{
"compared_with_test": {
"full_name": "linux.clang.integration.release_debug_no_symbols",
"name": "integration.release_debug_no_symbols",
"platform": {
"compiler": "clang",
"extras": [],
"os": "linux"
},
"platform_as_string": "linux.clang",
"revision": {
"branch": "main",
"revision_id": 62108
},
"state": "passed",
"test_id": 827189
},
"summary": {
"failed": 14,
"failed_tests": [
"ambiguous_nmr_distance_constraint",
"crosslinkermover_lanthionine",
"crosslinkermover_methyllanthionine",
"cyclization",
"database_md5",
"ddG_of_mutation",
"dehydro_aa_patch",
"design_glycans",
"features",
"fiber_diffraction_fad",
"fold_and_dock",
"number_of_residuetypes",
"output_schema",
"simple_cycpep_predict_lanthionine"
],
"total": 801
},
"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": "Brief Diff:\ndiff: /home/benchmark/working_dir/main:62108/ambiguous_nmr_distance_constraint: No such file or directory\r\n",
"state": "failed"
},
"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"
},
"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"
},
"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": "Brief Diff:\ndiff: /home/benchmark/working_dir/main:62108/crosslinkermover_lanthionine: No such file or directory\r\n",
"state": "failed"
},
"crosslinkermover_methyllanthionine": {
"log": "Brief Diff:\ndiff: /home/benchmark/working_dir/main:62108/crosslinkermover_methyllanthionine: No such file or directory\r\n",
"state": "failed"
},
"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": "Brief Diff:\nFiles /home/benchmark/working_dir/main:62108/cyclization/log_cyclize and /home/benchmark/working_dir/main:62109/cyclization/log_cyclize differ\r\n\n\nFull Diff:\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62108/cyclization/log_cyclize /home/benchmark/working_dir/main:62109/cyclization/log_cyclize\r\n7147a7148\r\n> core.chemical.Patch: Reading patch file: ROSETTA/database/chemical/residue_type_sets/fa_standard/patches/branching/C-linked_conjugation.txt\r\n7170a7172\r\n> core.chemical.Patch: Reading patch file: ROSETTA/database/chemical/residue_type_sets/fa_standard/patches/Nterm2_Oxobutrylation.txt\r\n10203a10206,10209\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET:NtermProteinFull\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET:N_formylated\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET:NtermProteinMethylated\r\n10295a10302,10305\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET:NtermProteinFull\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET:N_formylated\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET:NtermProteinMethylated\r\n10968a10979\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n10991a11003\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n11114a11127\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n11137a11151\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n11260a11275\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n11283a11299\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n11406a11423\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE\r\n11429a11447\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE\r\n11552a11571\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n11575a11595\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n11694a11715\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n11717a11739\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n11840a11863\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO\r\n11863a11887\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO\r\n11985a12010\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n12008a12034\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n12130a12157\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n12153a12181\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n12276a12305\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n12299a12329\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n12421a12452\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n12444a12476\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n12566a12599\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n12589a12623\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n12708a12743\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n12731a12767\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n12853a12890\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n12876a12914\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n12999a13038\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n13022a13062\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n13145a13186\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n13168a13210\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n13290a13333\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n13313a13357\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n13435a13480\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n13458a13504\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n13580a13627\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n13603a13651\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n13725a13774\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n13748a13798\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n13870a13921\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n13893a13945\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n14011a14064\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n14034a14088\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n14153a14208\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP\r\n14176a14232\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP\r\n14298a14355\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n14321a14379\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n14443a14502\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n14466a14526\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n14588a14649\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n14611a14673\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n14733a14796\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n14756a14820\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n14878a14943\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n14901a14967\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n15024a15091\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n15047a15115\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n15169a15238\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n15192a15262\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n15314a15385\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n15337a15409\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n15459a15532\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n15482a15556\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n15604a15679\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n15627a15703\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n15749a15826\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n15772a15850\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n15894a15973\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n15917a15997\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n16035a16116\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n16058a16140\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n16180a16263\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n16203a16287\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n16321a16406\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n16344a16430\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n16462a16549\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n16485a16573\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n16607a16696\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n16630a16720\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n16752a16843\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n16775a16867\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n16897a16990\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n16920a17014\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n17042a17137\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n17065a17161\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n17187a17284\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n17210a17308\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n17332a17431\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n17355a17455\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n17477a17578\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n17500a17602\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n17619a17722\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n17642a17746\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n17764a17869\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n17787a17893\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n17909a18016\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n17932a18040\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n18054a18163\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n18077a18187\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n18199a18310\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n18222a18334\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n18344a18457\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n18367a18481\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n18490a18605\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR\r\n18513a18629\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR\r\n18635a18752\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n18658a18776\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n18780a18899\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n18803a18923\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n18925a19046\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n18948a19070\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n19070a19193\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n19093a19217\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n19215a19340\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n19238a19364\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n19360a19487\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n19383a19511\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n19505a19634\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n19528a19658\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n19650a19781\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n19673a19805\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n19795a19928\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n19818a19952\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n19936a20071\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n19959a20095\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n20081a20218\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n20104a20242\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n20226a20365\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n20249a20389\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n20371a20512\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n20394a20536\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n20516a20659\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n20539a20683\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n20661a20806\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n20684a20830\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n20878a21025,21026\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP:CtermProteinFull\r\n20924a21073,21074\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP:CtermProteinFull\r\n",
"state": "failed"
},
"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": "Brief Diff:\nFiles /home/benchmark/working_dir/main:62108/database_md5/database_md5s.txt and /home/benchmark/working_dir/main:62109/database_md5/database_md5s.txt differ\r\n\n\nFull Diff:\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62108/database_md5/database_md5s.txt /home/benchmark/working_dir/main:62109/database_md5/database_md5s.txt\r\n16788c16788\r\n< c909bffbb3b7c665a99443665a77f5cb ./chemical/residue_type_sets/centroid/patches/protein_centroid_with_HA.txt\r\n---\r\n> 14a3a01ffc340912f5c70d5d52a06cdf ./chemical/residue_type_sets/centroid/patches/protein_centroid_with_HA.txt\r\n17803,17804c17803,17804\r\n< 1fdcb56b08a46f0a7c933961a4ddce66 ./chemical/residue_type_sets/fa_standard/patches/AcetylatedProteinNtermConnection.txt\r\n< 76ffba1f73c55a8f860af5ada10a4541 ./chemical/residue_type_sets/fa_standard/patches/AcetylatedProteinNterm.txt\r\n---\r\n> c7e446e38d20fa9c0b5f759cf62f2a4b ./chemical/residue_type_sets/fa_standard/patches/AcetylatedProteinNtermConnection.txt\r\n> cdf63b349b63e3da612ca92e33498a69 ./chemical/residue_type_sets/fa_standard/patches/AcetylatedProteinNterm.txt\r\n17806a17807\r\n> 6b383393986b317b64e733e19558172f ./chemical/residue_type_sets/fa_standard/patches/branching/C-linked_conjugation.txt\r\n17890c17891\r\n< 7a05abbb31a2b3fb59366ba3fd81aebd ./chemical/residue_type_sets/fa_standard/patches/N_acetylated.txt\r\n---\r\n> 85eff15e44054bb049c755304e801327 ./chemical/residue_type_sets/fa_standard/patches/N_acetylated.txt\r\n17892a17894\r\n> bac9fc639ef0b2e303e78aec734996b9 ./chemical/residue_type_sets/fa_standard/patches/Nterm2_Oxobutrylation.txt\r\n17895,17896c17897,17898\r\n< 12104d2b46ae245b6320ec989c71b286 ./chemical/residue_type_sets/fa_standard/patches/NtermProteinFull.txt\r\n< c9e918005ee889fbee792a5a2c2d37b2 ./chemical/residue_type_sets/fa_standard/patches/NtermProteinMethylated.txt\r\n---\r\n> 3b93d9b05e1da4c14f90596baf4fe9d3 ./chemical/residue_type_sets/fa_standard/patches/NtermProteinFull.txt\r\n> 3ed8fbd76e1b0cabe04f0cb35ad1b5dc ./chemical/residue_type_sets/fa_standard/patches/NtermProteinMethylated.txt\r\n17978c17980\r\n< d6f1bc231727569da7fd52218617f444 ./chemical/residue_type_sets/fa_standard/patches.txt\r\n---\r\n> 4e3c74aa7473f19472207aa35d53b2ad ./chemical/residue_type_sets/fa_standard/patches.txt\r\n",
"state": "failed"
},
"database_session_resource": {
"log": "",
"state": "passed"
},
"ddG_ensemble": {
"log": "",
"state": "passed"
},
"ddG_of_mutation": {
"log": "Brief Diff:\nFiles /home/benchmark/working_dir/main:62108/ddG_of_mutation/log and /home/benchmark/working_dir/main:62109/ddG_of_mutation/log differ\r\n\n\nFull Diff:\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62108/ddG_of_mutation/log /home/benchmark/working_dir/main:62109/ddG_of_mutation/log\r\n7135a7136\r\n> core.chemical.Patch: Reading patch file: ROSETTA/database/chemical/residue_type_sets/fa_standard/patches/branching/C-linked_conjugation.txt\r\n7158a7160\r\n> core.chemical.Patch: Reading patch file: ROSETTA/database/chemical/residue_type_sets/fa_standard/patches/Nterm2_Oxobutrylation.txt\r\n10174a10177,10179\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN:NtermProteinFull\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN:NtermProteinMethylated\r\n10243a10249,10251\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN:NtermProteinFull\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN:NtermProteinMethylated\r\n10880a10889\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n10903a10913\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n11026a11037\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n11049a11061\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n11172a11185\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n11195a11209\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n11318a11333\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n11341a11357\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n11464a11481\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP\r\n11487a11505\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP\r\n11610a11629\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO\r\n11633a11653\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO\r\n11755a11776\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n11778a11800\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n11900a11923\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n11923a11947\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n12046a12071\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n12069a12095\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n12192a12219\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n12215a12243\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n12333a12362\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n12356a12386\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n12479a12510\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n12502a12534\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n12624a12657\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n12647a12681\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n12769a12804\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n12792a12828\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n12914a12951\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n12937a12975\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n13060a13099,13117\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Patch 'C-conjugated' is relevant because this patch has atom name 1HB which is an atom name found in the PDB file\r\n> core.chemical.Patch: Attempting to patch: ALA with: C-conjugated\r\n> core.chemical.PatchOperations.hh: DeleteAtom::apply: deleting: 3HB\r\n> core.chemical.PatchOperations.hh: DeleteAtom::apply: deleting: 2HB\r\n> core.chemical.PatchOperations.hh: DeleteAtom::apply: deleting: 1HB\r\n> core.chemical.PatchOperations.hh: AddAtom::apply: 1HB HNbb H 0.31\r\n> core.chemical.PatchOperations.hh: AddAtom::apply: 2HB HNbb H 0.31\r\n> core.chemical.PatchOperations.hh: AddAtom::apply: V1 VIRT VIRT 0\r\n> core.chemical.PatchOperations.hh: AddBond::apply: CB 1HB\r\n> core.chemical.PatchOperations.hh: AddBond::apply: CB 2HB\r\n> core.chemical.PatchOperations.hh: AddBond::apply: CB V1\r\n> core.chemical.PatchOperations.hh: SetICoor::apply: 1HB CB CA CONN%LASTCONN\r\n> core.chemical.PatchOperations.hh: SetICoor::apply: 2HB CB CA CONN%LASTCONN\r\n> core.chemical.PatchOperations.hh: SetICoor::apply: V1 CB CA CONN%LASTCONN\r\n> core.chemical.PatchOperations.hh: RedefineChi::apply: N CA CB V1\r\n> core.chemical.PatchOperations.hh: DeleteProperty::apply: CANONICAL_AA\r\n> core.chemical.PatchOperations.hh: AddProperty::apply: BRANCH_POINT\r\n> core.chemical.Patch: successfully patched: ALA to: ALA:C-conjugated\r\n13061a13119\r\n> core.chemical.ResidueTypeFinder: Checking if patch Cterm_amidation applies to residue ALA:C-conjugated\r\n13062a13121\r\n> core.chemical.ResidueTypeFinder: Checking if patch Virtual_Residue applies to residue ALA:C-conjugated\r\n13063a13123\r\n> core.chemical.ResidueTypeFinder: Checking if patch VirtualNterm applies to residue ALA:C-conjugated\r\n13064a13125\r\n> core.chemical.ResidueTypeFinder: Checking if patch BulgeRNA applies to residue ALA:C-conjugated\r\n13065a13127\r\n> core.chemical.ResidueTypeFinder: Checking if patch 3prime_end_OH applies to residue ALA:C-conjugated\r\n13066a13129\r\n> core.chemical.ResidueTypeFinder: Checking if patch 5prime_end_OH applies to residue ALA:C-conjugated\r\n13067a13131\r\n> core.chemical.ResidueTypeFinder: Checking if patch 5prime_end_phosphate applies to residue ALA:C-conjugated\r\n13068a13133\r\n> core.chemical.ResidueTypeFinder: Checking if patch Protonated_N1_Adenosine applies to residue ALA:C-conjugated\r\n13069a13135\r\n> core.chemical.ResidueTypeFinder: Checking if patch Protonated_N3_Cytosine applies to residue ALA:C-conjugated\r\n13070a13137\r\n> core.chemical.ResidueTypeFinder: Checking if patch Protonated_N3_Adenosine applies to residue ALA:C-conjugated\r\n13071a13139\r\n> core.chemical.ResidueTypeFinder: Checking if patch Virtual_Backbone_Except_C1prime applies to residue ALA:C-conjugated\r\n13072a13141\r\n> core.chemical.ResidueTypeFinder: Checking if patch PtermProteinFull applies to residue ALA:C-conjugated\r\n13073a13143\r\n> core.chemical.ResidueTypeFinder: Checking if patch phosphorylated applies to residue ALA:C-conjugated\r\n13074a13145\r\n> core.chemical.ResidueTypeFinder: Checking if patch phosphorylated applies to residue ALA:C-conjugated\r\n13075a13147\r\n> core.chemical.ResidueTypeFinder: Checking if patch phosphorylated applies to residue ALA:C-conjugated\r\n13076a13149\r\n> core.chemical.ResidueTypeFinder: Checking if patch sulfated applies to residue ALA:C-conjugated\r\n13077a13151\r\n> core.chemical.ResidueTypeFinder: Checking if patch monomethylated applies to residue ALA:C-conjugated\r\n13078a13153\r\n> core.chemical.ResidueTypeFinder: Checking if patch dimethylated applies to residue ALA:C-conjugated\r\n13079a13155\r\n> core.chemical.ResidueTypeFinder: Checking if patch lys_trimethylated applies to residue ALA:C-conjugated\r\n13080a13157\r\n> core.chemical.ResidueTypeFinder: Checking if patch acetylated applies to residue ALA:C-conjugated\r\n13081a13159\r\n> core.chemical.ResidueTypeFinder: Checking if patch carboxylated applies to residue ALA:C-conjugated\r\n13082a13161\r\n> core.chemical.ResidueTypeFinder: Checking if patch acetylated applies to residue ALA:C-conjugated\r\n13083a13163,13165\r\n> core.chemical.ResidueTypeFinder: Checking if patch diiodinated applies to residue ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA:C-conjugated\r\n13084a13167\r\n> core.chemical.ResidueTypeFinder: Checking if patch methylated applies to residue ALA:C-conjugated\r\n13085a13169\r\n> core.chemical.ResidueTypeFinder: Checking if patch MethylatedCtermProteinFull applies to residue ALA:C-conjugated\r\n13086a13171\r\n> core.chemical.ResidueTypeFinder: Checking if patch AcetylatedNtermProteinFull applies to residue ALA:C-conjugated\r\n13087a13173\r\n> core.chemical.ResidueTypeFinder: Checking if patch AcetylatedNtermConnectionProteinFull applies to residue ALA:C-conjugated\r\n13088a13175\r\n> core.chemical.ResidueTypeFinder: Checking if patch DimethylatedCtermProteinFull applies to residue ALA:C-conjugated\r\n13089a13177\r\n> core.chemical.ResidueTypeFinder: Checking if patch NtermPeptoidFull applies to residue ALA:C-conjugated\r\n13090a13179\r\n> core.chemical.ResidueTypeFinder: Checking if patch CtermPeptoidFull applies to residue ALA:C-conjugated\r\n13091a13181\r\n> core.chemical.ResidueTypeFinder: Checking if patch AcetylatedNtermDimethylatedCtermPeptoidFull applies to residue ALA:C-conjugated\r\n13092a13183\r\n> core.chemical.ResidueTypeFinder: Checking if patch AcetylatedPeptoidNterm applies to residue ALA:C-conjugated\r\n13093a13185\r\n> core.chemical.ResidueTypeFinder: Checking if patch non-conjugated applies to residue ALA:C-conjugated\r\n13094a13187\r\n> core.chemical.ResidueTypeFinder: Checking if patch terpene_lower_full applies to residue ALA:C-conjugated\r\n13095a13189\r\n> core.chemical.ResidueTypeFinder: Checking if patch terpene_upper_full applies to residue ALA:C-conjugated\r\n13096a13191\r\n> core.chemical.ResidueTypeFinder: Checking if patch hbs_pre applies to residue ALA:C-conjugated\r\n13097a13193\r\n> core.chemical.ResidueTypeFinder: Checking if patch hbs_post applies to residue ALA:C-conjugated\r\n13098a13195\r\n> core.chemical.ResidueTypeFinder: Checking if patch a3b_hbs_pre applies to residue ALA:C-conjugated\r\n13099a13197\r\n> core.chemical.ResidueTypeFinder: Checking if patch a3b_hbs_post applies to residue ALA:C-conjugated\r\n13100a13199\r\n> core.chemical.ResidueTypeFinder: Checking if patch oop_pre applies to residue ALA:C-conjugated\r\n13101a13201\r\n> core.chemical.ResidueTypeFinder: Checking if patch oop_post applies to residue ALA:C-conjugated\r\n13102a13203\r\n> core.chemical.ResidueTypeFinder: Checking if patch triazolamerN applies to residue ALA:C-conjugated\r\n13103a13205\r\n> core.chemical.ResidueTypeFinder: Checking if patch triazolamerC applies to residue ALA:C-conjugated\r\n13104a13207\r\n> core.chemical.ResidueTypeFinder: Checking if patch VirtualWater applies to residue ALA:C-conjugated\r\n13105a13209\r\n> core.chemical.ResidueTypeFinder: Checking if patch ProteinReplsBB applies to residue ALA:C-conjugated\r\n13106a13211\r\n> core.chemical.ResidueTypeFinder: Checking if patch Ca2Coordinating applies to residue ALA:C-conjugated\r\n13107a13213\r\n> core.chemical.ResidueTypeFinder: Checking if patch Co2Coordinating applies to residue ALA:C-conjugated\r\n13108a13215\r\n> core.chemical.ResidueTypeFinder: Checking if patch Cu2Coordinating applies to residue ALA:C-conjugated\r\n13109a13217\r\n> core.chemical.ResidueTypeFinder: Checking if patch Dy3Coordinating applies to residue ALA:C-conjugated\r\n13110a13219\r\n> core.chemical.ResidueTypeFinder: Checking if patch Fe2Coordinating applies to residue ALA:C-conjugated\r\n13111a13221\r\n> core.chemical.ResidueTypeFinder: Checking if patch Fe3Coordinating applies to residue ALA:C-conjugated\r\n13112a13223\r\n> core.chemical.ResidueTypeFinder: Checking if patch La3Coordinating applies to residue ALA:C-conjugated\r\n13113a13225\r\n> core.chemical.ResidueTypeFinder: Checking if patch Lu3Coordinating applies to residue ALA:C-conjugated\r\n13114a13227\r\n> core.chemical.ResidueTypeFinder: Checking if patch Mg2Coordinating applies to residue ALA:C-conjugated\r\n13115a13229\r\n> core.chemical.ResidueTypeFinder: Checking if patch Mn2Coordinating applies to residue ALA:C-conjugated\r\n13116a13231\r\n> core.chemical.ResidueTypeFinder: Checking if patch Tb3Coordinating applies to residue ALA:C-conjugated\r\n13117a13233\r\n> core.chemical.ResidueTypeFinder: Checking if patch Tm3Coordinating applies to residue ALA:C-conjugated\r\n13118a13235\r\n> core.chemical.ResidueTypeFinder: Checking if patch Yb3Coordinating applies to residue ALA:C-conjugated\r\n13120,13121c13237,13239\r\n< core.chemical.ResidueTypeFinder: Patched up to 1 ResidueType(s).\r\n< core.chemical.ResidueTypeFinder: Discouraging 3 properties, going from 1 types to 1 types.\r\n---\r\n> core.chemical.ResidueTypeFinder: Checking if patch Er3Coordinating applies to residue ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: Patched up to 2 ResidueType(s).\r\n> core.chemical.ResidueTypeFinder: Discouraging 3 properties, going from 2 types to 2 types.\r\n13123,13125c13241,13243\r\n< core.chemical.ResidueTypeFinder: Going from ALA\r\n< core.chemical.ResidueTypeFinder: To ALA\r\n< core.chemical.ResidueTypeFinder: Encouraging 1 properties, going from 1 types to 1 types.\r\n---\r\n> core.chemical.ResidueTypeFinder: Going from ALA ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: To ALA ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: Encouraging 1 properties, going from 2 types to 2 types.\r\n13127,13129c13245,13250\r\n< core.chemical.ResidueTypeFinder: Going from ALA\r\n< core.chemical.ResidueTypeFinder: To ALA\r\n< core.chemical.ResidueTypeFinder: Keeping up to 1 ResidueType(s) after filtering.\r\n---\r\n> core.chemical.ResidueTypeFinder: Going from ALA ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: To ALA ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: Keeping up to 2 ResidueType(s) after filtering.\r\n> core.chemical.ResidueTypeFinder: Finding best match from among 2 ResidueTypes.\r\n> core.chemical.ResidueTypeFinder: ALA\r\n> core.chemical.ResidueTypeFinder: ALA:C-conjugated\r\n13205a13327\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n13228a13351\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n13350a13474\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n13373a13498\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n13495a13621\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n13518a13645\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n13641a13769\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n13664a13793\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n13786a13916\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n13809a13940\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n13932a14064\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n13955a14088\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n14078a14212\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n14101a14236\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n14223a14359\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n14246a14383\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n14368a14506\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO\r\n14391a14530\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO\r\n14513a14653\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n14536a14677\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n14658a14800,14801\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Patch 'C-conjugated' is relevant because this patch has atom name 1HB which is an atom name found in the PDB file\r\n14659a14803\r\n> core.chemical.ResidueTypeFinder: Checking if patch Cterm_amidation applies to residue ALA:C-conjugated\r\n14660a14805\r\n> core.chemical.ResidueTypeFinder: Checking if patch Virtual_Residue applies to residue ALA:C-conjugated\r\n14661a14807\r\n> core.chemical.ResidueTypeFinder: Checking if patch VirtualNterm applies to residue ALA:C-conjugated\r\n14662a14809\r\n> core.chemical.ResidueTypeFinder: Checking if patch BulgeRNA applies to residue ALA:C-conjugated\r\n14663a14811\r\n> core.chemical.ResidueTypeFinder: Checking if patch 3prime_end_OH applies to residue ALA:C-conjugated\r\n14664a14813\r\n> core.chemical.ResidueTypeFinder: Checking if patch 5prime_end_OH applies to residue ALA:C-conjugated\r\n14665a14815\r\n> core.chemical.ResidueTypeFinder: Checking if patch 5prime_end_phosphate applies to residue ALA:C-conjugated\r\n14666a14817\r\n> core.chemical.ResidueTypeFinder: Checking if patch Protonated_N1_Adenosine applies to residue ALA:C-conjugated\r\n14667a14819\r\n> core.chemical.ResidueTypeFinder: Checking if patch Protonated_N3_Cytosine applies to residue ALA:C-conjugated\r\n14668a14821\r\n> core.chemical.ResidueTypeFinder: Checking if patch Protonated_N3_Adenosine applies to residue ALA:C-conjugated\r\n14669a14823\r\n> core.chemical.ResidueTypeFinder: Checking if patch Virtual_Backbone_Except_C1prime applies to residue ALA:C-conjugated\r\n14670a14825\r\n> core.chemical.ResidueTypeFinder: Checking if patch PtermProteinFull applies to residue ALA:C-conjugated\r\n14671a14827\r\n> core.chemical.ResidueTypeFinder: Checking if patch phosphorylated applies to residue ALA:C-conjugated\r\n14672a14829\r\n> core.chemical.ResidueTypeFinder: Checking if patch phosphorylated applies to residue ALA:C-conjugated\r\n14673a14831\r\n> core.chemical.ResidueTypeFinder: Checking if patch phosphorylated applies to residue ALA:C-conjugated\r\n14674a14833\r\n> core.chemical.ResidueTypeFinder: Checking if patch sulfated applies to residue ALA:C-conjugated\r\n14675a14835\r\n> core.chemical.ResidueTypeFinder: Checking if patch monomethylated applies to residue ALA:C-conjugated\r\n14676a14837\r\n> core.chemical.ResidueTypeFinder: Checking if patch dimethylated applies to residue ALA:C-conjugated\r\n14677a14839\r\n> core.chemical.ResidueTypeFinder: Checking if patch lys_trimethylated applies to residue ALA:C-conjugated\r\n14678a14841\r\n> core.chemical.ResidueTypeFinder: Checking if patch acetylated applies to residue ALA:C-conjugated\r\n14679a14843\r\n> core.chemical.ResidueTypeFinder: Checking if patch carboxylated applies to residue ALA:C-conjugated\r\n14680a14845\r\n> core.chemical.ResidueTypeFinder: Checking if patch acetylated applies to residue ALA:C-conjugated\r\n14681a14847,14849\r\n> core.chemical.ResidueTypeFinder: Checking if patch diiodinated applies to residue ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA:C-conjugated\r\n14682a14851\r\n> core.chemical.ResidueTypeFinder: Checking if patch methylated applies to residue ALA:C-conjugated\r\n14683a14853\r\n> core.chemical.ResidueTypeFinder: Checking if patch MethylatedCtermProteinFull applies to residue ALA:C-conjugated\r\n14684a14855\r\n> core.chemical.ResidueTypeFinder: Checking if patch AcetylatedNtermProteinFull applies to residue ALA:C-conjugated\r\n14685a14857\r\n> core.chemical.ResidueTypeFinder: Checking if patch AcetylatedNtermConnectionProteinFull applies to residue ALA:C-conjugated\r\n14686a14859\r\n> core.chemical.ResidueTypeFinder: Checking if patch DimethylatedCtermProteinFull applies to residue ALA:C-conjugated\r\n14687a14861\r\n> core.chemical.ResidueTypeFinder: Checking if patch NtermPeptoidFull applies to residue ALA:C-conjugated\r\n14688a14863\r\n> core.chemical.ResidueTypeFinder: Checking if patch CtermPeptoidFull applies to residue ALA:C-conjugated\r\n14689a14865\r\n> core.chemical.ResidueTypeFinder: Checking if patch AcetylatedNtermDimethylatedCtermPeptoidFull applies to residue ALA:C-conjugated\r\n14690a14867\r\n> core.chemical.ResidueTypeFinder: Checking if patch AcetylatedPeptoidNterm applies to residue ALA:C-conjugated\r\n14691a14869\r\n> core.chemical.ResidueTypeFinder: Checking if patch non-conjugated applies to residue ALA:C-conjugated\r\n14692a14871\r\n> core.chemical.ResidueTypeFinder: Checking if patch terpene_lower_full applies to residue ALA:C-conjugated\r\n14693a14873\r\n> core.chemical.ResidueTypeFinder: Checking if patch terpene_upper_full applies to residue ALA:C-conjugated\r\n14694a14875\r\n> core.chemical.ResidueTypeFinder: Checking if patch hbs_pre applies to residue ALA:C-conjugated\r\n14695a14877\r\n> core.chemical.ResidueTypeFinder: Checking if patch hbs_post applies to residue ALA:C-conjugated\r\n14696a14879\r\n> core.chemical.ResidueTypeFinder: Checking if patch a3b_hbs_pre applies to residue ALA:C-conjugated\r\n14697a14881\r\n> core.chemical.ResidueTypeFinder: Checking if patch a3b_hbs_post applies to residue ALA:C-conjugated\r\n14698a14883\r\n> core.chemical.ResidueTypeFinder: Checking if patch oop_pre applies to residue ALA:C-conjugated\r\n14699a14885\r\n> core.chemical.ResidueTypeFinder: Checking if patch oop_post applies to residue ALA:C-conjugated\r\n14700a14887\r\n> core.chemical.ResidueTypeFinder: Checking if patch triazolamerN applies to residue ALA:C-conjugated\r\n14701a14889\r\n> core.chemical.ResidueTypeFinder: Checking if patch triazolamerC applies to residue ALA:C-conjugated\r\n14702a14891\r\n> core.chemical.ResidueTypeFinder: Checking if patch VirtualWater applies to residue ALA:C-conjugated\r\n14703a14893\r\n> core.chemical.ResidueTypeFinder: Checking if patch ProteinReplsBB applies to residue ALA:C-conjugated\r\n14704a14895\r\n> core.chemical.ResidueTypeFinder: Checking if patch Ca2Coordinating applies to residue ALA:C-conjugated\r\n14705a14897\r\n> core.chemical.ResidueTypeFinder: Checking if patch Co2Coordinating applies to residue ALA:C-conjugated\r\n14706a14899\r\n> core.chemical.ResidueTypeFinder: Checking if patch Cu2Coordinating applies to residue ALA:C-conjugated\r\n14707a14901\r\n> core.chemical.ResidueTypeFinder: Checking if patch Dy3Coordinating applies to residue ALA:C-conjugated\r\n14708a14903\r\n> core.chemical.ResidueTypeFinder: Checking if patch Fe2Coordinating applies to residue ALA:C-conjugated\r\n14709a14905\r\n> core.chemical.ResidueTypeFinder: Checking if patch Fe3Coordinating applies to residue ALA:C-conjugated\r\n14710a14907\r\n> core.chemical.ResidueTypeFinder: Checking if patch La3Coordinating applies to residue ALA:C-conjugated\r\n14711a14909\r\n> core.chemical.ResidueTypeFinder: Checking if patch Lu3Coordinating applies to residue ALA:C-conjugated\r\n14712a14911\r\n> core.chemical.ResidueTypeFinder: Checking if patch Mg2Coordinating applies to residue ALA:C-conjugated\r\n14713a14913\r\n> core.chemical.ResidueTypeFinder: Checking if patch Mn2Coordinating applies to residue ALA:C-conjugated\r\n14714a14915\r\n> core.chemical.ResidueTypeFinder: Checking if patch Tb3Coordinating applies to residue ALA:C-conjugated\r\n14715a14917\r\n> core.chemical.ResidueTypeFinder: Checking if patch Tm3Coordinating applies to residue ALA:C-conjugated\r\n14716a14919\r\n> core.chemical.ResidueTypeFinder: Checking if patch Yb3Coordinating applies to residue ALA:C-conjugated\r\n14718,14719c14921,14923\r\n< core.chemical.ResidueTypeFinder: Patched up to 1 ResidueType(s).\r\n< core.chemical.ResidueTypeFinder: Discouraging 3 properties, going from 1 types to 1 types.\r\n---\r\n> core.chemical.ResidueTypeFinder: Checking if patch Er3Coordinating applies to residue ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: Patched up to 2 ResidueType(s).\r\n> core.chemical.ResidueTypeFinder: Discouraging 3 properties, going from 2 types to 2 types.\r\n14721,14723c14925,14927\r\n< core.chemical.ResidueTypeFinder: Going from ALA\r\n< core.chemical.ResidueTypeFinder: To ALA\r\n< core.chemical.ResidueTypeFinder: Encouraging 1 properties, going from 1 types to 1 types.\r\n---\r\n> core.chemical.ResidueTypeFinder: Going from ALA ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: To ALA ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: Encouraging 1 properties, going from 2 types to 2 types.\r\n14725,14727c14929,14934\r\n< core.chemical.ResidueTypeFinder: Going from ALA\r\n< core.chemical.ResidueTypeFinder: To ALA\r\n< core.chemical.ResidueTypeFinder: Keeping up to 1 ResidueType(s) after filtering.\r\n---\r\n> core.chemical.ResidueTypeFinder: Going from ALA ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: To ALA ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: Keeping up to 2 ResidueType(s) after filtering.\r\n> core.chemical.ResidueTypeFinder: Finding best match from among 2 ResidueTypes.\r\n> core.chemical.ResidueTypeFinder: ALA\r\n> core.chemical.ResidueTypeFinder: ALA:C-conjugated\r\n14803a15011\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n14826a15035\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n14948a15158\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n14971a15182\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n15093a15305\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n15116a15329\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n15238a15452\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n15261a15476\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n15383a15599\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n15406a15623\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n15528a15746\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO\r\n15551a15770\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO\r\n15673a15893\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n15696a15917\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n15818a16040\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n15841a16064\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n15959a16183\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n15982a16207\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n16104a16330\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n16127a16354\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n16249a16477\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n16272a16501\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n16394a16624\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n16417a16648\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n16540a16772\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET\r\n16563a16796\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET\r\n16685a16919\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n16708a16943\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n16831a17067\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR\r\n16854a17091\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR\r\n16977a17215\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n17000a17239\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n17122a17362\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n17145a17386\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n17267a17509\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n17290a17533\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n17412a17656\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n17435a17680\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n17557a17803\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n17580a17827\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n17702a17950\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n17725a17974\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n17847a18097\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n17870a18121\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n17993a18245\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE\r\n18016a18269\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE\r\n18138a18392\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n18161a18416\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n18283a18539\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n18306a18563\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n18428a18686\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n18451a18710\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n18573a18833\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n18596a18857\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n18718a18980\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n18741a19004\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n18863a19127\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n18886a19151\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n19008a19274\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n19031a19298\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n19153a19421,19422\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Patch 'C-conjugated' is relevant because this patch has atom name 1HB which is an atom name found in the PDB file\r\n19154a19424\r\n> core.chemical.ResidueTypeFinder: Checking if patch Cterm_amidation applies to residue ALA:C-conjugated\r\n19155a19426\r\n> core.chemical.ResidueTypeFinder: Checking if patch Virtual_Residue applies to residue ALA:C-conjugated\r\n19156a19428\r\n> core.chemical.ResidueTypeFinder: Checking if patch VirtualNterm applies to residue ALA:C-conjugated\r\n19157a19430\r\n> core.chemical.ResidueTypeFinder: Checking if patch BulgeRNA applies to residue ALA:C-conjugated\r\n19158a19432\r\n> core.chemical.ResidueTypeFinder: Checking if patch 3prime_end_OH applies to residue ALA:C-conjugated\r\n19159a19434\r\n> core.chemical.ResidueTypeFinder: Checking if patch 5prime_end_OH applies to residue ALA:C-conjugated\r\n19160a19436\r\n> core.chemical.ResidueTypeFinder: Checking if patch 5prime_end_phosphate applies to residue ALA:C-conjugated\r\n19161a19438\r\n> core.chemical.ResidueTypeFinder: Checking if patch Protonated_N1_Adenosine applies to residue ALA:C-conjugated\r\n19162a19440\r\n> core.chemical.ResidueTypeFinder: Checking if patch Protonated_N3_Cytosine applies to residue ALA:C-conjugated\r\n19163a19442\r\n> core.chemical.ResidueTypeFinder: Checking if patch Protonated_N3_Adenosine applies to residue ALA:C-conjugated\r\n19164a19444\r\n> core.chemical.ResidueTypeFinder: Checking if patch Virtual_Backbone_Except_C1prime applies to residue ALA:C-conjugated\r\n19165a19446\r\n> core.chemical.ResidueTypeFinder: Checking if patch PtermProteinFull applies to residue ALA:C-conjugated\r\n19166a19448\r\n> core.chemical.ResidueTypeFinder: Checking if patch phosphorylated applies to residue ALA:C-conjugated\r\n19167a19450\r\n> core.chemical.ResidueTypeFinder: Checking if patch phosphorylated applies to residue ALA:C-conjugated\r\n19168a19452\r\n> core.chemical.ResidueTypeFinder: Checking if patch phosphorylated applies to residue ALA:C-conjugated\r\n19169a19454\r\n> core.chemical.ResidueTypeFinder: Checking if patch sulfated applies to residue ALA:C-conjugated\r\n19170a19456\r\n> core.chemical.ResidueTypeFinder: Checking if patch monomethylated applies to residue ALA:C-conjugated\r\n19171a19458\r\n> core.chemical.ResidueTypeFinder: Checking if patch dimethylated applies to residue ALA:C-conjugated\r\n19172a19460\r\n> core.chemical.ResidueTypeFinder: Checking if patch lys_trimethylated applies to residue ALA:C-conjugated\r\n19173a19462\r\n> core.chemical.ResidueTypeFinder: Checking if patch acetylated applies to residue ALA:C-conjugated\r\n19174a19464\r\n> core.chemical.ResidueTypeFinder: Checking if patch carboxylated applies to residue ALA:C-conjugated\r\n19175a19466\r\n> core.chemical.ResidueTypeFinder: Checking if patch acetylated applies to residue ALA:C-conjugated\r\n19176a19468,19470\r\n> core.chemical.ResidueTypeFinder: Checking if patch diiodinated applies to residue ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA:C-conjugated\r\n19177a19472\r\n> core.chemical.ResidueTypeFinder: Checking if patch methylated applies to residue ALA:C-conjugated\r\n19178a19474\r\n> core.chemical.ResidueTypeFinder: Checking if patch MethylatedCtermProteinFull applies to residue ALA:C-conjugated\r\n19179a19476\r\n> core.chemical.ResidueTypeFinder: Checking if patch AcetylatedNtermProteinFull applies to residue ALA:C-conjugated\r\n19180a19478\r\n> core.chemical.ResidueTypeFinder: Checking if patch AcetylatedNtermConnectionProteinFull applies to residue ALA:C-conjugated\r\n19181a19480\r\n> core.chemical.ResidueTypeFinder: Checking if patch DimethylatedCtermProteinFull applies to residue ALA:C-conjugated\r\n19182a19482\r\n> core.chemical.ResidueTypeFinder: Checking if patch NtermPeptoidFull applies to residue ALA:C-conjugated\r\n19183a19484\r\n> core.chemical.ResidueTypeFinder: Checking if patch CtermPeptoidFull applies to residue ALA:C-conjugated\r\n19184a19486\r\n> core.chemical.ResidueTypeFinder: Checking if patch AcetylatedNtermDimethylatedCtermPeptoidFull applies to residue ALA:C-conjugated\r\n19185a19488\r\n> core.chemical.ResidueTypeFinder: Checking if patch AcetylatedPeptoidNterm applies to residue ALA:C-conjugated\r\n19186a19490\r\n> core.chemical.ResidueTypeFinder: Checking if patch non-conjugated applies to residue ALA:C-conjugated\r\n19187a19492\r\n> core.chemical.ResidueTypeFinder: Checking if patch terpene_lower_full applies to residue ALA:C-conjugated\r\n19188a19494\r\n> core.chemical.ResidueTypeFinder: Checking if patch terpene_upper_full applies to residue ALA:C-conjugated\r\n19189a19496\r\n> core.chemical.ResidueTypeFinder: Checking if patch hbs_pre applies to residue ALA:C-conjugated\r\n19190a19498\r\n> core.chemical.ResidueTypeFinder: Checking if patch hbs_post applies to residue ALA:C-conjugated\r\n19191a19500\r\n> core.chemical.ResidueTypeFinder: Checking if patch a3b_hbs_pre applies to residue ALA:C-conjugated\r\n19192a19502\r\n> core.chemical.ResidueTypeFinder: Checking if patch a3b_hbs_post applies to residue ALA:C-conjugated\r\n19193a19504\r\n> core.chemical.ResidueTypeFinder: Checking if patch oop_pre applies to residue ALA:C-conjugated\r\n19194a19506\r\n> core.chemical.ResidueTypeFinder: Checking if patch oop_post applies to residue ALA:C-conjugated\r\n19195a19508\r\n> core.chemical.ResidueTypeFinder: Checking if patch triazolamerN applies to residue ALA:C-conjugated\r\n19196a19510\r\n> core.chemical.ResidueTypeFinder: Checking if patch triazolamerC applies to residue ALA:C-conjugated\r\n19197a19512\r\n> core.chemical.ResidueTypeFinder: Checking if patch VirtualWater applies to residue ALA:C-conjugated\r\n19198a19514\r\n> core.chemical.ResidueTypeFinder: Checking if patch ProteinReplsBB applies to residue ALA:C-conjugated\r\n19199a19516\r\n> core.chemical.ResidueTypeFinder: Checking if patch Ca2Coordinating applies to residue ALA:C-conjugated\r\n19200a19518\r\n> core.chemical.ResidueTypeFinder: Checking if patch Co2Coordinating applies to residue ALA:C-conjugated\r\n19201a19520\r\n> core.chemical.ResidueTypeFinder: Checking if patch Cu2Coordinating applies to residue ALA:C-conjugated\r\n19202a19522\r\n> core.chemical.ResidueTypeFinder: Checking if patch Dy3Coordinating applies to residue ALA:C-conjugated\r\n19203a19524\r\n> core.chemical.ResidueTypeFinder: Checking if patch Fe2Coordinating applies to residue ALA:C-conjugated\r\n19204a19526\r\n> core.chemical.ResidueTypeFinder: Checking if patch Fe3Coordinating applies to residue ALA:C-conjugated\r\n19205a19528\r\n> core.chemical.ResidueTypeFinder: Checking if patch La3Coordinating applies to residue ALA:C-conjugated\r\n19206a19530\r\n> core.chemical.ResidueTypeFinder: Checking if patch Lu3Coordinating applies to residue ALA:C-conjugated\r\n19207a19532\r\n> core.chemical.ResidueTypeFinder: Checking if patch Mg2Coordinating applies to residue ALA:C-conjugated\r\n19208a19534\r\n> core.chemical.ResidueTypeFinder: Checking if patch Mn2Coordinating applies to residue ALA:C-conjugated\r\n19209a19536\r\n> core.chemical.ResidueTypeFinder: Checking if patch Tb3Coordinating applies to residue ALA:C-conjugated\r\n19210a19538\r\n> core.chemical.ResidueTypeFinder: Checking if patch Tm3Coordinating applies to residue ALA:C-conjugated\r\n19211a19540\r\n> core.chemical.ResidueTypeFinder: Checking if patch Yb3Coordinating applies to residue ALA:C-conjugated\r\n19213,19214c19542,19544\r\n< core.chemical.ResidueTypeFinder: Patched up to 1 ResidueType(s).\r\n< core.chemical.ResidueTypeFinder: Discouraging 3 properties, going from 1 types to 1 types.\r\n---\r\n> core.chemical.ResidueTypeFinder: Checking if patch Er3Coordinating applies to residue ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: Patched up to 2 ResidueType(s).\r\n> core.chemical.ResidueTypeFinder: Discouraging 3 properties, going from 2 types to 2 types.\r\n19216,19218c19546,19548\r\n< core.chemical.ResidueTypeFinder: Going from ALA\r\n< core.chemical.ResidueTypeFinder: To ALA\r\n< core.chemical.ResidueTypeFinder: Encouraging 1 properties, going from 1 types to 1 types.\r\n---\r\n> core.chemical.ResidueTypeFinder: Going from ALA ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: To ALA ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: Encouraging 1 properties, going from 2 types to 2 types.\r\n19220,19222c19550,19555\r\n< core.chemical.ResidueTypeFinder: Going from ALA\r\n< core.chemical.ResidueTypeFinder: To ALA\r\n< core.chemical.ResidueTypeFinder: Keeping up to 1 ResidueType(s) after filtering.\r\n---\r\n> core.chemical.ResidueTypeFinder: Going from ALA ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: To ALA ALA:C-conjugated\r\n> core.chemical.ResidueTypeFinder: Keeping up to 2 ResidueType(s) after filtering.\r\n> core.chemical.ResidueTypeFinder: Finding best match from among 2 ResidueTypes.\r\n> core.chemical.ResidueTypeFinder: ALA\r\n> core.chemical.ResidueTypeFinder: ALA:C-conjugated\r\n19298a19632\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n19321a19656\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n19443a19779\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n19466a19803\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n19588a19926\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO\r\n19611a19950\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO\r\n19733a20073\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n19756a20097\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n19878a20220\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n19901a20244\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n20095a20439,20440\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY:CtermProteinFull\r\n20141a20487,20488\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY:CtermProteinFull\r\n24855a25203,25204\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA:NtermProteinFull\r\n24901a25251,25252\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA:NtermProteinFull\r\n25113a25465,25466\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue CYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue CYS:NtermProteinFull\r\n25159a25513,25514\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue CYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue CYS:NtermProteinFull\r\n25371a25727,25728\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP:NtermProteinFull\r\n25417a25775,25776\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP:NtermProteinFull\r\n25629a25989,25990\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU:NtermProteinFull\r\n25675a26037,26038\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU:NtermProteinFull\r\n25887a26251,26252\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE:NtermProteinFull\r\n25933a26299,26300\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE:NtermProteinFull\r\n26146a26514,26515\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY:NtermProteinFull\r\n26192a26562,26563\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY:NtermProteinFull\r\n26404a26776,26777\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS:NtermProteinFull\r\n26450a26824,26825\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS:NtermProteinFull\r\n26662a27038,27039\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS_D\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS_D:NtermProteinFull\r\n26708a27086,27087\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS_D\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS_D:NtermProteinFull\r\n26920a27300,27301\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE:NtermProteinFull\r\n26966a27348,27349\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE:NtermProteinFull\r\n27178a27562,27563\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS:NtermProteinFull\r\n27224a27610,27611\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS:NtermProteinFull\r\n27436a27824,27825\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU:NtermProteinFull\r\n27482a27872,27873\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU:NtermProteinFull\r\n27694a28086,28087\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET:NtermProteinFull\r\n27740a28134,28135\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET:NtermProteinFull\r\n27932a28328,28329\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN:NtermProteinFull\r\n27978a28376,28377\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN:NtermProteinFull\r\n28200a28600,28601\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO:NtermProteinFull\r\n28246a28648,28649\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO:NtermProteinFull\r\n28458a28862,28863\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN:NtermProteinFull\r\n28504a28910,28911\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN:NtermProteinFull\r\n28716a29124,29125\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG:NtermProteinFull\r\n28762a29172,29173\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG:NtermProteinFull\r\n28974a29386,29387\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER:NtermProteinFull\r\n29020a29434,29435\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER:NtermProteinFull\r\n29232a29648,29649\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR:NtermProteinFull\r\n29278a29696,29697\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR:NtermProteinFull\r\n29490a29910,29911\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL:NtermProteinFull\r\n29536a29958,29959\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL:NtermProteinFull\r\n29748a30172,30173\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP:NtermProteinFull\r\n29794a30220,30221\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP:NtermProteinFull\r\n30006a30434,30435\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR:NtermProteinFull\r\n30052a30482,30483\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR:NtermProteinFull\r\n30189a30621\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n30212a30645\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n30313a30747\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue CYS\r\n30336a30771\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue CYS\r\n30437a30873\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n30460a30897\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n30561a30999\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n30584a31023\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n30685a31125\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE\r\n30708a31149\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE\r\n30809a31251\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n30832a31275\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n30933a31377\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS\r\n30956a31401\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS\r\n31057a31503\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS_D\r\n31080a31527\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS_D\r\n31181a31629\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n31204a31653\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n31305a31755\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n31328a31779\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n31429a31881\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n31452a31905\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n31553a32007\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET\r\n31576a32031\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET\r\n31677a32133\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n31700a32157\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n31801a32259\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO\r\n31824a32283\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO\r\n31925a32385\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n31948a32409\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n32049a32511\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n32072a32535\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n32173a32637\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n32196a32661\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n32297a32763\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n32320a32787\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n32421a32889\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n32444a32913\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n32545a33015\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP\r\n32568a33039\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP\r\n32669a33141\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR\r\n32692a33165\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR\r\n34167a34641,34642\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA:CtermProteinFull\r\n34213a34689,34690\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA:CtermProteinFull\r\n34422a34900,34901\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue CYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue CYS:CtermProteinFull\r\n34468a34948,34949\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue CYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue CYS:CtermProteinFull\r\n34677a35159,35160\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP:CtermProteinFull\r\n34723a35207,35208\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP:CtermProteinFull\r\n34932a35418,35419\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU:CtermProteinFull\r\n34978a35466,35467\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU:CtermProteinFull\r\n35187a35677,35678\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE:CtermProteinFull\r\n35233a35725,35726\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE:CtermProteinFull\r\n35426a35920,35921\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY:CtermProteinFull\r\n35472a35968,35969\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY:CtermProteinFull\r\n35681a36179,36180\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS:CtermProteinFull\r\n35727a36227,36228\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS:CtermProteinFull\r\n35936a36438,36439\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS_D\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS_D:CtermProteinFull\r\n35982a36486,36487\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS_D\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS_D:CtermProteinFull\r\n36191a36697,36698\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE:CtermProteinFull\r\n36237a36745,36746\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE:CtermProteinFull\r\n36446a36956,36957\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS:CtermProteinFull\r\n36492a37004,37005\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS:CtermProteinFull\r\n36701a37215,37216\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU:CtermProteinFull\r\n36747a37263,37264\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU:CtermProteinFull\r\n36956a37474,37475\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET:CtermProteinFull\r\n37002a37522,37523\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET:CtermProteinFull\r\n37211a37733,37734\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN:CtermProteinFull\r\n37257a37781,37782\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN:CtermProteinFull\r\n37466a37992,37993\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO:CtermProteinFull\r\n37512a38040,38041\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO:CtermProteinFull\r\n37721a38251,38252\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN:CtermProteinFull\r\n37767a38299,38300\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN:CtermProteinFull\r\n37976a38510,38511\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG:CtermProteinFull\r\n38022a38558,38559\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG:CtermProteinFull\r\n38231a38769,38770\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER:CtermProteinFull\r\n38277a38817,38818\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER:CtermProteinFull\r\n38486a39028,39029\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR:CtermProteinFull\r\n38532a39076,39077\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR:CtermProteinFull\r\n38741a39287,39288\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL:CtermProteinFull\r\n38787a39335,39336\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL:CtermProteinFull\r\n38996a39546,39547\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP:CtermProteinFull\r\n39042a39594,39595\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP:CtermProteinFull\r\n39251a39805,39806\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR:CtermProteinFull\r\n39297a39853,39854\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR:CtermProteinFull\r\n",
"state": "failed"
},
"ddG_scan": {
"log": "",
"state": "passed"
},
"ddG_sym": {
"log": "",
"state": "passed"
},
"dehydro_aa_patch": {
"log": "Brief Diff:\ndiff: /home/benchmark/working_dir/main:62108/dehydro_aa_patch: No such file or directory\r\n",
"state": "failed"
},
"density_denovo": {
"log": "",
"state": "passed"
},
"density_refine": {
"log": "",
"state": "passed"
},
"density_refine_symm": {
"log": "",
"state": "passed"
},
"density_tools": {
"log": "",
"state": "passed"
},
"design_glycans": {
"log": "Brief Diff:\nFiles /home/benchmark/working_dir/main:62108/design_glycans/info.log and /home/benchmark/working_dir/main:62109/design_glycans/info.log differ\r\n\n\nFull Diff:\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62108/design_glycans/info.log /home/benchmark/working_dir/main:62109/design_glycans/info.log\r\n620a621\r\n> core.pack.palette.PackerPalette: Adding ALA:C-conjugated at position 2.\r\n",
"state": "failed"
},
"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"
},
"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": "Brief Diff:\nFiles /home/benchmark/working_dir/main:62108/features/log_db_output and /home/benchmark/working_dir/main:62109/features/log_db_output differ\r\n\n\nFull Diff:\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62108/features/log_db_output /home/benchmark/working_dir/main:62109/features/log_db_output\r\n708,710d707\r\n< basic.io.database: Database file opened: scoring/score_functions/custom_pair_distance/pos_charge_repulsion\r\n< basic.io.database: Database file opened: scoring/score_functions/custom_pair_distance/neg_charge_repulsion\r\n< core.scoring.custom_pair_distance.FullatomCustomPairDistanceEnergy: Added 8 AtomPairFuncList lists\r\n",
"state": "failed"
},
"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": "Brief Diff:\nFiles /home/benchmark/working_dir/main:62108/fiber_diffraction_fad/log and /home/benchmark/working_dir/main:62109/fiber_diffraction_fad/log differ\r\n\n\nFull Diff:\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62108/fiber_diffraction_fad/log /home/benchmark/working_dir/main:62109/fiber_diffraction_fad/log\r\n7556a7557\r\n> core.chemical.Patch: Reading patch file: ROSETTA/database/chemical/residue_type_sets/fa_standard/patches/branching/C-linked_conjugation.txt\r\n7579a7581\r\n> core.chemical.Patch: Reading patch file: ROSETTA/database/chemical/residue_type_sets/fa_standard/patches/Nterm2_Oxobutrylation.txt\r\n17458a17461,17462\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA:NtermProteinFull\r\n17504a17509,17510\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA:NtermProteinFull\r\n17716a17723,17724\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue CYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue CYS:NtermProteinFull\r\n17762a17771,17772\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue CYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue CYS:NtermProteinFull\r\n17974a17985,17986\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP:NtermProteinFull\r\n18020a18033,18034\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP:NtermProteinFull\r\n18232a18247,18248\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU:NtermProteinFull\r\n18278a18295,18296\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU:NtermProteinFull\r\n18490a18509,18510\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE:NtermProteinFull\r\n18536a18557,18558\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE:NtermProteinFull\r\n18749a18772,18773\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY:NtermProteinFull\r\n18795a18820,18821\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY:NtermProteinFull\r\n19007a19034,19035\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS:NtermProteinFull\r\n19053a19082,19083\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS:NtermProteinFull\r\n19265a19296,19297\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS_D\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS_D:NtermProteinFull\r\n19311a19344,19345\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS_D\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS_D:NtermProteinFull\r\n19523a19558,19559\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE:NtermProteinFull\r\n19569a19606,19607\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE:NtermProteinFull\r\n19781a19820,19821\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS:NtermProteinFull\r\n19827a19868,19869\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS:NtermProteinFull\r\n20039a20082,20083\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU:NtermProteinFull\r\n20085a20130,20131\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU:NtermProteinFull\r\n20277a20324,20325\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET:NtermProteinFull\r\n20323a20372,20373\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET:NtermProteinFull\r\n20535a20586,20587\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN:NtermProteinFull\r\n20581a20634,20635\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN:NtermProteinFull\r\n20803a20858,20859\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO:NtermProteinFull\r\n20849a20906,20907\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO:NtermProteinFull\r\n21061a21120,21121\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN:NtermProteinFull\r\n21107a21168,21169\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN:NtermProteinFull\r\n21319a21382,21383\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG:NtermProteinFull\r\n21365a21430,21431\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG:NtermProteinFull\r\n21577a21644,21645\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER:NtermProteinFull\r\n21623a21692,21693\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER:NtermProteinFull\r\n21835a21906,21907\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR:NtermProteinFull\r\n21881a21954,21955\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR:NtermProteinFull\r\n22093a22168,22169\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL:NtermProteinFull\r\n22139a22216,22217\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL:NtermProteinFull\r\n22351a22430,22431\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP:NtermProteinFull\r\n22397a22478,22479\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP:NtermProteinFull\r\n22609a22692,22693\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR:NtermProteinFull\r\n22655a22740,22741\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR:NtermProteinFull\r\n22792a22879\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n22815a22903\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n22916a23005\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue CYS\r\n22939a23029\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue CYS\r\n23040a23131\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n23063a23155\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n23164a23257\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n23187a23281\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n23288a23383\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE\r\n23311a23407\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE\r\n23412a23509\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n23435a23533\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n23536a23635\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS\r\n23559a23659\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS\r\n23660a23761\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS_D\r\n23683a23785\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS_D\r\n23784a23887\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n23807a23911\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n23908a24013\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n23931a24037\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n24032a24139\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n24055a24163\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n24156a24265\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET\r\n24179a24289\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET\r\n24280a24391\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n24303a24415\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n24404a24517\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO\r\n24427a24541\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO\r\n24528a24643\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n24551a24667\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n24652a24769\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n24675a24793\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n24776a24895\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n24799a24919\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n24900a25021\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n24923a25045\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n25024a25147\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n25047a25171\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n25148a25273\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP\r\n25171a25297\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP\r\n25272a25399\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR\r\n25295a25423\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR\r\n25615a25744,25745\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA:CtermProteinFull\r\n25661a25792,25793\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA:CtermProteinFull\r\n25870a26003,26004\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue CYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue CYS:CtermProteinFull\r\n25916a26051,26052\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue CYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue CYS:CtermProteinFull\r\n26125a26262,26263\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP:CtermProteinFull\r\n26171a26310,26311\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP:CtermProteinFull\r\n26380a26521,26522\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU:CtermProteinFull\r\n26426a26569,26570\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU:CtermProteinFull\r\n26635a26780,26781\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE:CtermProteinFull\r\n26681a26828,26829\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE:CtermProteinFull\r\n26874a27023,27024\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY:CtermProteinFull\r\n26920a27071,27072\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY:CtermProteinFull\r\n27129a27282,27283\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS:CtermProteinFull\r\n27175a27330,27331\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS:CtermProteinFull\r\n27384a27541,27542\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS_D\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS_D:CtermProteinFull\r\n27430a27589,27590\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS_D\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS_D:CtermProteinFull\r\n27639a27800,27801\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE:CtermProteinFull\r\n27685a27848,27849\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE:CtermProteinFull\r\n27894a28059,28060\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS:CtermProteinFull\r\n27940a28107,28108\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS:CtermProteinFull\r\n28149a28318,28319\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU:CtermProteinFull\r\n28195a28366,28367\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU:CtermProteinFull\r\n28404a28577,28578\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET:CtermProteinFull\r\n28450a28625,28626\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET:CtermProteinFull\r\n28659a28836,28837\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN:CtermProteinFull\r\n28705a28884,28885\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN:CtermProteinFull\r\n28914a29095,29096\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO:CtermProteinFull\r\n28960a29143,29144\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO:CtermProteinFull\r\n29169a29354,29355\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN:CtermProteinFull\r\n29215a29402,29403\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN:CtermProteinFull\r\n29424a29613,29614\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG:CtermProteinFull\r\n29470a29661,29662\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG:CtermProteinFull\r\n29679a29872,29873\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER:CtermProteinFull\r\n29725a29920,29921\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER:CtermProteinFull\r\n29934a30131,30132\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR:CtermProteinFull\r\n29980a30179,30180\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR:CtermProteinFull\r\n30189a30390,30391\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL:CtermProteinFull\r\n30235a30438,30439\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL:CtermProteinFull\r\n30444a30649,30650\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP:CtermProteinFull\r\n30490a30697,30698\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP:CtermProteinFull\r\n30699a30908,30909\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR:CtermProteinFull\r\n30745a30956,30957\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR:CtermProteinFull\r\n",
"state": "failed"
},
"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": "Brief Diff:\nFiles /home/benchmark/working_dir/main:62108/fold_and_dock/log and /home/benchmark/working_dir/main:62109/fold_and_dock/log differ\r\n\n\nFull Diff:\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62108/fold_and_dock/log /home/benchmark/working_dir/main:62109/fold_and_dock/log\r\n7309a7310\r\n> core.chemical.Patch: Reading patch file: ROSETTA/database/chemical/residue_type_sets/fa_standard/patches/branching/C-linked_conjugation.txt\r\n7332a7334\r\n> core.chemical.Patch: Reading patch file: ROSETTA/database/chemical/residue_type_sets/fa_standard/patches/Nterm2_Oxobutrylation.txt\r\n10069a10072,10074\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL:NtermProteinFull\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL:NtermProteinMethylated\r\n10138a10144,10146\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL:NtermProteinFull\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL:NtermProteinMethylated\r\n10775a10784\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n10798a10808\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n10921a10932\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n10944a10956\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n11067a11080\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n11090a11104\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n11213a11228\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n11236a11252\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n11358a11375\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n11381a11399\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n11504a11523\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n11527a11547\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n11649a11670\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n11672a11694\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n11794a11817\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n11817a11841\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n11940a11965\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n11963a11989\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n12085a12112\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n12108a12136\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n12230a12259\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n12253a12283\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n12376a12407\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n12399a12431\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n12522a12555\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n12545a12579\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n12667a12702\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n12690a12726\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n12813a12850\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n12836a12874\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n12959a12998\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n12982a13022\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n13104a13145\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n13127a13169\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n13249a13292\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n13272a13316\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n13394a13439\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n13417a13463\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n13539a13586\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n13562a13610\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n13684a13733\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n13707a13757\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n13829a13880\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n13852a13904\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n13974a14027\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n13997a14051\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n14119a14174\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n14142a14198\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n14264a14321\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n14287a14345\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n14409a14468\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n14432a14492\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n14555a14616\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n14578a14640\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n14700a14763\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n14723a14787\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n14845a14910\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n14868a14934\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n14990a15057\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n15013a15081\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n15207a15276,15277\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS:CtermProteinFull\r\n15253a15324,15325\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS:CtermProteinFull\r\n15553a15626,15628\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL:NtermProteinFull\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL:NtermProteinMethylated\r\n15622a15698,15700\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL:NtermProteinFull\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL:NtermProteinMethylated\r\n15978a16057\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n16001a16081\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n16123a16204\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n16146a16228\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n16268a16351\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n16291a16375\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n16413a16498\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n16436a16522\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n16558a16645\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n16581a16669\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n16703a16792\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n16726a16816\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n16848a16939\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n16871a16963\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n16993a17086\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n17016a17110\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n17138a17233\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n17161a17257\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n17283a17380\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n17306a17404\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n17428a17527\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n17451a17551\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n17573a17674\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n17596a17698\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n17718a17821\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n17741a17845\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n17863a17968\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n17886a17992\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n18008a18115\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n18031a18139\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n18153a18262\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n18176a18286\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n18298a18409\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n18321a18433\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n18443a18556\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n18466a18580\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n18588a18703\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n18611a18727\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n18733a18850\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n18756a18874\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n18878a18997\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n18901a19021\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n19023a19144\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n19046a19168\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n19168a19291\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n19191a19315\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n19313a19438\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n19336a19462\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n19458a19585\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n19481a19609\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n19603a19732\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n19626a19756\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n19748a19879\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n19771a19903\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n19893a20026\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n19916a20050\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n20038a20173\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n20061a20197\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n20183a20320\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n20206a20344\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n20384a20523,20524\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS:CtermProteinFull\r\n20430a20571,20572\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS:CtermProteinFull\r\n20693a20836,20838\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL:NtermProteinFull\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL:NtermProteinMethylated\r\n20762a20908,20910\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL:NtermProteinFull\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL:NtermProteinMethylated\r\n21118a21267\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n21141a21291\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n21263a21414\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n21286a21438\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n21408a21561\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n21431a21585\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n21553a21708\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n21576a21732\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n21698a21855\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n21721a21879\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n21843a22002\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n21866a22026\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n21988a22149\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n22011a22173\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n22133a22296\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n22156a22320\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n22278a22443\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n22301a22467\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n22423a22590\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n22446a22614\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n22568a22737\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n22591a22761\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n22713a22884\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n22736a22908\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n22858a23031\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n22881a23055\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n23003a23178\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n23026a23202\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n23148a23325\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n23171a23349\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n23293a23472\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n23316a23496\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n23438a23619\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n23461a23643\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n23583a23766\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n23606a23790\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n23728a23913\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n23751a23937\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n23873a24060\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n23896a24084\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n24018a24207\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n24041a24231\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n24163a24354\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n24186a24378\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n24308a24501\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n24331a24525\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n24453a24648\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n24476a24672\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n24598a24795\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n24621a24819\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n24743a24942\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n24766a24966\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n24888a25089\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n24911a25113\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n25033a25236\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n25056a25260\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n25178a25383\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n25201a25407\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n25323a25530\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n25346a25554\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n25524a25733,25734\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS:CtermProteinFull\r\n25570a25781,25782\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS:CtermProteinFull\r\n33200a33413,33414\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA:NtermProteinFull\r\n33246a33461,33462\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA:NtermProteinFull\r\n33458a33675,33676\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue CYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue CYS:NtermProteinFull\r\n33504a33723,33724\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue CYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue CYS:NtermProteinFull\r\n33716a33937,33938\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP:NtermProteinFull\r\n33762a33985,33986\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP:NtermProteinFull\r\n33974a34199,34200\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU:NtermProteinFull\r\n34020a34247,34248\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU:NtermProteinFull\r\n34232a34461,34462\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE:NtermProteinFull\r\n34278a34509,34510\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE:NtermProteinFull\r\n34491a34724,34725\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY:NtermProteinFull\r\n34537a34772,34773\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY:NtermProteinFull\r\n34749a34986,34987\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS:NtermProteinFull\r\n34795a35034,35035\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS:NtermProteinFull\r\n35007a35248,35249\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS_D\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS_D:NtermProteinFull\r\n35053a35296,35297\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS_D\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS_D:NtermProteinFull\r\n35265a35510,35511\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE:NtermProteinFull\r\n35311a35558,35559\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE:NtermProteinFull\r\n35523a35772,35773\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS:NtermProteinFull\r\n35569a35820,35821\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS:NtermProteinFull\r\n35781a36034,36035\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU:NtermProteinFull\r\n35827a36082,36083\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU:NtermProteinFull\r\n36039a36296,36297\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET:NtermProteinFull\r\n36085a36344,36345\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET:NtermProteinFull\r\n36297a36558,36559\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN:NtermProteinFull\r\n36343a36606,36607\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN:NtermProteinFull\r\n36565a36830,36831\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO:NtermProteinFull\r\n36611a36878,36879\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO:NtermProteinFull\r\n36823a37092,37093\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN:NtermProteinFull\r\n36869a37140,37141\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN:NtermProteinFull\r\n37081a37354,37355\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG:NtermProteinFull\r\n37127a37402,37403\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG:NtermProteinFull\r\n37339a37616,37617\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER:NtermProteinFull\r\n37385a37664,37665\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER:NtermProteinFull\r\n37597a37878,37879\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR:NtermProteinFull\r\n37643a37926,37927\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR:NtermProteinFull\r\n37835a38120,38121\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL:NtermProteinFull\r\n37881a38168,38169\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL:NtermProteinFull\r\n38093a38382,38383\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP:NtermProteinFull\r\n38139a38430,38431\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP:NtermProteinFull\r\n38351a38644,38645\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR:NtermProteinFull\r\n38397a38692,38693\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR:NtermProteinFull\r\n38534a38831\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n38557a38855\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n38658a38957\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue CYS\r\n38681a38981\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue CYS\r\n38782a39083\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n38805a39107\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n38906a39209\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n38929a39233\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n39030a39335\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE\r\n39053a39359\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE\r\n39154a39461\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n39177a39485\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n39278a39587\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS\r\n39301a39611\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS\r\n39402a39713\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS_D\r\n39425a39737\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS_D\r\n39526a39839\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n39549a39863\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n39650a39965\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n39673a39989\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n39774a40091\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n39797a40115\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n39898a40217\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET\r\n39921a40241\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET\r\n40022a40343\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n40045a40367\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n40146a40469\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO\r\n40169a40493\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO\r\n40270a40595\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n40293a40619\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n40394a40721\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n40417a40745\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n40518a40847\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n40541a40871\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n40642a40973\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n40665a40997\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n40766a41099\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n40789a41123\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n40890a41225\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP\r\n40913a41249\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP\r\n41014a41351\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR\r\n41037a41375\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR\r\n41819a42158,42159\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA:CtermProteinFull\r\n41865a42206,42207\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA:CtermProteinFull\r\n42074a42417,42418\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue CYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue CYS:CtermProteinFull\r\n42120a42465,42466\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue CYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue CYS:CtermProteinFull\r\n42329a42676,42677\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASP:CtermProteinFull\r\n42375a42724,42725\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASP:CtermProteinFull\r\n42584a42935,42936\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU:CtermProteinFull\r\n42630a42983,42984\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU:CtermProteinFull\r\n42839a43194,43195\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE:CtermProteinFull\r\n42885a43242,43243\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE:CtermProteinFull\r\n43094a43453,43454\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY:CtermProteinFull\r\n43140a43501,43502\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY:CtermProteinFull\r\n43349a43712,43713\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS:CtermProteinFull\r\n43395a43760,43761\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS:CtermProteinFull\r\n43604a43971,43972\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS_D\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue HIS_D:CtermProteinFull\r\n43650a44019,44020\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS_D\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue HIS_D:CtermProteinFull\r\n43859a44230,44231\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE:CtermProteinFull\r\n43905a44278,44279\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE:CtermProteinFull\r\n44098a44473,44474\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS:CtermProteinFull\r\n44144a44521,44522\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS:CtermProteinFull\r\n44353a44732,44733\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU:CtermProteinFull\r\n44399a44780,44781\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU:CtermProteinFull\r\n44608a44991,44992\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET:CtermProteinFull\r\n44654a45039,45040\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET:CtermProteinFull\r\n44863a45250,45251\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN:CtermProteinFull\r\n44909a45298,45299\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN:CtermProteinFull\r\n45118a45509,45510\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO:CtermProteinFull\r\n45164a45557,45558\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO:CtermProteinFull\r\n45373a45768,45769\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLN:CtermProteinFull\r\n45419a45816,45817\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLN:CtermProteinFull\r\n45628a46027,46028\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG:CtermProteinFull\r\n45674a46075,46076\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG:CtermProteinFull\r\n45883a46286,46287\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER:CtermProteinFull\r\n45929a46334,46335\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER:CtermProteinFull\r\n46138a46545,46546\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR:CtermProteinFull\r\n46184a46593,46594\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR:CtermProteinFull\r\n46393a46804,46805\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL:CtermProteinFull\r\n46439a46852,46853\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL:CtermProteinFull\r\n46648a47063,47064\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP:CtermProteinFull\r\n46694a47111,47112\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP:CtermProteinFull\r\n46903a47322,47323\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR\r\n> core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR:CtermProteinFull\r\n46949a47370,47371\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR\r\n> core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR:CtermProteinFull\r\n",
"state": "failed"
},
"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": "",
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},
"glycosylation": {
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},
"grid_scores_features": {
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"hbnet": {
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"log": "",
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},
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},
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},
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},
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},
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},
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"helical_bundle_predict": {
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},
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},
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"log": "",
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"log": "",
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},
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"homodimer_fnd_ref2015_memb": {
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"hybridization": {
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"hydrate": {
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"iphold": {
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"jd2test_PDBIO": {
"log": "",
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},
"jd2test_PDBin_mmCIFout_extra_data_separate": {
"log": "",
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},
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},
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},
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},
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},
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},
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},
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},
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},
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},
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},
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},
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},
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"mf_flexbb_sc": {
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},
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},
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},
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},
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},
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},
"motif_extraction": {
"log": "",
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},
"motif_score_filter": {
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},
"mp_dock": {
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},
"mp_dock_ensemble": {
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},
"mp_dock_prepack": {
"log": "",
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},
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},
"mp_domain_assembly": {
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},
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},
"mp_find_interface": {
"log": "",
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},
"mp_interface_statistics": {
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},
"mp_ligand_interface": {
"log": "",
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},
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},
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},
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},
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},
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},
"mp_relax": {
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},
"mp_score_jd2": {
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},
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},
"mp_span_from_pdb": {
"log": "",
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},
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},
"mp_symmetry_load": {
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},
"mp_transform": {
"log": "",
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},
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},
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"log": "",
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},
"mpi_simple_cycpep_predict": {
"log": "",
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},
"mpi_simple_cycpep_predict_4level": {
"log": "",
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},
"mpi_simple_cycpep_predict_computing_pnear_to_all": {
"log": "",
"state": "passed"
},
"mpil_find_pore_ahelical": {
"log": "",
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},
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"log": "",
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},
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},
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},
"multistage_rosetta_scripts": {
"log": "",
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},
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},
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"log": "",
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"log": "",
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},
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"mutate": {
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"number_of_residuetypes": {
"log": "Brief Diff:\nFiles /home/benchmark/working_dir/main:62108/number_of_residuetypes/log and /home/benchmark/working_dir/main:62109/number_of_residuetypes/log differ\r\n\n\nFull Diff:\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62108/number_of_residuetypes/log /home/benchmark/working_dir/main:62109/number_of_residuetypes/log\r\n9c9\r\n< apps.pilot.doug.number_of_residuetypes: The FA_STANDARD ResidueTypeSet contains 985 base ResidueTypes, 120 Patches, and 0 unpatchable ResidueTypes \r\n---\r\n> apps.pilot.doug.number_of_residuetypes: The FA_STANDARD ResidueTypeSet contains 985 base ResidueTypes, 122 Patches, and 0 unpatchable ResidueTypes \r\n",
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"oop_create": {
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},
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"state": "passed"
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"state": "passed"
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"orbitals": {
"log": "",
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"output_schema": {
"log": "Brief Diff:\nFiles /home/benchmark/working_dir/main:62108/output_schema/current_rosettascripts_schema.xsd and /home/benchmark/working_dir/main:62109/output_schema/current_rosettascripts_schema.xsd differ\r\n\n\nFull Diff:\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62108/output_schema/current_rosettascripts_schema.xsd /home/benchmark/working_dir/main:62109/output_schema/current_rosettascripts_schema.xsd\r\n21284c21284\r\n< The name of the type of linker to use. For example, use TBMB for 1,3,5-tris(bromomethyl)benzene. (Allowed options are TBMB|1_4_BBMB|TMA|thioether|tetrahedral_metal|octahedral_metal|trigonal_planar_metal|trigonal_pyramidal_metal|square_planar_metal|square_pyramidal_metal.)\r\n---\r\n> The name of the type of linker to use. For example, use TBMB for 1,3,5-tris(bromomethyl)benzene. (Allowed options are TBMB|1_4_BBMB|TMA|lanthionine|thioether|tetrahedral_metal|octahedral_metal|trigonal_planar_metal|trigonal_pyramidal_metal|square_planar_metal|square_pyramidal_metal.)\r\n",
"state": "failed"
},
"pH_mode": {
"log": "",
"state": "passed"
},
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"log": "",
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},
"per_residue_energies": {
"log": "",
"state": "passed"
},
"per_residue_sc_sasa": {
"log": "",
"state": "passed"
},
"per_residue_solvent_exposure": {
"log": "",
"state": "passed"
},
"pertmin": {
"log": "",
"state": "passed"
},
"perturb_helical_bundle": {
"log": "",
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"perturb_helical_bundle_copying_pitch": {
"log": "",
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"perturb_helical_bundle_epsilon": {
"log": "",
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"perturb_helical_bundle_setting": {
"log": "",
"state": "passed"
},
"perturb_helical_bundle_z_offset": {
"log": "",
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"phiselector": {
"log": "",
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},
"phosphonate": {
"log": "",
"state": "passed"
},
"phosphorylation": {
"log": "",
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},
"place_simultaneously": {
"log": "",
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"pmut_scan": {
"log": "",
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"pna": {
"log": "",
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},
"pna_base_pairs": {
"log": "",
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},
"pocket_measure": {
"log": "",
"state": "passed"
},
"pocket_relax": {
"log": "",
"state": "passed"
},
"pocket_suggest_targets": {
"log": "",
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},
"polyaramid_test_trivial": {
"log": "",
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},
"pose_sewing": {
"log": "",
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},
"posttranslationalmod_io": {
"log": "",
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},
"ppi_v3_suiteA": {
"log": "",
"state": "passed"
},
"ppi_v3_suiteB": {
"log": "",
"state": "passed"
},
"ppi_v3_suiteC": {
"log": "",
"state": "passed"
},
"ppi_v3_suiteD": {
"log": "",
"state": "passed"
},
"ppi_v3_suiteE": {
"log": "",
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},
"ppi_v3_suiteF": {
"log": "",
"state": "passed"
},
"ppi_v3_suiteG": {
"log": "",
"state": "passed"
},
"ppk": {
"log": "",
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},
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"log": "",
"state": "passed"
},
"protocol_metric": {
"log": "",
"state": "passed"
},
"pwsho": {
"log": "",
"state": "passed"
},
"pymol_cif": {
"log": "",
"state": "passed"
},
"r_pdb2top": {
"log": "",
"state": "passed"
},
"r_rmsf": {
"log": "",
"state": "passed"
},
"ralford_dump_rotamers": {
"log": "",
"state": "passed"
},
"rama_mutation_selector": {
"log": "",
"state": "passed"
},
"range_relax_w_cst": {
"log": "",
"state": "passed"
},
"rb_recces": {
"log": "",
"state": "passed"
},
"rdkit_metrics": {
"log": "",
"state": "passed"
},
"read_polymeric_components": {
"log": "",
"state": "passed"
},
"readin_dna_rna_protein": {
"log": "",
"state": "passed"
},
"real_virt_mover": {
"log": "",
"state": "passed"
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"recces_turner": {
"log": "",
"state": "passed"
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"recon_design": {
"log": "",
"state": "passed"
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"recon_design_mpi": {
"log": "",
"state": "passed"
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"referencepose_mutateresidue": {
"log": "",
"state": "passed"
},
"relax_w_allatom_cst": {
"log": "",
"state": "passed"
},
"remodel_disulfides_rosettascripts": {
"log": "",
"state": "passed"
},
"remodel_helical_repeat": {
"log": "",
"state": "passed"
},
"repack_with_elec_dens": {
"log": "",
"state": "passed"
},
"repeat_propagate": {
"log": "",
"state": "passed"
},
"repeat_propagate_v2": {
"log": "",
"state": "passed"
},
"repeat_propagate_v3": {
"log": "",
"state": "passed"
},
"repeat_relax": {
"log": "",
"state": "passed"
},
"replica_docking": {
"log": "",
"state": "passed"
},
"report_hbonds_for_plugin": {
"log": "",
"state": "passed"
},
"res_lipo_ref2015_memb": {
"log": "",
"state": "passed"
},
"residue_energy_breakdown": {
"log": "",
"state": "passed"
},
"resource_database_locator": {
"log": "",
"state": "passed"
},
"restype_converter": {
"log": "",
"state": "passed"
},
"rings": {
"log": "",
"state": "passed"
},
"rna_add_WC_stats": {
"log": "",
"state": "passed"
},
"rna_assemble": {
"log": "",
"state": "passed"
},
"rna_cluster": {
"log": "",
"state": "passed"
},
"rna_denovo": {
"log": "",
"state": "passed"
},
"rna_denovo_RNP_low_res": {
"log": "",
"state": "passed"
},
"rna_denovo_RNP_refine_native": {
"log": "",
"state": "passed"
},
"rna_denovo_base_pair_constraints": {
"log": "",
"state": "passed"
},
"rna_denovo_base_pair_setup": {
"log": "",
"state": "passed"
},
"rna_denovo_bps": {
"log": "",
"state": "passed"
},
"rna_denovo_bps_fixed_ends": {
"log": "",
"state": "passed"
},
"rna_denovo_bps_helix_ends": {
"log": "",
"state": "passed"
},
"rna_denovo_dna_bridge": {
"log": "",
"state": "passed"
},
"rna_denovo_fragment_homology_exclusion": {
"log": "",
"state": "passed"
},
"rna_denovo_grid_vdw": {
"log": "",
"state": "passed"
},
"rna_denovo_lariat": {
"log": "",
"state": "passed"
},
"rna_denovo_new_FT_2in_dens": {
"log": "",
"state": "passed"
},
"rna_denovo_new_FT_5P_j12_leadzyme": {
"log": "",
"state": "passed"
},
"rna_denovo_new_FT_RNP_2prot_dens": {
"log": "",
"state": "passed"
},
"rna_denovo_new_FT_rna_two_chains": {
"log": "",
"state": "passed"
},
"rna_denovo_new_libs": {
"log": "",
"state": "passed"
},
"rna_denovo_symm_hack": {
"log": "",
"state": "passed"
},
"rna_design": {
"log": "",
"state": "passed"
},
"rna_farfar_block_stack": {
"log": "",
"state": "passed"
},
"rna_farfar_noncanonical_hairpin": {
"log": "",
"state": "passed"
},
"rna_farfar_syn_chi_res": {
"log": "",
"state": "passed"
},
"rna_helix": {
"log": "",
"state": "passed"
},
"rna_minimize": {
"log": "",
"state": "passed"
},
"rna_minimize_6D_loop_close": {
"log": "",
"state": "passed"
},
"rna_motif": {
"log": "",
"state": "passed"
},
"rna_predict_chem_map": {
"log": "",
"state": "passed"
},
"rna_puzzle11_H2H3H4_run3_connectU40": {
"log": "",
"state": "passed"
},
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"log": "",
"state": "passed"
},
"rna_puzzle5_P15P3P8_noP4P6_4RB_G208phosphate_ligation": {
"log": "",
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},
"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": "",
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},
"rnp_ddg_relax_finalize": {
"log": "",
"state": "passed"
},
"rnp_ddg_relax_setup": {
"log": "",
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},
"rollmover": {
"log": "",
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},
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"log": "",
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},
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"log": "",
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},
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"log": "",
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},
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},
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"log": "",
"state": "passed"
},
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"log": "",
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},
"rosie_ligand_docking": {
"log": "",
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},
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"log": "",
"state": "passed"
},
"rotamer_recovery": {
"log": "",
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},
"rotamer_recovery_compare_two_structures": {
"log": "",
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},
"rs_flexbbmoves": {
"log": "",
"state": "passed"
},
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"log": "",
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},
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"log": "",
"state": "passed"
},
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"log": "",
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},
"score12_docking": {
"log": "",
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},
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"log": "",
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},
"score_jd2": {
"log": "",
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},
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"log": "",
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},
"sdf_reader": {
"log": "",
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},
"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": "",
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},
"sequence_tolerance": {
"log": "",
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},
"set_torsion": {
"log": "",
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},
"shobuns": {
"log": "",
"state": "passed"
},
"silent2frag": {
"log": "",
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},
"simple_cycpep_predict": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_1_4_bbmb": {
"log": "",
"state": "passed"
},
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"log": "",
"state": "passed"
},
"simple_cycpep_predict_anglelength": {
"log": "",
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},
"simple_cycpep_predict_beta_thioether_lariat": {
"log": "",
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"log": "",
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"simple_cycpep_predict_cartesian": {
"log": "",
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},
"simple_cycpep_predict_cispro": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_cterm_isopeptide_lariat": {
"log": "",
"state": "passed"
},
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"log": "",
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},
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"log": "",
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},
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},
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"log": "",
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},
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"log": "",
"state": "passed"
},
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"log": "",
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},
"simple_cycpep_predict_octahedral_metal": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_peptoid": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_setting": {
"log": "",
"state": "passed"
},
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"log": "",
"state": "passed"
},
"simple_cycpep_predict_sidechain_isopeptide_reverse": {
"log": "",
"state": "passed"
},
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"log": "",
"state": "passed"
},
"simple_cycpep_predict_square_pyramidal_metal": {
"log": "",
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},
"simple_cycpep_predict_symm_gly": {
"log": "",
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},
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"log": "",
"state": "passed"
},
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"log": "",
"state": "passed"
},
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"log": "",
"state": "passed"
},
"simple_cycpep_predict_terminal_disulfide_internal_permutations": {
"log": "",
"state": "passed"
},
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"log": "",
"state": "passed"
},
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"log": "",
"state": "passed"
},
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"log": "",
"state": "passed"
},
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"log": "",
"state": "passed"
},
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"log": "",
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},
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"log": "",
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"log": "",
"state": "passed"
},
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"log": "",
"state": "passed"
},
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"log": "",
"state": "passed"
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"log": "",
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},
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"log": "",
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},
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"log": "",
"state": "passed"
},
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"log": "",
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},
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"log": "",
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},
"simple_metric_cache": {
"log": "",
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},
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"log": "",
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},
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"log": "",
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},
"simple_metrics": {
"log": "",
"state": "passed"
},
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"log": "",
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},
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"log": "",
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},
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"log": "",
"state": "passed"
},
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"log": "",
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},
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"log": "",
"state": "passed"
},
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},
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"log": "",
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"log": "",
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},
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},
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},
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"log": "",
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},
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},
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"log": "",
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},
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"log": "",
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},
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"log": "",
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},
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"log": "",
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"log": "",
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"log": "",
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},
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"log": "",
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},
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"log": "",
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},
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"log": "",
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},
"supercharge": {
"log": "",
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},
"surface_docking": {
"log": "",
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},
"swa_protein_CCDclose": {
"log": "",
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},
"swa_protein_build_at_Cterminus": {
"log": "",
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},
"swa_protein_build_at_Nterminus": {
"log": "",
"state": "passed"
},
"swa_protein_cluster": {
"log": "",
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},
"swa_protein_combine_loops": {
"log": "",
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},
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"log": "",
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},
"swa_protein_prepack": {
"log": "",
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},
"swa_rna_erraser": {
"log": "",
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},
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"log": "",
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},
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"log": "",
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"log": "",
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"log": "",
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"log": "",
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"log": "",
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"log": "",
"state": "passed"
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"log": "",
"state": "passed"
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"swa_rna_gagu_09_sample_virtual_ribose": {
"log": "",
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"log": "",
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"log": "",
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"log": "",
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"log": "",
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},
"swa_rna_gagu_14_combine_long_loop_filtering": {
"log": "",
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"log": "",
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},
"swa_rna_gagu_16_prepend_dinucleotide_on_dinucleotide": {
"log": "",
"state": "passed"
},
"swa_rna_gagu_17_append_floating_base": {
"log": "",
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"swa_rna_gagu_18_rebuild_bulge": {
"log": "",
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},
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"log": "",
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},
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"log": "",
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},
"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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},
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"log": "",
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},
"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": "",
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},
"swm_build_full_model": {
"log": "",
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},
"swm_dna_bridge": {
"log": "",
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},
"swm_dna_loop": {
"log": "",
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},
"swm_general_polymer_sampler": {
"log": "",
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},
"swm_l_rna": {
"log": "",
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},
"swm_protein_CCDmove": {
"log": "",
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},
"swm_protein_from_scratch": {
"log": "",
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},
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"log": "",
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},
"swm_protein_move_inside_coiledcoil_by_bond": {
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},
"swm_protein_move_inside_helix_by_bond": {
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},
"swm_protein_preminimize": {
"log": "",
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},
"swm_rna_base_pair_constraints": {
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},
"swm_rna_checkpoint_partition": {
"log": "",
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},
"swm_rna_fourwayjunction": {
"log": "",
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},
"swm_rna_loop_design": {
"log": "",
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},
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"log": "",
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"swm_rna_move_inside_helix_by_bond": {
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},
"swm_rna_move_inside_helix_by_jump": {
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},
"swm_rna_move_two_strands": {
"log": "",
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},
"swm_rna_nickedhelix": {
"log": "",
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},
"swm_rna_protonated_adenosine": {
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},
"swm_rna_singleloop": {
"log": "",
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},
"swm_rna_srl_triplet": {
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},
"symm_disulfidize": {
"log": "",
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},
"symm_rotamer_boltzmann": {
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"symmetric_cycpep_align_and_symmetrize": {
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"symmetric_docking": {
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"symmetrical_residue_selector": {
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"symmetry_data_resource": {
"log": "",
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"symmetry_multicomponent": {
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},
"target_clash": {
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"task_selector": {
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"tcrmodel": {
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},
"template_features": {
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},
"tensorflow_connection_test": {
"log": "",
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},
"tensorflow_manager": {
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},
"tensorflow_simple_model_load_and_evaluate": {
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"test1_benchmark": {
"log": "",
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"test_computed_saxs_spectrum": {
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"test_d_l_readin": {
"log": "",
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},
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},
"test_rosetta_thread_manager_basic_API": {
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"thermal_sampler": {
"log": "",
"state": "passed"
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"thread_local_tracers_check": {
"log": "",
"state": "passed"
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"threefold_symm_peptide_design": {
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},
"threefoldlinkermover_tbmb": {
"log": "",
"state": "passed"
},
"threefoldlinkermover_tbmb_symmetric": {
"log": "",
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},
"tna_base_pairs": {
"log": "",
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},
"torsion_restricted_sampling": {
"log": "",
"state": "passed"
},
"trRosetta": {
"log": "",
"state": "passed"
},
"trRosettaConstraintGenerator": {
"log": "",
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},
"trRosettaConstraintGenerator_rosettascripts": {
"log": "",
"state": "passed"
},
"trRosettaProtocolMover": {
"log": "",
"state": "passed"
},
"trRosettaProtocolMover_rosettascripts": {
"log": "",
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},
"trRosettaProtocolMover_rosettascripts_diskwrite": {
"log": "",
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},
"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": {
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"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"
}
}
}