6, type is Npro \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: ATOM k: 11 Name: C16\r\n> apps.pilot.ligand_motifs: Connected triplet is: 4, type is aroC; 5, type is aroC; 11, type is aroC \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: 11\r\n> apps.pilot.ligand_motifs: ATOM j: 14 Name: C19\r\n> apps.pilot.ligand_motifs: ATOM k: 4 Name: C14\r\n> apps.pilot.ligand_motifs: Connected triplet is: 4, type is aroC; 14, type is aroC; 4, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 13 Name: C18\r\n> apps.pilot.ligand_motifs: Connected triplet is: 4, type is aroC; 14, 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: 14\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 C15\r\n> apps.pilot.ligand_motifs: ATOM j: 4 Name: C14\r\n> apps.pilot.ligand_motifs: ATOM k: 3 Name: C13\r\n> apps.pilot.ligand_motifs: Connected triplet is: 5, type is aroC; 4, type is aroC; 3, 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: 3\r\n> apps.pilot.ligand_motifs: ATOM k: 5 Name: C15\r\n> apps.pilot.ligand_motifs: Connected triplet is: 5, type is aroC; 4, type is aroC; 5, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 14 Name: C19\r\n> apps.pilot.ligand_motifs: Connected triplet is: 5, type is aroC; 4, type is aroC; 14, type is aroC \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: 14\r\n> apps.pilot.ligand_motifs: ATOM j: 6 Name: N4 \r\n> apps.pilot.ligand_motifs: ATOM k: 5 Name: C15\r\n> apps.pilot.ligand_motifs: Connected triplet is: 5, type is aroC; 6, type is Npro; 5, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 7 Name: N5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 5, type is aroC; 6, type is Npro; 7, type is Nhis \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: ATOM k: 10 Name: N6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 5, type is aroC; 6, type is Npro; 10, type is Nhis \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: 10\r\n> apps.pilot.ligand_motifs: ATOM j: 11 Name: C16\r\n> apps.pilot.ligand_motifs: ATOM k: 5 Name: C15\r\n> apps.pilot.ligand_motifs: Connected triplet is: 5, type is aroC; 11, type is aroC; 5, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 12 Name: C17\r\n> apps.pilot.ligand_motifs: Connected triplet is: 5, type is aroC; 11, type is aroC; 12, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 5\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 6\r\n> apps.pilot.ligand_motifs: atom name is N4 \r\n> apps.pilot.ligand_motifs: ATOM j: 5 Name: C15\r\n> apps.pilot.ligand_motifs: ATOM k: 4 Name: C14\r\n> apps.pilot.ligand_motifs: Connected triplet is: 6, type is Npro; 5, type is aroC; 4, type is aroC \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: N4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 6, type is Npro; 5, type is aroC; 6, type is Npro \r\n> apps.pilot.ligand_motifs: ATOM k: 11 Name: C16\r\n> apps.pilot.ligand_motifs: Connected triplet is: 6, type is Npro; 5, type is aroC; 11, type is aroC \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: 11\r\n> apps.pilot.ligand_motifs: ATOM j: 7 Name: N5 \r\n> apps.pilot.ligand_motifs: ATOM k: 6 Name: N4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 6, type is Npro; 7, type is Nhis; 6, type is Npro \r\n> apps.pilot.ligand_motifs: ATOM k: 8 Name: C20\r\n> apps.pilot.ligand_motifs: Connected triplet is: 6, type is Npro; 7, type is Nhis; 8, type is aroC \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: ATOM j: 10 Name: N6 \r\n> apps.pilot.ligand_motifs: ATOM k: 6 Name: N4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 6, type is Npro; 10, type is Nhis; 6, type is Npro \r\n> apps.pilot.ligand_motifs: ATOM k: 9 Name: C21\r\n> apps.pilot.ligand_motifs: Connected triplet is: 6, type is Npro; 10, type is Nhis; 9, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 6\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: in atom iterate block, atom num is 7\r\n> apps.pilot.ligand_motifs: atom name is N5 \r\n> apps.pilot.ligand_motifs: ATOM j: 6 Name: N4 \r\n> apps.pilot.ligand_motifs: ATOM k: 5 Name: C15\r\n> apps.pilot.ligand_motifs: Connected triplet is: 7, type is Nhis; 6, type is Npro; 5, type is aroC \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: N5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 7, type is Nhis; 6, type is Npro; 7, type is Nhis \r\n> apps.pilot.ligand_motifs: ATOM k: 10 Name: N6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 7, type is Nhis; 6, type is Npro; 10, type is Nhis \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: 10\r\n> apps.pilot.ligand_motifs: ATOM j: 8 Name: C20\r\n> apps.pilot.ligand_motifs: ATOM k: 7 Name: N5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 7, type is Nhis; 8, type is aroC; 7, type is Nhis \r\n> apps.pilot.ligand_motifs: ATOM k: 9 Name: C21\r\n> apps.pilot.ligand_motifs: Connected triplet is: 7, type is Nhis; 8, type is aroC; 9, type is aroC \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 C20\r\n> apps.pilot.ligand_motifs: ATOM j: 7 Name: N5 \r\n> apps.pilot.ligand_motifs: ATOM k: 6 Name: N4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 8, type is aroC; 7, type is Nhis; 6, type is Npro \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: C20\r\n> apps.pilot.ligand_motifs: Connected triplet is: 8, type is aroC; 7, type is Nhis; 8, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 9 Name: C21\r\n> apps.pilot.ligand_motifs: ATOM k: 8 Name: C20\r\n> apps.pilot.ligand_motifs: Connected triplet is: 8, type is aroC; 9, type is aroC; 8, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 10 Name: N6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 8, type is aroC; 9, type is aroC; 10, type is Nhis \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 C21\r\n> apps.pilot.ligand_motifs: ATOM j: 8 Name: C20\r\n> apps.pilot.ligand_motifs: ATOM k: 7 Name: N5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 8, type is aroC; 7, type is Nhis \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: C21\r\n> apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 8, type is aroC; 9, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 10 Name: N6 \r\n> apps.pilot.ligand_motifs: ATOM k: 6 Name: N4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 10, type is Nhis; 6, type is Npro \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: 6\r\n> apps.pilot.ligand_motifs: ATOM k: 9 Name: C21\r\n> apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 10, type is Nhis; 9, type is aroC \r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 10\r\n> apps.pilot.ligand_motifs: atom name is N6 \r\n> apps.pilot.ligand_motifs: ATOM j: 6 Name: N4 \r\n> apps.pilot.ligand_motifs: ATOM k: 5 Name: C15\r\n> apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 6, type is Npro; 5, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 10\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: N5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 6, type is Npro; 7, type is Nhis \r\n> apps.pilot.ligand_motifs: atom_i: 10\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: ATOM k: 10 Name: N6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 6, type is Npro; 10, type is Nhis \r\n> apps.pilot.ligand_motifs: ATOM j: 9 Name: C21\r\n> apps.pilot.ligand_motifs: ATOM k: 8 Name: C20\r\n> apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 9, type is aroC; 8, type is aroC \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: N6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 9, type is aroC; 10, type is Nhis \r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 11\r\n> apps.pilot.ligand_motifs: atom name is C16\r\n> apps.pilot.ligand_motifs: ATOM j: 5 Name: C15\r\n> apps.pilot.ligand_motifs: ATOM k: 4 Name: C14\r\n> apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 5, type is aroC; 4, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 11\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: N4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 5, type is aroC; 6, type is Npro \r\n> apps.pilot.ligand_motifs: atom_i: 11\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: ATOM k: 11 Name: C16\r\n> apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 5, type is aroC; 11, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 12 Name: C17\r\n> apps.pilot.ligand_motifs: ATOM k: 11 Name: C16\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: C18\r\n> apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 12, type is aroC; 13, type is aroC \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 C17\r\n> apps.pilot.ligand_motifs: ATOM j: 11 Name: C16\r\n> apps.pilot.ligand_motifs: ATOM k: 5 Name: C15\r\n> apps.pilot.ligand_motifs: Connected triplet is: 12, type is aroC; 11, type is aroC; 5, type is aroC \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: 5\r\n> apps.pilot.ligand_motifs: ATOM k: 12 Name: C17\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: C18\r\n> apps.pilot.ligand_motifs: ATOM k: 12 Name: C17\r\n> apps.pilot.ligand_motifs: Connected triplet is: 12, type is aroC; 13, type is aroC; 12, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 14 Name: C19\r\n> apps.pilot.ligand_motifs: Connected triplet is: 12, type is aroC; 13, type is aroC; 14, type is aroC \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: ATOM k: 15 Name: C22\r\n> apps.pilot.ligand_motifs: Connected triplet is: 12, type is aroC; 13, type is aroC; 15, type is CH3 \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: 15\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 13\r\n> apps.pilot.ligand_motifs: atom name is C18\r\n> apps.pilot.ligand_motifs: ATOM j: 12 Name: C17\r\n> apps.pilot.ligand_motifs: ATOM k: 11 Name: C16\r\n> apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 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: C18\r\n> apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 12, type is aroC; 13, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 14 Name: C19\r\n> apps.pilot.ligand_motifs: ATOM k: 4 Name: C14\r\n> apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 14, type is aroC; 4, type is aroC \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: 4\r\n> apps.pilot.ligand_motifs: ATOM k: 13 Name: C18\r\n> apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 14, type is aroC; 13, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 15 Name: C22\r\n> apps.pilot.ligand_motifs: ATOM k: 13 Name: C18\r\n> apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 15, type is CH3; 13, type is aroC \r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 14\r\n> apps.pilot.ligand_motifs: atom name is C19\r\n> apps.pilot.ligand_motifs: ATOM j: 4 Name: C14\r\n> apps.pilot.ligand_motifs: ATOM k: 3 Name: C13\r\n> apps.pilot.ligand_motifs: Connected triplet is: 14, type is aroC; 4, type is aroC; 3, type is COO \r\n> apps.pilot.ligand_motifs: atom_i: 14\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 4\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 3\r\n> apps.pilot.ligand_motifs: ATOM k: 5 Name: C15\r\n> apps.pilot.ligand_motifs: Connected triplet is: 14, type is aroC; 4, type is aroC; 5, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 14\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: ATOM k: 14 Name: C19\r\n> apps.pilot.ligand_motifs: Connected triplet is: 14, type is aroC; 4, type is aroC; 14, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 13 Name: C18\r\n> apps.pilot.ligand_motifs: ATOM k: 12 Name: C17\r\n> apps.pilot.ligand_motifs: Connected triplet is: 14, type is aroC; 13, type is aroC; 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: C19\r\n> apps.pilot.ligand_motifs: Connected triplet is: 14, type is aroC; 13, type is aroC; 14, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 15 Name: C22\r\n> apps.pilot.ligand_motifs: Connected triplet is: 14, type is aroC; 13, type is aroC; 15, type is CH3 \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: 15\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 15\r\n> apps.pilot.ligand_motifs: atom name is C22\r\n> apps.pilot.ligand_motifs: ATOM j: 13 Name: C18\r\n> apps.pilot.ligand_motifs: ATOM k: 12 Name: C17\r\n> apps.pilot.ligand_motifs: Connected triplet is: 15, type is CH3; 13, type is aroC; 12, 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: 12\r\n> apps.pilot.ligand_motifs: ATOM k: 14 Name: C19\r\n> apps.pilot.ligand_motifs: Connected triplet is: 15, type is CH3; 13, type is aroC; 14, 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: 14\r\n> apps.pilot.ligand_motifs: ATOM k: 15 Name: C22\r\n> apps.pilot.ligand_motifs: Connected triplet is: 15, type is CH3; 13, type is aroC; 15, type is CH3 \r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 16\r\n> apps.pilot.ligand_motifs: atom name is O2 \r\n> apps.pilot.ligand_motifs: ATOM j: 3 Name: C13\r\n> apps.pilot.ligand_motifs: ATOM k: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 16, type is ONH2; 3, type is COO; 2, type is Npro \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: 2\r\n> apps.pilot.ligand_motifs: ATOM k: 4 Name: C14\r\n> apps.pilot.ligand_motifs: Connected triplet is: 16, type is ONH2; 3, type is COO; 4, 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: 4\r\n> apps.pilot.ligand_motifs: ATOM k: 16 Name: O2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 16, type is ONH2; 3, type is COO; 16, type is ONH2 \r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 17\r\n> apps.pilot.ligand_motifs: atom name is C10\r\n> apps.pilot.ligand_motifs: ATOM j: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: ATOM k: 1 Name: C9 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH1; 2, type is Npro; 1, 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: 1\r\n> apps.pilot.ligand_motifs: ATOM k: 3 Name: C13\r\n> apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH1; 2, type is Npro; 3, type is COO \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: 3\r\n> apps.pilot.ligand_motifs: ATOM k: 17 Name: C10\r\n> apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH1; 2, type is Npro; 17, type is CH1 \r\n> apps.pilot.ligand_motifs: ATOM j: 18 Name: C23\r\n> apps.pilot.ligand_motifs: ATOM k: 17 Name: C10\r\n> apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH1; 18, type is CH3; 17, type is CH1 \r\n> apps.pilot.ligand_motifs: ATOM j: 19 Name: C11\r\n> apps.pilot.ligand_motifs: ATOM k: 17 Name: C10\r\n> apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH1; 19, type is CH2; 17, type is CH1 \r\n> apps.pilot.ligand_motifs: ATOM k: 20 Name: C12\r\n> apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH1; 19, type is CH2; 20, type is CH2 \r\n> apps.pilot.ligand_motifs: atom_i: 17\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 18\r\n> apps.pilot.ligand_motifs: atom name is C23\r\n> apps.pilot.ligand_motifs: ATOM j: 17 Name: C10\r\n> apps.pilot.ligand_motifs: ATOM k: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH3; 17, type is CH1; 2, type is Npro \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: C23\r\n> apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH3; 17, type is CH1; 18, type is CH3 \r\n> apps.pilot.ligand_motifs: ATOM k: 19 Name: C11\r\n> apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH3; 17, type is CH1; 19, 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: 19\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 19\r\n> apps.pilot.ligand_motifs: atom name is C11\r\n> apps.pilot.ligand_motifs: ATOM j: 17 Name: C10\r\n> apps.pilot.ligand_motifs: ATOM k: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH2; 17, type is CH1; 2, type is Npro \r\n> apps.pilot.ligand_motifs: atom_i: 19\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: C23\r\n> apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH2; 17, type is CH1; 18, type is CH3 \r\n> apps.pilot.ligand_motifs: atom_i: 19\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 k: 19 Name: C11\r\n> apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH2; 17, type is CH1; 19, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM j: 20 Name: C12\r\n> apps.pilot.ligand_motifs: ATOM k: 19 Name: C11\r\n> apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH2; 20, type is CH2; 19, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM k: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH2; 20, type is CH2; 21, type is Nhis \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: in atom iterate block, atom num is 20\r\n> apps.pilot.ligand_motifs: atom name is C12\r\n> apps.pilot.ligand_motifs: ATOM j: 19 Name: C11\r\n> apps.pilot.ligand_motifs: ATOM k: 17 Name: C10\r\n> apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 19, type is CH2; 17, type is CH1 \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: 17\r\n> apps.pilot.ligand_motifs: ATOM k: 20 Name: C12\r\n> apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 19, type is CH2; 20, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM j: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: ATOM k: 20 Name: C12\r\n> apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 21, type is Nhis; 20, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM k: 22 Name: C8 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 21, type is Nhis; 22, type is CH2 \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: 22\r\n> apps.pilot.ligand_motifs: ATOM k: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 21, type is Nhis; 23, type is aroC \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: 23\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 21\r\n> apps.pilot.ligand_motifs: atom name is N1 \r\n> apps.pilot.ligand_motifs: ATOM j: 20 Name: C12\r\n> apps.pilot.ligand_motifs: ATOM k: 19 Name: C11\r\n> apps.pilot.ligand_motifs: Connected triplet is: 21, type is Nhis; 20, type is CH2; 19, type is CH2 \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: N1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 21, type is Nhis; 20, type is CH2; 21, type is Nhis \r\n> apps.pilot.ligand_motifs: ATOM j: 22 Name: C8 \r\n> apps.pilot.ligand_motifs: ATOM k: 1 Name: C9 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 21, type is Nhis; 22, type is CH2; 1, type is CH2 \r\n> apps.pilot.ligand_motifs: atom_i: 21\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 22\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 1\r\n> apps.pilot.ligand_motifs: ATOM k: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 21, type is Nhis; 22, type is CH2; 21, type is Nhis \r\n> apps.pilot.ligand_motifs: ATOM j: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: ATOM k: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 21, type is Nhis; 23, type is aroC; 21, type is Nhis \r\n> apps.pilot.ligand_motifs: ATOM k: 24 Name: O1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 21, type is Nhis; 23, type is aroC; 24, type is Oaro \r\n> apps.pilot.ligand_motifs: atom_i: 21\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: 31 Name: N2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 21, type is Nhis; 23, type is aroC; 31, type is Nhis \r\n> apps.pilot.ligand_motifs: atom_i: 21\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 23\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 22\r\n> apps.pilot.ligand_motifs: atom name is C8 \r\n> apps.pilot.ligand_motifs: ATOM j: 1 Name: C9 \r\n> apps.pilot.ligand_motifs: ATOM k: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 22, type is CH2; 1, type is CH2; 2, type is Npro \r\n> apps.pilot.ligand_motifs: atom_i: 22\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: 22 Name: C8 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 22, type is CH2; 1, type is CH2; 22, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM j: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: ATOM k: 20 Name: C12\r\n> apps.pilot.ligand_motifs: Connected triplet is: 22, type is CH2; 21, type is Nhis; 20, type is CH2 \r\n> apps.pilot.ligand_motifs: atom_i: 22\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: ATOM k: 22 Name: C8 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 22, type is CH2; 21, type is Nhis; 22, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM k: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 22, type is CH2; 21, type is Nhis; 23, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 22\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 21\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 23\r\n> apps.pilot.ligand_motifs: atom name is C1 \r\n> apps.pilot.ligand_motifs: ATOM j: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: ATOM k: 20 Name: C12\r\n> apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 21, type is Nhis; 20, type is CH2 \r\n> apps.pilot.ligand_motifs: atom_i: 23\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: ATOM k: 22 Name: C8 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 21, type is Nhis; 22, type is CH2 \r\n> apps.pilot.ligand_motifs: atom_i: 23\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 21\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 22\r\n> apps.pilot.ligand_motifs: ATOM k: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 21, type is Nhis; 23, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 24 Name: O1 \r\n> apps.pilot.ligand_motifs: ATOM k: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 24, type is Oaro; 23, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 25 Name: C7 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 24, type is Oaro; 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: 31 Name: N2 \r\n> apps.pilot.ligand_motifs: ATOM k: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 31, type is Nhis; 23, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 31, type is Nhis; 30, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 23\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 31\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 24\r\n> apps.pilot.ligand_motifs: atom name is O1 \r\n> apps.pilot.ligand_motifs: ATOM j: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: ATOM k: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 24, type is Oaro; 23, type is aroC; 21, type is Nhis \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: 21\r\n> apps.pilot.ligand_motifs: ATOM k: 24 Name: O1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 24, type is Oaro; 23, type is aroC; 24, type is Oaro \r\n> apps.pilot.ligand_motifs: ATOM k: 31 Name: N2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 24, type is Oaro; 23, type is aroC; 31, type is Nhis \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: 31\r\n> apps.pilot.ligand_motifs: ATOM j: 25 Name: C7 \r\n> apps.pilot.ligand_motifs: ATOM k: 24 Name: O1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 24, type is Oaro; 25, type is aroC; 24, type is Oaro \r\n> apps.pilot.ligand_motifs: ATOM k: 26 Name: C6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 24, type is Oaro; 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: ATOM k: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 24, type is Oaro; 25, type is aroC; 30, 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: 30\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 25\r\n> apps.pilot.ligand_motifs: atom name is C7 \r\n> apps.pilot.ligand_motifs: ATOM j: 24 Name: O1 \r\n> apps.pilot.ligand_motifs: ATOM k: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 24, type is Oaro; 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: C7 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 24, type is Oaro; 25, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 26 Name: C6 \r\n> apps.pilot.ligand_motifs: ATOM k: 25 Name: C7 \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: C5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 26, type is aroC; 27, type is CH2 \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: ATOM j: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: ATOM k: 25 Name: C7 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 30, type is aroC; 25, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 29 Name: C3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 30, type is aroC; 29, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 25\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: ATOM k: 31 Name: N2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 30, type is aroC; 31, type is Nhis \r\n> apps.pilot.ligand_motifs: atom_i: 25\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 30\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 26\r\n> apps.pilot.ligand_motifs: atom name is C6 \r\n> apps.pilot.ligand_motifs: ATOM j: 25 Name: C7 \r\n> apps.pilot.ligand_motifs: ATOM k: 24 Name: O1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 25, type is aroC; 24, type is Oaro \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: C6 \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 k: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 25, type is aroC; 30, 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: 30\r\n> apps.pilot.ligand_motifs: ATOM j: 27 Name: C5 \r\n> apps.pilot.ligand_motifs: ATOM k: 26 Name: C6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 27, type is CH2; 26, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 28 Name: C4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 27, type is CH2; 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: in atom iterate block, atom num is 27\r\n> apps.pilot.ligand_motifs: atom name is C5 \r\n> apps.pilot.ligand_motifs: ATOM j: 26 Name: C6 \r\n> apps.pilot.ligand_motifs: ATOM k: 25 Name: C7 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 27, type is CH2; 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: C5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 27, type is CH2; 26, type is aroC; 27, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM j: 28 Name: C4 \r\n> apps.pilot.ligand_motifs: ATOM k: 27 Name: C5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 27, type is CH2; 28, type is aroC; 27, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM k: 29 Name: C3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 27, type is CH2; 28, type is aroC; 29, 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: 29\r\n> apps.pilot.ligand_motifs: ATOM k: 32 Name: CL1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 27, type is CH2; 28, type is aroC; 32, type is Cl \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: 32\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 28\r\n> apps.pilot.ligand_motifs: atom name is C4 \r\n> apps.pilot.ligand_motifs: ATOM j: 27 Name: C5 \r\n> apps.pilot.ligand_motifs: ATOM k: 26 Name: C6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 27, type is CH2; 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: C4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 27, type is CH2; 28, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 29 Name: C3 \r\n> apps.pilot.ligand_motifs: ATOM k: 28 Name: C4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 29, type is aroC; 28, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 29, type is aroC; 30, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 28\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: ATOM j: 32 Name: CL1 \r\n> apps.pilot.ligand_motifs: ATOM k: 28 Name: C4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 32, type is Cl; 28, type is aroC \r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 29\r\n> apps.pilot.ligand_motifs: atom name is C3 \r\n> apps.pilot.ligand_motifs: ATOM j: 28 Name: C4 \r\n> apps.pilot.ligand_motifs: ATOM k: 27 Name: C5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 28, type is aroC; 27, type is CH2 \r\n> apps.pilot.ligand_motifs: atom_i: 29\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: ATOM k: 29 Name: C3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 28, type is aroC; 29, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 32 Name: CL1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 28, type is aroC; 32, type is Cl \r\n> apps.pilot.ligand_motifs: atom_i: 29\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 28\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 32\r\n> apps.pilot.ligand_motifs: ATOM j: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: ATOM k: 25 Name: C7 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 30, type is aroC; 25, type is aroC \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: 25\r\n> apps.pilot.ligand_motifs: ATOM k: 29 Name: C3 \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: ATOM k: 31 Name: N2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 30, type is aroC; 31, 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: 31\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 30\r\n> apps.pilot.ligand_motifs: atom name is C2 \r\n> apps.pilot.ligand_motifs: ATOM j: 25 Name: C7 \r\n> apps.pilot.ligand_motifs: ATOM k: 24 Name: O1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 25, type is aroC; 24, type is Oaro \r\n> apps.pilot.ligand_motifs: atom_i: 30\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: C6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 25, type is aroC; 26, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 30\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: ATOM k: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 25, type is aroC; 30, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 29 Name: C3 \r\n> apps.pilot.ligand_motifs: ATOM k: 28 Name: C4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 29, type is aroC; 28, type is aroC \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: 28\r\n> apps.pilot.ligand_motifs: ATOM k: 30 Name: C2 \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: ATOM j: 31 Name: N2 \r\n> apps.pilot.ligand_motifs: ATOM k: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 31, type is Nhis; 23, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 30\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 31\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 23\r\n> apps.pilot.ligand_motifs: ATOM k: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 31, type is Nhis; 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 N2 \r\n> apps.pilot.ligand_motifs: ATOM j: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: ATOM k: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 31, type is Nhis; 23, type is aroC; 21, type is Nhis \r\n> apps.pilot.ligand_motifs: atom_i: 31\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 23\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 21\r\n> apps.pilot.ligand_motifs: ATOM k: 24 Name: O1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 31, type is Nhis; 23, type is aroC; 24, type is Oaro \r\n> apps.pilot.ligand_motifs: atom_i: 31\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: 31 Name: N2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 31, type is Nhis; 23, type is aroC; 31, type is Nhis \r\n> apps.pilot.ligand_motifs: ATOM j: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: ATOM k: 25 Name: C7 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 31, type is Nhis; 30, type is aroC; 25, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 31\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 30\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 25\r\n> apps.pilot.ligand_motifs: ATOM k: 29 Name: C3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 31, type is Nhis; 30, type is aroC; 29, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 31\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: ATOM k: 31 Name: N2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 31, type is Nhis; 30, type is aroC; 31, type is Nhis \r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 32\r\n> apps.pilot.ligand_motifs: atom name is CL1 \r\n> apps.pilot.ligand_motifs: ATOM j: 28 Name: C4 \r\n> apps.pilot.ligand_motifs: ATOM k: 27 Name: C5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 32, type is Cl; 28, type is aroC; 27, type is CH2 \r\n> apps.pilot.ligand_motifs: atom_i: 32\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: ATOM k: 29 Name: C3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 32, type is Cl; 28, type is aroC; 29, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 32\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 28\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 29\r\n> apps.pilot.ligand_motifs: ATOM k: 32 Name: CL1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 32, type is Cl; 28, type is aroC; 32, type is Cl \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: -2.03199, hbond score: 0, for a total score of: -2.03199\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 49: 27-28-32Writing THR62A_Z0_Ligatoms_27_28_32_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 82 passed energy cut with pack score: -2.19745, hbond score: 0, for a total score of: -2.19745\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 42: 24-25-30Writing PRO82A_Z0_Ligatoms_24_25_30_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 85 passed energy cut with pack score: -5.12186, hbond score: 0, for a total score of: -5.12186\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> protocols.motifs.Motif: Res1 name is GLN\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> apps.pilot.ligand_motifs: 26: 11-12-13Writing GLN85A_Z0_Ligatoms_11_12_13_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 86 passed energy cut with pack score: -1.24512, hbond score: 0, for a total score of: -1.24512\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 37: 22-21-23Writing THR86A_Z0_Ligatoms_22_21_23_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 134 passed energy cut with pack score: -2.38535, hbond score: 0, for a total score of: -2.38535\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 32: 19-20-21Writing GLN134A_Z0_Ligatoms_19_20_21_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 169 passed energy cut with pack score: -2.19109, hbond score: 0, for a total score of: -2.19109\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 25: 8-9-10Writing PHE169A_Z0_Ligatoms_8_9_10_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 419 passed energy cut with pack score: -2.98131, hbond score: 0, for a total score of: -2.98131\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 25: 8-9-10Writing ILE419A_Z0_Ligatoms_8_9_10_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 423 passed energy cut with pack score: -2.37074, hbond score: -0.655702, for a total score of: -3.02644\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 12: 4-3-16Writing ASN423A_Z0_Ligatoms_4_3_16_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 447 passed energy cut with pack score: -2.58216, hbond score: 0, for a total score of: -2.58216\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 29: 14-13-15Writing HIS447A_Z0_Ligatoms_14_13_15_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 450 passed energy cut with pack score: -1.21028, hbond score: 0, for a total score of: -1.21028\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 26: 11-12-13Writing VAL450A_Z0_Ligatoms_11_12_13_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 451 passed energy cut with pack score: -1.26157, hbond score: 0, for a total score of: -1.26157\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 49: 27-28-32Writing TYR451A_Z0_Ligatoms_27_28_32_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Motif index contains: 1-2-3\r\n> apps.pilot.ligand_motifs: Motif index contains: 1-2-17\r\n> apps.pilot.ligand_motifs: Motif index contains: 1-22-21\r\n> apps.pilot.ligand_motifs: Motif index contains: 2-1-22\r\n> apps.pilot.ligand_motifs: Motif index contains: 2-3-4\r\n> apps.pilot.ligand_motifs: Motif index contains: 2-3-16\r\n> apps.pilot.ligand_motifs: Motif index contains: 2-17-18\r\n> apps.pilot.ligand_motifs: Motif index contains: 2-17-19\r\n> apps.pilot.ligand_motifs: Motif index contains: 3-2-17\r\n> apps.pilot.ligand_motifs: Motif index contains: 3-4-5\r\n> apps.pilot.ligand_motifs: Motif index contains: 3-4-14\r\n> apps.pilot.ligand_motifs: Motif index contains: 4-3-16\r\n> apps.pilot.ligand_motifs: Motif index contains: 4-5-6\r\n> apps.pilot.ligand_motifs: Motif index contains: 4-5-11\r\n> apps.pilot.ligand_motifs: Motif index contains: 4-14-13\r\n> apps.pilot.ligand_motifs: Motif index contains: 5-4-14\r\n> apps.pilot.ligand_motifs: Motif index contains: 5-6-7\r\n> apps.pilot.ligand_motifs: Motif index contains: 5-6-10\r\n> apps.pilot.ligand_motifs: Motif index contains: 5-11-12\r\n> apps.pilot.ligand_motifs: Motif index contains: 6-5-11\r\n> apps.pilot.ligand_motifs: Motif index contains: 6-7-8\r\n> apps.pilot.ligand_motifs: Motif index contains: 6-10-9\r\n> apps.pilot.ligand_motifs: Motif index contains: 7-6-10\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: 11-12-13\r\n> apps.pilot.ligand_motifs: Motif index contains: 12-13-14\r\n> apps.pilot.ligand_motifs: Motif index contains: 12-13-15\r\n> apps.pilot.ligand_motifs: Motif index contains: 14-13-15\r\n> apps.pilot.ligand_motifs: Motif index contains: 17-19-20\r\n> apps.pilot.ligand_motifs: Motif index contains: 18-17-19\r\n> apps.pilot.ligand_motifs: Motif index contains: 19-20-21\r\n> apps.pilot.ligand_motifs: Motif index contains: 20-21-22\r\n> apps.pilot.ligand_motifs: Motif index contains: 20-21-23\r\n> apps.pilot.ligand_motifs: Motif index contains: 21-23-24\r\n> apps.pilot.ligand_motifs: Motif index contains: 21-23-31\r\n> apps.pilot.ligand_motifs: Motif index contains: 22-21-23\r\n> apps.pilot.ligand_motifs: Motif index contains: 23-24-25\r\n> apps.pilot.ligand_motifs: Motif index contains: 23-31-30\r\n> apps.pilot.ligand_motifs: Motif index contains: 24-23-31\r\n> apps.pilot.ligand_motifs: Motif index contains: 24-25-26\r\n> apps.pilot.ligand_motifs: Motif index contains: 24-25-30\r\n> apps.pilot.ligand_motifs: Motif index contains: 25-26-27\r\n> apps.pilot.ligand_motifs: Motif index contains: 25-30-29\r\n> apps.pilot.ligand_motifs: Motif index contains: 25-30-31\r\n> apps.pilot.ligand_motifs: Motif index contains: 26-25-30\r\n> apps.pilot.ligand_motifs: Motif index contains: 26-27-28\r\n> apps.pilot.ligand_motifs: Motif index contains: 27-28-29\r\n> apps.pilot.ligand_motifs: Motif index contains: 27-28-32\r\n> apps.pilot.ligand_motifs: Motif index contains: 28-29-30\r\n> apps.pilot.ligand_motifs: Motif index contains: 29-28-32\r\n> apps.pilot.ligand_motifs: Motif index contains: 29-30-31\r\n> LigandDiscoverySearch_out: Ligand placement created 11 total motifs\r\n> LigandDiscoverySearch_out: Ligand placement created motifs against significant residues: 447,450,419,134,86,423,85,\r\n> LigandDiscoverySearch_out: Ligand placement created 7 motifs for significant residues\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_delta_-24.612108_motifs_11_sigmotifs_7.pdb\r\n358,360d1701\r\n< LigandDiscoverySearch_out: Trio is C16 C15 C14\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n366,368d1706\r\n< LigandDiscoverySearch_out: Trio is C16 C15 N4 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n374,376d1711\r\n< LigandDiscoverySearch_out: Trio is C16 C17 C18\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n382,384d1716\r\n< LigandDiscoverySearch_out: Trio is C17 C16 C15\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n390,392d1721\r\n< LigandDiscoverySearch_out: Trio is C17 C18 C19\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n398,400d1726\r\n< LigandDiscoverySearch_out: Trio is C17 C18 C22\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n406,408d1731\r\n< LigandDiscoverySearch_out: Trio is C18 C17 C16\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n414,416d1736\r\n< LigandDiscoverySearch_out: Trio is C18 C19 C14\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n422,424d1741\r\n< LigandDiscoverySearch_out: Trio is C19 C14 C13\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n430,432c1747,1748\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---\r\n> LigandDiscoverySearch_export_space_fill_matrix_as_C_H_O_N_pdb: Preparing to make visualization pose for 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio46_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120951_SubRatio_0.776593.pdb\r\n> LigandDiscoverySearch_export_space_fill_matrix_as_C_H_O_N_pdb: Making viualization pdb 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio46_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120951_SubRatio_0.776593.pdb\r\n434c1750\r\n< LigandDiscoverySearch_out: # clashing cases for this trio = 1\r\n---\r\n> LigandDiscoverySearch_out: # clashing cases for this trio = 0\r\n436c1752\r\n< LigandDiscoverySearch_out: Total cases for trio: 1\r\n---\r\n> LigandDiscoverySearch_out: Total cases for trio: 0\r\n438,440d1753\r\n< LigandDiscoverySearch_out: Trio is C19 C18 C17\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n446,448d1758\r\n< LigandDiscoverySearch_out: Trio is C19 C18 C22\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n454,456d1763\r\n< LigandDiscoverySearch_out: Trio is C22 C18 C17\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n462,464d1768\r\n< LigandDiscoverySearch_out: Trio is C22 C18 C19\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n470,472d1773\r\n< LigandDiscoverySearch_out: Trio is O2 C13 N3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n478,481c1779,1785\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---\r\n> LigandDiscoverySearch_export_space_fill_matrix_as_C_H_O_N_pdb: Preparing to make visualization pose for 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000_WholeRatio_0.120987_SubRatio_0.801185.pdb\r\n> LigandDiscoverySearch_export_space_fill_matrix_as_C_H_O_N_pdb: Making viualization pdb 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000_WholeRatio_0.120987_SubRatio_0.801185.pdb\r\n> LigandDiscoverySearch_out: Pre-move delta score = -23.0626, fa_atr = -18.0683, fa_rep = 8.77181, fa_atr_rep before = 5581.19\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\n489,491c1793,3220\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---\r\n> protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: -1199.58 -1199.58\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 C9 \r\n> apps.pilot.ligand_motifs: ATOM j: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: ATOM k: 1 Name: C9 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 1, type is CH2; 2, type is Npro; 1, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM k: 3 Name: C13\r\n> apps.pilot.ligand_motifs: Connected triplet is: 1, type is CH2; 2, type is Npro; 3, type is COO \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: 3\r\n> apps.pilot.ligand_motifs: ATOM k: 17 Name: C10\r\n> apps.pilot.ligand_motifs: Connected triplet is: 1, type is CH2; 2, type is Npro; 17, type is CH1 \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 j: 22 Name: C8 \r\n> apps.pilot.ligand_motifs: ATOM k: 1 Name: C9 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 1, type is CH2; 22, type is CH2; 1, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM k: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 1, type is CH2; 22, type is CH2; 21, type is Nhis \r\n> apps.pilot.ligand_motifs: atom_i: 1\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 22\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 21\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 2\r\n> apps.pilot.ligand_motifs: atom name is N3 \r\n> apps.pilot.ligand_motifs: ATOM j: 1 Name: C9 \r\n> apps.pilot.ligand_motifs: ATOM k: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 2, type is Npro; 1, type is CH2; 2, type is Npro \r\n> apps.pilot.ligand_motifs: ATOM k: 22 Name: C8 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 2, type is Npro; 1, type is CH2; 22, 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: 22\r\n> apps.pilot.ligand_motifs: ATOM j: 3 Name: C13\r\n> apps.pilot.ligand_motifs: ATOM k: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 2, type is Npro; 3, type is COO; 2, type is Npro \r\n> apps.pilot.ligand_motifs: ATOM k: 4 Name: C14\r\n> apps.pilot.ligand_motifs: Connected triplet is: 2, type is Npro; 3, type is COO; 4, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 2\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 3\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 4\r\n> apps.pilot.ligand_motifs: ATOM k: 16 Name: O2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 2, type is Npro; 3, type is COO; 16, type is ONH2 \r\n> apps.pilot.ligand_motifs: atom_i: 2\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: 17 Name: C10\r\n> apps.pilot.ligand_motifs: ATOM k: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 2, type is Npro; 17, type is CH1; 2, type is Npro \r\n> apps.pilot.ligand_motifs: ATOM k: 18 Name: C23\r\n> apps.pilot.ligand_motifs: Connected triplet is: 2, type is Npro; 17, type is CH1; 18, type is CH3 \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 k: 19 Name: C11\r\n> apps.pilot.ligand_motifs: Connected triplet is: 2, type is Npro; 17, type is CH1; 19, 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: 19\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 3\r\n> apps.pilot.ligand_motifs: atom name is C13\r\n> apps.pilot.ligand_motifs: ATOM j: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: ATOM k: 1 Name: C9 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 3, type is COO; 2, type is Npro; 1, type is CH2 \r\n> apps.pilot.ligand_motifs: atom_i: 3\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: 3 Name: C13\r\n> apps.pilot.ligand_motifs: Connected triplet is: 3, type is COO; 2, type is Npro; 3, type is COO \r\n> apps.pilot.ligand_motifs: ATOM k: 17 Name: C10\r\n> apps.pilot.ligand_motifs: Connected triplet is: 3, type is COO; 2, type is Npro; 17, type is CH1 \r\n> apps.pilot.ligand_motifs: atom_i: 3\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 j: 4 Name: C14\r\n> apps.pilot.ligand_motifs: ATOM k: 3 Name: C13\r\n> apps.pilot.ligand_motifs: Connected triplet is: 3, type is COO; 4, type is aroC; 3, type is COO \r\n> apps.pilot.ligand_motifs: ATOM k: 5 Name: C15\r\n> apps.pilot.ligand_motifs: Connected triplet is: 3, type is COO; 4, type is aroC; 5, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 3\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: ATOM k: 14 Name: C19\r\n> apps.pilot.ligand_motifs: Connected triplet is: 3, type is COO; 4, type is aroC; 14, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 3\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 4\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 14\r\n> apps.pilot.ligand_motifs: ATOM j: 16 Name: O2 \r\n> apps.pilot.ligand_motifs: ATOM k: 3 Name: C13\r\n> apps.pilot.ligand_motifs: Connected triplet is: 3, type is COO; 16, type is ONH2; 3, type is COO \r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 4\r\n> apps.pilot.ligand_motifs: atom name is C14\r\n> apps.pilot.ligand_motifs: ATOM j: 3 Name: C13\r\n> apps.pilot.ligand_motifs: ATOM k: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 4, type is aroC; 3, type is COO; 2, type is Npro \r\n> apps.pilot.ligand_motifs: atom_i: 4\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 3\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 2\r\n> apps.pilot.ligand_motifs: ATOM k: 4 Name: C14\r\n> apps.pilot.ligand_motifs: Connected triplet is: 4, type is aroC; 3, type is COO; 4, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 16 Name: O2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 4, type is aroC; 3, type is COO; 16, type is ONH2 \r\n> apps.pilot.ligand_motifs: atom_i: 4\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: C15\r\n> apps.pilot.ligand_motifs: ATOM k: 4 Name: C14\r\n> apps.pilot.ligand_motifs: Connected triplet is: 4, type is aroC; 5, type is aroC; 4, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 6 Name: N4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 4, type is aroC; 5, type is aroC; 6, type is Npro \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: ATOM k: 11 Name: C16\r\n> apps.pilot.ligand_motifs: Connected triplet is: 4, type is aroC; 5, type is aroC; 11, type is aroC \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: 11\r\n> apps.pilot.ligand_motifs: ATOM j: 14 Name: C19\r\n> apps.pilot.ligand_motifs: ATOM k: 4 Name: C14\r\n> apps.pilot.ligand_motifs: Connected triplet is: 4, type is aroC; 14, type is aroC; 4, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 13 Name: C18\r\n> apps.pilot.ligand_motifs: Connected triplet is: 4, type is aroC; 14, 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: 14\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 C15\r\n> apps.pilot.ligand_motifs: ATOM j: 4 Name: C14\r\n> apps.pilot.ligand_motifs: ATOM k: 3 Name: C13\r\n> apps.pilot.ligand_motifs: Connected triplet is: 5, type is aroC; 4, type is aroC; 3, 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: 3\r\n> apps.pilot.ligand_motifs: ATOM k: 5 Name: C15\r\n> apps.pilot.ligand_motifs: Connected triplet is: 5, type is aroC; 4, type is aroC; 5, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 14 Name: C19\r\n> apps.pilot.ligand_motifs: Connected triplet is: 5, type is aroC; 4, type is aroC; 14, type is aroC \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: 14\r\n> apps.pilot.ligand_motifs: ATOM j: 6 Name: N4 \r\n> apps.pilot.ligand_motifs: ATOM k: 5 Name: C15\r\n> apps.pilot.ligand_motifs: Connected triplet is: 5, type is aroC; 6, type is Npro; 5, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 7 Name: N5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 5, type is aroC; 6, type is Npro; 7, type is Nhis \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: ATOM k: 10 Name: N6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 5, type is aroC; 6, type is Npro; 10, type is Nhis \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: 10\r\n> apps.pilot.ligand_motifs: ATOM j: 11 Name: C16\r\n> apps.pilot.ligand_motifs: ATOM k: 5 Name: C15\r\n> apps.pilot.ligand_motifs: Connected triplet is: 5, type is aroC; 11, type is aroC; 5, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 12 Name: C17\r\n> apps.pilot.ligand_motifs: Connected triplet is: 5, type is aroC; 11, type is aroC; 12, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 5\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 6\r\n> apps.pilot.ligand_motifs: atom name is N4 \r\n> apps.pilot.ligand_motifs: ATOM j: 5 Name: C15\r\n> apps.pilot.ligand_motifs: ATOM k: 4 Name: C14\r\n> apps.pilot.ligand_motifs: Connected triplet is: 6, type is Npro; 5, type is aroC; 4, type is aroC \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: N4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 6, type is Npro; 5, type is aroC; 6, type is Npro \r\n> apps.pilot.ligand_motifs: ATOM k: 11 Name: C16\r\n> apps.pilot.ligand_motifs: Connected triplet is: 6, type is Npro; 5, type is aroC; 11, type is aroC \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: 11\r\n> apps.pilot.ligand_motifs: ATOM j: 7 Name: N5 \r\n> apps.pilot.ligand_motifs: ATOM k: 6 Name: N4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 6, type is Npro; 7, type is Nhis; 6, type is Npro \r\n> apps.pilot.ligand_motifs: ATOM k: 8 Name: C20\r\n> apps.pilot.ligand_motifs: Connected triplet is: 6, type is Npro; 7, type is Nhis; 8, type is aroC \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: ATOM j: 10 Name: N6 \r\n> apps.pilot.ligand_motifs: ATOM k: 6 Name: N4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 6, type is Npro; 10, type is Nhis; 6, type is Npro \r\n> apps.pilot.ligand_motifs: ATOM k: 9 Name: C21\r\n> apps.pilot.ligand_motifs: Connected triplet is: 6, type is Npro; 10, type is Nhis; 9, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 6\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: in atom iterate block, atom num is 7\r\n> apps.pilot.ligand_motifs: atom name is N5 \r\n> apps.pilot.ligand_motifs: ATOM j: 6 Name: N4 \r\n> apps.pilot.ligand_motifs: ATOM k: 5 Name: C15\r\n> apps.pilot.ligand_motifs: Connected triplet is: 7, type is Nhis; 6, type is Npro; 5, type is aroC \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: N5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 7, type is Nhis; 6, type is Npro; 7, type is Nhis \r\n> apps.pilot.ligand_motifs: ATOM k: 10 Name: N6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 7, type is Nhis; 6, type is Npro; 10, type is Nhis \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: 10\r\n> apps.pilot.ligand_motifs: ATOM j: 8 Name: C20\r\n> apps.pilot.ligand_motifs: ATOM k: 7 Name: N5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 7, type is Nhis; 8, type is aroC; 7, type is Nhis \r\n> apps.pilot.ligand_motifs: ATOM k: 9 Name: C21\r\n> apps.pilot.ligand_motifs: Connected triplet is: 7, type is Nhis; 8, type is aroC; 9, type is aroC \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 C20\r\n> apps.pilot.ligand_motifs: ATOM j: 7 Name: N5 \r\n> apps.pilot.ligand_motifs: ATOM k: 6 Name: N4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 8, type is aroC; 7, type is Nhis; 6, type is Npro \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: C20\r\n> apps.pilot.ligand_motifs: Connected triplet is: 8, type is aroC; 7, type is Nhis; 8, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 9 Name: C21\r\n> apps.pilot.ligand_motifs: ATOM k: 8 Name: C20\r\n> apps.pilot.ligand_motifs: Connected triplet is: 8, type is aroC; 9, type is aroC; 8, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 10 Name: N6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 8, type is aroC; 9, type is aroC; 10, type is Nhis \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 C21\r\n> apps.pilot.ligand_motifs: ATOM j: 8 Name: C20\r\n> apps.pilot.ligand_motifs: ATOM k: 7 Name: N5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 8, type is aroC; 7, type is Nhis \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: C21\r\n> apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 8, type is aroC; 9, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 10 Name: N6 \r\n> apps.pilot.ligand_motifs: ATOM k: 6 Name: N4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 10, type is Nhis; 6, type is Npro \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: 6\r\n> apps.pilot.ligand_motifs: ATOM k: 9 Name: C21\r\n> apps.pilot.ligand_motifs: Connected triplet is: 9, type is aroC; 10, type is Nhis; 9, type is aroC \r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 10\r\n> apps.pilot.ligand_motifs: atom name is N6 \r\n> apps.pilot.ligand_motifs: ATOM j: 6 Name: N4 \r\n> apps.pilot.ligand_motifs: ATOM k: 5 Name: C15\r\n> apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 6, type is Npro; 5, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 10\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: N5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 6, type is Npro; 7, type is Nhis \r\n> apps.pilot.ligand_motifs: atom_i: 10\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: ATOM k: 10 Name: N6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 6, type is Npro; 10, type is Nhis \r\n> apps.pilot.ligand_motifs: ATOM j: 9 Name: C21\r\n> apps.pilot.ligand_motifs: ATOM k: 8 Name: C20\r\n> apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 9, type is aroC; 8, type is aroC \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: N6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 10, type is Nhis; 9, type is aroC; 10, type is Nhis \r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 11\r\n> apps.pilot.ligand_motifs: atom name is C16\r\n> apps.pilot.ligand_motifs: ATOM j: 5 Name: C15\r\n> apps.pilot.ligand_motifs: ATOM k: 4 Name: C14\r\n> apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 5, type is aroC; 4, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 11\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: N4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 5, type is aroC; 6, type is Npro \r\n> apps.pilot.ligand_motifs: atom_i: 11\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: ATOM k: 11 Name: C16\r\n> apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 5, type is aroC; 11, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 12 Name: C17\r\n> apps.pilot.ligand_motifs: ATOM k: 11 Name: C16\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: C18\r\n> apps.pilot.ligand_motifs: Connected triplet is: 11, type is aroC; 12, type is aroC; 13, type is aroC \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 C17\r\n> apps.pilot.ligand_motifs: ATOM j: 11 Name: C16\r\n> apps.pilot.ligand_motifs: ATOM k: 5 Name: C15\r\n> apps.pilot.ligand_motifs: Connected triplet is: 12, type is aroC; 11, type is aroC; 5, type is aroC \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: 5\r\n> apps.pilot.ligand_motifs: ATOM k: 12 Name: C17\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: C18\r\n> apps.pilot.ligand_motifs: ATOM k: 12 Name: C17\r\n> apps.pilot.ligand_motifs: Connected triplet is: 12, type is aroC; 13, type is aroC; 12, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 14 Name: C19\r\n> apps.pilot.ligand_motifs: Connected triplet is: 12, type is aroC; 13, type is aroC; 14, type is aroC \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: ATOM k: 15 Name: C22\r\n> apps.pilot.ligand_motifs: Connected triplet is: 12, type is aroC; 13, type is aroC; 15, type is CH3 \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: 15\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 13\r\n> apps.pilot.ligand_motifs: atom name is C18\r\n> apps.pilot.ligand_motifs: ATOM j: 12 Name: C17\r\n> apps.pilot.ligand_motifs: ATOM k: 11 Name: C16\r\n> apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 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: C18\r\n> apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 12, type is aroC; 13, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 14 Name: C19\r\n> apps.pilot.ligand_motifs: ATOM k: 4 Name: C14\r\n> apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 14, type is aroC; 4, type is aroC \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: 4\r\n> apps.pilot.ligand_motifs: ATOM k: 13 Name: C18\r\n> apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 14, type is aroC; 13, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 15 Name: C22\r\n> apps.pilot.ligand_motifs: ATOM k: 13 Name: C18\r\n> apps.pilot.ligand_motifs: Connected triplet is: 13, type is aroC; 15, type is CH3; 13, type is aroC \r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 14\r\n> apps.pilot.ligand_motifs: atom name is C19\r\n> apps.pilot.ligand_motifs: ATOM j: 4 Name: C14\r\n> apps.pilot.ligand_motifs: ATOM k: 3 Name: C13\r\n> apps.pilot.ligand_motifs: Connected triplet is: 14, type is aroC; 4, type is aroC; 3, type is COO \r\n> apps.pilot.ligand_motifs: atom_i: 14\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 4\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 3\r\n> apps.pilot.ligand_motifs: ATOM k: 5 Name: C15\r\n> apps.pilot.ligand_motifs: Connected triplet is: 14, type is aroC; 4, type is aroC; 5, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 14\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: ATOM k: 14 Name: C19\r\n> apps.pilot.ligand_motifs: Connected triplet is: 14, type is aroC; 4, type is aroC; 14, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 13 Name: C18\r\n> apps.pilot.ligand_motifs: ATOM k: 12 Name: C17\r\n> apps.pilot.ligand_motifs: Connected triplet is: 14, type is aroC; 13, type is aroC; 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: C19\r\n> apps.pilot.ligand_motifs: Connected triplet is: 14, type is aroC; 13, type is aroC; 14, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 15 Name: C22\r\n> apps.pilot.ligand_motifs: Connected triplet is: 14, type is aroC; 13, type is aroC; 15, type is CH3 \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: 15\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 15\r\n> apps.pilot.ligand_motifs: atom name is C22\r\n> apps.pilot.ligand_motifs: ATOM j: 13 Name: C18\r\n> apps.pilot.ligand_motifs: ATOM k: 12 Name: C17\r\n> apps.pilot.ligand_motifs: Connected triplet is: 15, type is CH3; 13, type is aroC; 12, 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: 12\r\n> apps.pilot.ligand_motifs: ATOM k: 14 Name: C19\r\n> apps.pilot.ligand_motifs: Connected triplet is: 15, type is CH3; 13, type is aroC; 14, 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: 14\r\n> apps.pilot.ligand_motifs: ATOM k: 15 Name: C22\r\n> apps.pilot.ligand_motifs: Connected triplet is: 15, type is CH3; 13, type is aroC; 15, type is CH3 \r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 16\r\n> apps.pilot.ligand_motifs: atom name is O2 \r\n> apps.pilot.ligand_motifs: ATOM j: 3 Name: C13\r\n> apps.pilot.ligand_motifs: ATOM k: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 16, type is ONH2; 3, type is COO; 2, type is Npro \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: 2\r\n> apps.pilot.ligand_motifs: ATOM k: 4 Name: C14\r\n> apps.pilot.ligand_motifs: Connected triplet is: 16, type is ONH2; 3, type is COO; 4, 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: 4\r\n> apps.pilot.ligand_motifs: ATOM k: 16 Name: O2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 16, type is ONH2; 3, type is COO; 16, type is ONH2 \r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 17\r\n> apps.pilot.ligand_motifs: atom name is C10\r\n> apps.pilot.ligand_motifs: ATOM j: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: ATOM k: 1 Name: C9 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH1; 2, type is Npro; 1, 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: 1\r\n> apps.pilot.ligand_motifs: ATOM k: 3 Name: C13\r\n> apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH1; 2, type is Npro; 3, type is COO \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: 3\r\n> apps.pilot.ligand_motifs: ATOM k: 17 Name: C10\r\n> apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH1; 2, type is Npro; 17, type is CH1 \r\n> apps.pilot.ligand_motifs: ATOM j: 18 Name: C23\r\n> apps.pilot.ligand_motifs: ATOM k: 17 Name: C10\r\n> apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH1; 18, type is CH3; 17, type is CH1 \r\n> apps.pilot.ligand_motifs: ATOM j: 19 Name: C11\r\n> apps.pilot.ligand_motifs: ATOM k: 17 Name: C10\r\n> apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH1; 19, type is CH2; 17, type is CH1 \r\n> apps.pilot.ligand_motifs: ATOM k: 20 Name: C12\r\n> apps.pilot.ligand_motifs: Connected triplet is: 17, type is CH1; 19, type is CH2; 20, type is CH2 \r\n> apps.pilot.ligand_motifs: atom_i: 17\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 18\r\n> apps.pilot.ligand_motifs: atom name is C23\r\n> apps.pilot.ligand_motifs: ATOM j: 17 Name: C10\r\n> apps.pilot.ligand_motifs: ATOM k: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH3; 17, type is CH1; 2, type is Npro \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: C23\r\n> apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH3; 17, type is CH1; 18, type is CH3 \r\n> apps.pilot.ligand_motifs: ATOM k: 19 Name: C11\r\n> apps.pilot.ligand_motifs: Connected triplet is: 18, type is CH3; 17, type is CH1; 19, 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: 19\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 19\r\n> apps.pilot.ligand_motifs: atom name is C11\r\n> apps.pilot.ligand_motifs: ATOM j: 17 Name: C10\r\n> apps.pilot.ligand_motifs: ATOM k: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH2; 17, type is CH1; 2, type is Npro \r\n> apps.pilot.ligand_motifs: atom_i: 19\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: C23\r\n> apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH2; 17, type is CH1; 18, type is CH3 \r\n> apps.pilot.ligand_motifs: atom_i: 19\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 k: 19 Name: C11\r\n> apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH2; 17, type is CH1; 19, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM j: 20 Name: C12\r\n> apps.pilot.ligand_motifs: ATOM k: 19 Name: C11\r\n> apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH2; 20, type is CH2; 19, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM k: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 19, type is CH2; 20, type is CH2; 21, type is Nhis \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: in atom iterate block, atom num is 20\r\n> apps.pilot.ligand_motifs: atom name is C12\r\n> apps.pilot.ligand_motifs: ATOM j: 19 Name: C11\r\n> apps.pilot.ligand_motifs: ATOM k: 17 Name: C10\r\n> apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 19, type is CH2; 17, type is CH1 \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: 17\r\n> apps.pilot.ligand_motifs: ATOM k: 20 Name: C12\r\n> apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 19, type is CH2; 20, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM j: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: ATOM k: 20 Name: C12\r\n> apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 21, type is Nhis; 20, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM k: 22 Name: C8 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 21, type is Nhis; 22, type is CH2 \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: 22\r\n> apps.pilot.ligand_motifs: ATOM k: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 20, type is CH2; 21, type is Nhis; 23, type is aroC \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: 23\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 21\r\n> apps.pilot.ligand_motifs: atom name is N1 \r\n> apps.pilot.ligand_motifs: ATOM j: 20 Name: C12\r\n> apps.pilot.ligand_motifs: ATOM k: 19 Name: C11\r\n> apps.pilot.ligand_motifs: Connected triplet is: 21, type is Nhis; 20, type is CH2; 19, type is CH2 \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: N1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 21, type is Nhis; 20, type is CH2; 21, type is Nhis \r\n> apps.pilot.ligand_motifs: ATOM j: 22 Name: C8 \r\n> apps.pilot.ligand_motifs: ATOM k: 1 Name: C9 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 21, type is Nhis; 22, type is CH2; 1, type is CH2 \r\n> apps.pilot.ligand_motifs: atom_i: 21\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 22\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 1\r\n> apps.pilot.ligand_motifs: ATOM k: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 21, type is Nhis; 22, type is CH2; 21, type is Nhis \r\n> apps.pilot.ligand_motifs: ATOM j: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: ATOM k: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 21, type is Nhis; 23, type is aroC; 21, type is Nhis \r\n> apps.pilot.ligand_motifs: ATOM k: 24 Name: O1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 21, type is Nhis; 23, type is aroC; 24, type is Oaro \r\n> apps.pilot.ligand_motifs: atom_i: 21\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: 31 Name: N2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 21, type is Nhis; 23, type is aroC; 31, type is Nhis \r\n> apps.pilot.ligand_motifs: atom_i: 21\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 23\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 22\r\n> apps.pilot.ligand_motifs: atom name is C8 \r\n> apps.pilot.ligand_motifs: ATOM j: 1 Name: C9 \r\n> apps.pilot.ligand_motifs: ATOM k: 2 Name: N3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 22, type is CH2; 1, type is CH2; 2, type is Npro \r\n> apps.pilot.ligand_motifs: atom_i: 22\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: 22 Name: C8 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 22, type is CH2; 1, type is CH2; 22, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM j: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: ATOM k: 20 Name: C12\r\n> apps.pilot.ligand_motifs: Connected triplet is: 22, type is CH2; 21, type is Nhis; 20, type is CH2 \r\n> apps.pilot.ligand_motifs: atom_i: 22\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: ATOM k: 22 Name: C8 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 22, type is CH2; 21, type is Nhis; 22, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM k: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 22, type is CH2; 21, type is Nhis; 23, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 22\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 21\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 23\r\n> apps.pilot.ligand_motifs: atom name is C1 \r\n> apps.pilot.ligand_motifs: ATOM j: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: ATOM k: 20 Name: C12\r\n> apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 21, type is Nhis; 20, type is CH2 \r\n> apps.pilot.ligand_motifs: atom_i: 23\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: ATOM k: 22 Name: C8 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 21, type is Nhis; 22, type is CH2 \r\n> apps.pilot.ligand_motifs: atom_i: 23\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 21\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 22\r\n> apps.pilot.ligand_motifs: ATOM k: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 21, type is Nhis; 23, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 24 Name: O1 \r\n> apps.pilot.ligand_motifs: ATOM k: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 24, type is Oaro; 23, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 25 Name: C7 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 24, type is Oaro; 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: 31 Name: N2 \r\n> apps.pilot.ligand_motifs: ATOM k: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 31, type is Nhis; 23, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 23, type is aroC; 31, type is Nhis; 30, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 23\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 31\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 24\r\n> apps.pilot.ligand_motifs: atom name is O1 \r\n> apps.pilot.ligand_motifs: ATOM j: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: ATOM k: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 24, type is Oaro; 23, type is aroC; 21, type is Nhis \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: 21\r\n> apps.pilot.ligand_motifs: ATOM k: 24 Name: O1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 24, type is Oaro; 23, type is aroC; 24, type is Oaro \r\n> apps.pilot.ligand_motifs: ATOM k: 31 Name: N2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 24, type is Oaro; 23, type is aroC; 31, type is Nhis \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: 31\r\n> apps.pilot.ligand_motifs: ATOM j: 25 Name: C7 \r\n> apps.pilot.ligand_motifs: ATOM k: 24 Name: O1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 24, type is Oaro; 25, type is aroC; 24, type is Oaro \r\n> apps.pilot.ligand_motifs: ATOM k: 26 Name: C6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 24, type is Oaro; 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: ATOM k: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 24, type is Oaro; 25, type is aroC; 30, 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: 30\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 25\r\n> apps.pilot.ligand_motifs: atom name is C7 \r\n> apps.pilot.ligand_motifs: ATOM j: 24 Name: O1 \r\n> apps.pilot.ligand_motifs: ATOM k: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 24, type is Oaro; 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: C7 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 24, type is Oaro; 25, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 26 Name: C6 \r\n> apps.pilot.ligand_motifs: ATOM k: 25 Name: C7 \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: C5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 26, type is aroC; 27, type is CH2 \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: ATOM j: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: ATOM k: 25 Name: C7 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 30, type is aroC; 25, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 29 Name: C3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 30, type is aroC; 29, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 25\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: ATOM k: 31 Name: N2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 25, type is aroC; 30, type is aroC; 31, type is Nhis \r\n> apps.pilot.ligand_motifs: atom_i: 25\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 30\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 26\r\n> apps.pilot.ligand_motifs: atom name is C6 \r\n> apps.pilot.ligand_motifs: ATOM j: 25 Name: C7 \r\n> apps.pilot.ligand_motifs: ATOM k: 24 Name: O1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 25, type is aroC; 24, type is Oaro \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: C6 \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 k: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 25, type is aroC; 30, 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: 30\r\n> apps.pilot.ligand_motifs: ATOM j: 27 Name: C5 \r\n> apps.pilot.ligand_motifs: ATOM k: 26 Name: C6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 27, type is CH2; 26, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 28 Name: C4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 26, type is aroC; 27, type is CH2; 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: in atom iterate block, atom num is 27\r\n> apps.pilot.ligand_motifs: atom name is C5 \r\n> apps.pilot.ligand_motifs: ATOM j: 26 Name: C6 \r\n> apps.pilot.ligand_motifs: ATOM k: 25 Name: C7 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 27, type is CH2; 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: C5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 27, type is CH2; 26, type is aroC; 27, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM j: 28 Name: C4 \r\n> apps.pilot.ligand_motifs: ATOM k: 27 Name: C5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 27, type is CH2; 28, type is aroC; 27, type is CH2 \r\n> apps.pilot.ligand_motifs: ATOM k: 29 Name: C3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 27, type is CH2; 28, type is aroC; 29, 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: 29\r\n> apps.pilot.ligand_motifs: ATOM k: 32 Name: CL1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 27, type is CH2; 28, type is aroC; 32, type is Cl \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: 32\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 28\r\n> apps.pilot.ligand_motifs: atom name is C4 \r\n> apps.pilot.ligand_motifs: ATOM j: 27 Name: C5 \r\n> apps.pilot.ligand_motifs: ATOM k: 26 Name: C6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 27, type is CH2; 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: C4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 27, type is CH2; 28, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 29 Name: C3 \r\n> apps.pilot.ligand_motifs: ATOM k: 28 Name: C4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 29, type is aroC; 28, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 29, type is aroC; 30, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 28\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: ATOM j: 32 Name: CL1 \r\n> apps.pilot.ligand_motifs: ATOM k: 28 Name: C4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 28, type is aroC; 32, type is Cl; 28, type is aroC \r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 29\r\n> apps.pilot.ligand_motifs: atom name is C3 \r\n> apps.pilot.ligand_motifs: ATOM j: 28 Name: C4 \r\n> apps.pilot.ligand_motifs: ATOM k: 27 Name: C5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 28, type is aroC; 27, type is CH2 \r\n> apps.pilot.ligand_motifs: atom_i: 29\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: ATOM k: 29 Name: C3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 28, type is aroC; 29, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM k: 32 Name: CL1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 28, type is aroC; 32, type is Cl \r\n> apps.pilot.ligand_motifs: atom_i: 29\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 28\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 32\r\n> apps.pilot.ligand_motifs: ATOM j: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: ATOM k: 25 Name: C7 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 30, type is aroC; 25, type is aroC \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: 25\r\n> apps.pilot.ligand_motifs: ATOM k: 29 Name: C3 \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: ATOM k: 31 Name: N2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 29, type is aroC; 30, type is aroC; 31, 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: 31\r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 30\r\n> apps.pilot.ligand_motifs: atom name is C2 \r\n> apps.pilot.ligand_motifs: ATOM j: 25 Name: C7 \r\n> apps.pilot.ligand_motifs: ATOM k: 24 Name: O1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 25, type is aroC; 24, type is Oaro \r\n> apps.pilot.ligand_motifs: atom_i: 30\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: C6 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 25, type is aroC; 26, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 30\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: ATOM k: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 25, type is aroC; 30, type is aroC \r\n> apps.pilot.ligand_motifs: ATOM j: 29 Name: C3 \r\n> apps.pilot.ligand_motifs: ATOM k: 28 Name: C4 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 29, type is aroC; 28, type is aroC \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: 28\r\n> apps.pilot.ligand_motifs: ATOM k: 30 Name: C2 \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: ATOM j: 31 Name: N2 \r\n> apps.pilot.ligand_motifs: ATOM k: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 31, type is Nhis; 23, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 30\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 31\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 23\r\n> apps.pilot.ligand_motifs: ATOM k: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 30, type is aroC; 31, type is Nhis; 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 N2 \r\n> apps.pilot.ligand_motifs: ATOM j: 23 Name: C1 \r\n> apps.pilot.ligand_motifs: ATOM k: 21 Name: N1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 31, type is Nhis; 23, type is aroC; 21, type is Nhis \r\n> apps.pilot.ligand_motifs: atom_i: 31\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 23\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 21\r\n> apps.pilot.ligand_motifs: ATOM k: 24 Name: O1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 31, type is Nhis; 23, type is aroC; 24, type is Oaro \r\n> apps.pilot.ligand_motifs: atom_i: 31\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: 31 Name: N2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 31, type is Nhis; 23, type is aroC; 31, type is Nhis \r\n> apps.pilot.ligand_motifs: ATOM j: 30 Name: C2 \r\n> apps.pilot.ligand_motifs: ATOM k: 25 Name: C7 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 31, type is Nhis; 30, type is aroC; 25, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 31\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 30\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 25\r\n> apps.pilot.ligand_motifs: ATOM k: 29 Name: C3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 31, type is Nhis; 30, type is aroC; 29, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 31\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: ATOM k: 31 Name: N2 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 31, type is Nhis; 30, type is aroC; 31, type is Nhis \r\n> apps.pilot.ligand_motifs: in atom iterate block, atom num is 32\r\n> apps.pilot.ligand_motifs: atom name is CL1 \r\n> apps.pilot.ligand_motifs: ATOM j: 28 Name: C4 \r\n> apps.pilot.ligand_motifs: ATOM k: 27 Name: C5 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 32, type is Cl; 28, type is aroC; 27, type is CH2 \r\n> apps.pilot.ligand_motifs: atom_i: 32\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: ATOM k: 29 Name: C3 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 32, type is Cl; 28, type is aroC; 29, type is aroC \r\n> apps.pilot.ligand_motifs: atom_i: 32\r\n> apps.pilot.ligand_motifs: atom_i to atom_j: 28\r\n> apps.pilot.ligand_motifs: atom_j to atom_k: 29\r\n> apps.pilot.ligand_motifs: ATOM k: 32 Name: CL1 \r\n> apps.pilot.ligand_motifs: Connected triplet is: 32, type is Cl; 28, type is aroC; 32, type is Cl \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: -1.99531, hbond score: 0, for a total score of: -1.99531\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 49: 27-28-32Writing THR62A_Z0_Ligatoms_27_28_32_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 82 passed energy cut with pack score: -2.06568, hbond score: 0, for a total score of: -2.06568\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 42: 24-25-30Writing PRO82A_Z0_Ligatoms_24_25_30_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 85 passed energy cut with pack score: -5.17614, hbond score: 0, for a total score of: -5.17614\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 42: 24-25-30Writing GLN85A_Z0_Ligatoms_24_25_30_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 86 passed energy cut with pack score: -1.18238, hbond score: 0, for a total score of: -1.18238\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 37: 22-21-23Writing THR86A_Z0_Ligatoms_22_21_23_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 134 passed energy cut with pack score: -2.09506, hbond score: 0, for a total score of: -2.09506\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 32: 19-20-21Writing GLN134A_Z0_Ligatoms_19_20_21_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 169 passed energy cut with pack score: -2.04138, hbond score: 0, for a total score of: -2.04138\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 25: 8-9-10Writing PHE169A_Z0_Ligatoms_8_9_10_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 419 passed energy cut with pack score: -3.35941, hbond score: 0, for a total score of: -3.35941\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 25: 8-9-10Writing ILE419A_Z0_Ligatoms_8_9_10_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 423 passed energy cut with pack score: -2.54004, hbond score: -0.738491, for a total score of: -3.27853\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 12: 4-3-16Writing ASN423A_Z0_Ligatoms_4_3_16_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 447 passed energy cut with pack score: -2.68983, hbond score: 0, for a total score of: -2.68983\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 29: 14-13-15Writing HIS447A_Z0_Ligatoms_14_13_15_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 450 passed energy cut with pack score: -1.42878, hbond score: 0, for a total score of: -1.42878\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 26: 11-12-13Writing VAL450A_Z0_Ligatoms_11_12_13_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Residue 451 passed energy cut with pack score: -1.3488, hbond score: 0, for a total score of: -1.3488\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> apps.pilot.ligand_motifs: Skipping motif whose closest atom-atom distance is no closer than 5.0 angstroms\r\n> 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> 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> apps.pilot.ligand_motifs: 29: 14-13-15Writing TYR451A_Z0_Ligatoms_14_13_15_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\n> apps.pilot.ligand_motifs: Motif index contains: 1-2-3\r\n> apps.pilot.ligand_motifs: Motif index contains: 1-2-17\r\n> apps.pilot.ligand_motifs: Motif index contains: 1-22-21\r\n> apps.pilot.ligand_motifs: Motif index contains: 2-1-22\r\n> apps.pilot.ligand_motifs: Motif index contains: 2-3-4\r\n> apps.pilot.ligand_motifs: Motif index contains: 2-3-16\r\n> apps.pilot.ligand_motifs: Motif index contains: 2-17-18\r\n> apps.pilot.ligand_motifs: Motif index contains: 2-17-19\r\n> apps.pilot.ligand_motifs: Motif index contains: 3-2-17\r\n> apps.pilot.ligand_motifs: Motif index contains: 3-4-5\r\n> apps.pilot.ligand_motifs: Motif index contains: 3-4-14\r\n> apps.pilot.ligand_motifs: Motif index contains: 4-3-16\r\n> apps.pilot.ligand_motifs: Motif index contains: 4-5-6\r\n> apps.pilot.ligand_motifs: Motif index contains: 4-5-11\r\n> apps.pilot.ligand_motifs: Motif index contains: 4-14-13\r\n> apps.pilot.ligand_motifs: Motif index contains: 5-4-14\r\n> apps.pilot.ligand_motifs: Motif index contains: 5-6-7\r\n> apps.pilot.ligand_motifs: Motif index contains: 5-6-10\r\n> apps.pilot.ligand_motifs: Motif index contains: 5-11-12\r\n> apps.pilot.ligand_motifs: Motif index contains: 6-5-11\r\n> apps.pilot.ligand_motifs: Motif index contains: 6-7-8\r\n> apps.pilot.ligand_motifs: Motif index contains: 6-10-9\r\n> apps.pilot.ligand_motifs: Motif index contains: 7-6-10\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: 11-12-13\r\n> apps.pilot.ligand_motifs: Motif index contains: 12-13-14\r\n> apps.pilot.ligand_motifs: Motif index contains: 12-13-15\r\n> apps.pilot.ligand_motifs: Motif index contains: 14-13-15\r\n> apps.pilot.ligand_motifs: Motif index contains: 17-19-20\r\n> apps.pilot.ligand_motifs: Motif index contains: 18-17-19\r\n> apps.pilot.ligand_motifs: Motif index contains: 19-20-21\r\n> apps.pilot.ligand_motifs: Motif index contains: 20-21-22\r\n> apps.pilot.ligand_motifs: Motif index contains: 20-21-23\r\n> apps.pilot.ligand_motifs: Motif index contains: 21-23-24\r\n> apps.pilot.ligand_motifs: Motif index contains: 21-23-31\r\n> apps.pilot.ligand_motifs: Motif index contains: 22-21-23\r\n> apps.pilot.ligand_motifs: Motif index contains: 23-24-25\r\n> apps.pilot.ligand_motifs: Motif index contains: 23-31-30\r\n> apps.pilot.ligand_motifs: Motif index contains: 24-23-31\r\n> apps.pilot.ligand_motifs: Motif index contains: 24-25-26\r\n> apps.pilot.ligand_motifs: Motif index contains: 24-25-30\r\n> apps.pilot.ligand_motifs: Motif index contains: 25-26-27\r\n> apps.pilot.ligand_motifs: Motif index contains: 25-30-29\r\n> apps.pilot.ligand_motifs: Motif index contains: 25-30-31\r\n> apps.pilot.ligand_motifs: Motif index contains: 26-25-30\r\n> apps.pilot.ligand_motifs: Motif index contains: 26-27-28\r\n> apps.pilot.ligand_motifs: Motif index contains: 27-28-29\r\n> apps.pilot.ligand_motifs: Motif index contains: 27-28-32\r\n> apps.pilot.ligand_motifs: Motif index contains: 28-29-30\r\n> apps.pilot.ligand_motifs: Motif index contains: 29-28-32\r\n> apps.pilot.ligand_motifs: Motif index contains: 29-30-31\r\n> LigandDiscoverySearch_out: Ligand placement created 11 total motifs\r\n> LigandDiscoverySearch_out: Ligand placement created motifs against significant residues: 447,450,419,134,86,423,85,\r\n> LigandDiscoverySearch_out: Ligand placement created 7 motifs for significant residues\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_delta_-25.058549_motifs_11_sigmotifs_7.pdb\r\n497,499d3225\r\n< LigandDiscoverySearch_out: Trio is C10 N3 C9 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n505,507d3230\r\n< LigandDiscoverySearch_out: Trio is C10 N3 C13\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n513,515d3235\r\n< LigandDiscoverySearch_out: Trio is C10 C11 C12\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n521,523d3240\r\n< LigandDiscoverySearch_out: Trio is C23 C10 N3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n529,531d3245\r\n< LigandDiscoverySearch_out: Trio is C23 C10 C11\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n537,539d3250\r\n< LigandDiscoverySearch_out: Trio is C11 C10 N3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n545,547d3255\r\n< LigandDiscoverySearch_out: Trio is C11 C10 C23\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n553,555d3260\r\n< LigandDiscoverySearch_out: Trio is C11 C12 N1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n561,563d3265\r\n< LigandDiscoverySearch_out: Trio is C12 C11 C10\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n569,571d3270\r\n< LigandDiscoverySearch_out: Trio is C12 N1 C8 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n577,579d3275\r\n< LigandDiscoverySearch_out: Trio is C12 N1 C1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n585,587d3280\r\n< LigandDiscoverySearch_out: Trio is N1 C12 C11\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n593,595d3285\r\n< LigandDiscoverySearch_out: Trio is N1 C8 C9 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n601,603d3290\r\n< LigandDiscoverySearch_out: Trio is N1 C1 O1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n609,611d3295\r\n< LigandDiscoverySearch_out: Trio is N1 C1 N2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n617,619d3300\r\n< LigandDiscoverySearch_out: Trio is C8 C9 N3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n625,627d3305\r\n< LigandDiscoverySearch_out: Trio is C8 N1 C12\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n633,635d3310\r\n< LigandDiscoverySearch_out: Trio is C8 N1 C1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n641,643d3315\r\n< LigandDiscoverySearch_out: Trio is C1 N1 C12\r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n649,651d3320\r\n< LigandDiscoverySearch_out: Trio is C1 N1 C8 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n657,659d3325\r\n< LigandDiscoverySearch_out: Trio is C1 O1 C7 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n665,667d3330\r\n< LigandDiscoverySearch_out: Trio is C1 N2 C2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n673,675d3335\r\n< LigandDiscoverySearch_out: Trio is O1 C1 N1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n681,683d3340\r\n< LigandDiscoverySearch_out: Trio is O1 C1 N2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n689,691d3345\r\n< LigandDiscoverySearch_out: Trio is O1 C7 C6 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n697,699d3350\r\n< LigandDiscoverySearch_out: Trio is O1 C7 C2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n705,707d3355\r\n< LigandDiscoverySearch_out: Trio is C7 O1 C1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n713,715d3360\r\n< LigandDiscoverySearch_out: Trio is C7 C6 C5 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n721,723d3365\r\n< LigandDiscoverySearch_out: Trio is C7 C2 C3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n729,731d3370\r\n< LigandDiscoverySearch_out: Trio is C7 C2 N2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n737,739d3375\r\n< LigandDiscoverySearch_out: Trio is C6 C7 O1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n745,747d3380\r\n< LigandDiscoverySearch_out: Trio is C6 C7 C2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n753,755d3385\r\n< LigandDiscoverySearch_out: Trio is C6 C5 C4 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n761,763d3390\r\n< LigandDiscoverySearch_out: Trio is C5 C6 C7 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n769,771d3395\r\n< LigandDiscoverySearch_out: Trio is C5 C4 C3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n777,779d3400\r\n< LigandDiscoverySearch_out: Trio is C5 C4 CL1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n785,787d3405\r\n< LigandDiscoverySearch_out: Trio is C4 C5 C6 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n793,795d3410\r\n< LigandDiscoverySearch_out: Trio is C4 C3 C2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n801,803d3415\r\n< LigandDiscoverySearch_out: Trio is C3 C4 C5 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n809,811d3420\r\n< LigandDiscoverySearch_out: Trio is C3 C4 CL1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n817,819d3425\r\n< LigandDiscoverySearch_out: Trio is C3 C2 C7 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n825,827d3430\r\n< LigandDiscoverySearch_out: Trio is C3 C2 N2 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n833,835d3435\r\n< LigandDiscoverySearch_out: Trio is C2 C7 O1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n841,843d3440\r\n< LigandDiscoverySearch_out: Trio is C2 C7 C6 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n849,851c3446,3447\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---\r\n> LigandDiscoverySearch_export_space_fill_matrix_as_C_H_O_N_pdb: Preparing to make visualization pose for 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio97_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120951_SubRatio_0.802667.pdb\r\n> LigandDiscoverySearch_export_space_fill_matrix_as_C_H_O_N_pdb: Making viualization pdb 4s0v_receptor_only_ResPos_423_ResID_ASN_Trio97_suv_motif_5z6y_BF6.pdb ASN121 BF6 Packing score: -5.020643 Hbond score: 0.000000_WholeRatio_0.120951_SubRatio_0.802667.pdb\r\n857,859d3452\r\n< LigandDiscoverySearch_out: Trio is C2 N2 C1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n865,867d3457\r\n< LigandDiscoverySearch_out: Trio is N2 C1 N1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n873,875d3462\r\n< LigandDiscoverySearch_out: Trio is N2 C1 O1 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n881,883d3467\r\n< LigandDiscoverySearch_out: Trio is N2 C2 C7 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n889,891d3472\r\n< LigandDiscoverySearch_out: Trio is N2 C2 C3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n897,899d3477\r\n< LigandDiscoverySearch_out: Trio is CL1 C4 C5 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n905,907d3482\r\n< LigandDiscoverySearch_out: Trio is CL1 C4 C3 \r\n< LigandDiscoverySearch_out: Looking through all motifs\r\n< LigandDiscoverySearch_out: #motifs = 24\r\n914c3489\r\n< LigandDiscoverySearch_out: Total clashing attempts for ligand is 4\r\n---\r\n> LigandDiscoverySearch_out: Total clashing attempts for ligand is 2\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: PHE169A_Z0_Ligatoms_8_9_10_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: PHE169A_Z0_Ligatoms_8_9_10_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: PRO82A_Z0_Ligatoms_24_25_30_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: PRO82A_Z0_Ligatoms_24_25_30_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: THR62A_Z0_Ligatoms_27_28_32_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: THR62A_Z0_Ligatoms_27_28_32_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: THR86A_Z0_Ligatoms_22_21_23_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: THR86A_Z0_Ligatoms_22_21_23_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: TYR451A_Z0_Ligatoms_14_13_15_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: TYR451A_Z0_Ligatoms_27_28_32_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: VAL450A_Z0_Ligatoms_11_12_13_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio36_suv_motif_6hq4_CMP.pdb ASN113 CMP Packing score: -1.226982 Hbond score: 0.000000.pdb\r\nOnly in /home/benchmark/working_dir/commits:20420/ligand_motif_discovery: VAL450A_Z0_Ligatoms_11_12_13_^_4s0v_receptor_only_ResPos_423_ResID_ASN_Trio52_suv_motif_4s0v_SUV.pdb ASN324 SUV Packing score: -2.429506 Hbond score: 0.000000.pdb\r\n",
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"ligand_motif_identification": {
"log": "",
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"ligand_water_docking": {
"log": "",
"state": "passed"
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"longest_continuous_polar_segment_filter": {
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"loop_creation": {
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"loop_grower_N_term_symm": {
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"loop_hash": {
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"loop_modeling": {
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},
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"log": "",
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"membrane_abinitio": {
"log": "",
"state": "passed"
},
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"log": "",
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},
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"mhc_epitope": {
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"oop_create": {
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"remove_duplicate_motifs": {
"log": "Brief Diff:\ndiff: /home/benchmark/working_dir/main:62109/remove_duplicate_motifs: No such file or directory\r\n",
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},
"rna_denovo_bps_helix_ends": {
"log": "",
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},
"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": "",
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},
"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": "",
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},
"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": "",
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},
"score12_docking": {
"log": "",
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},
"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"
},
"simple_cycpep_predict": {
"log": "",
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},
"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": "",
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},
"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": "",
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},
"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": "",
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},
"splice_in_4loops_longer": {
"log": "",
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},
"splice_in_4loops_shorter": {
"log": "",
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},
"splice_out_H1_H2_longer": {
"log": "",
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},
"splice_out_H1_H2_same": {
"log": "",
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},
"splice_out_H1_H2_shorter": {
"log": "",
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},
"splice_out_H3_longer": {
"log": "",
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},
"splice_out_H3_same": {
"log": "",
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},
"splice_out_H3_shorter": {
"log": "",
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},
"splice_out_L1_L2_longer": {
"log": "",
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},
"splice_out_L1_L2_same": {
"log": "",
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},
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"log": "",
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},
"splice_out_L3_longer": {
"log": "",
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},
"splice_out_L3_same": {
"log": "",
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},
"splice_out_L3_shorter": {
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},
"startfrom_file": {
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},
"stepwise_lores": {
"log": "",
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},
"stored_residue_subset": {
"log": "",
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},
"struc_set_fragment_picker": {
"log": "",
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},
"super_aln": {
"log": "",
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},
"supercharge": {
"log": "",
"state": "passed"
},
"surface_docking": {
"log": "",
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},
"swa_protein_CCDclose": {
"log": "",
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},
"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": "",
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},
"swa_rna_gagu_02_prepend": {
"log": "",
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},
"swa_rna_gagu_03_append_to_silent": {
"log": "",
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},
"swa_rna_gagu_04_clustering": {
"log": "",
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},
"swa_rna_gagu_05_prepend_to_5primeterminus": {
"log": "",
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},
"swa_rna_gagu_06_append_to_3primeterminus": {
"log": "",
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},
"swa_rna_gagu_07_prepend_dinucleotide": {
"log": "",
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},
"swa_rna_gagu_08_append_dinucleotide": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_09_sample_virtual_ribose": {
"log": "",
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},
"swa_rna_gagu_10_prepend_and_ccd_close": {
"log": "",
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},
"swa_rna_gagu_11_append_and_ccd_close": {
"log": "",
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},
"swa_rna_gagu_12_helix_addition": {
"log": "",
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},
"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": "",
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},
"swa_rna_gagu_23_append_and_kic_close": {
"log": "",
"state": "passed"
},
"swa_rna_loop_clusterer": {
"log": "",
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},
"swa_rna_loop_sampler": {
"log": "",
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},
"sweep_respair_energies": {
"log": "",
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},
"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"
}
}
}