{
"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": "master",
"revision_id": 62040
},
"state": "failed",
"test_id": 806842
},
"summary": {
"failed": 6,
"failed_tests": [
"simple_cycpep_predict_square_pyramidal_metal",
"energy_based_clustering_alpha_aa_scorefile",
"glycan_tree_relax",
"ddG_of_mutation",
"dgdp_script",
"ligand_dock_ensemble"
],
"total": 790
},
"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_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"
},
"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"
},
"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_octahedral": {
"log": "",
"state": "passed"
},
"crosslinkermover_octahedral_s2_symm": {
"log": "",
"state": "passed"
},
"crosslinkermover_square_planar": {
"log": "",
"state": "passed"
},
"crosslinkermover_square_planar_d2_symm": {
"log": "",
"state": "passed"
},
"crosslinkermover_square_pyramidal": {
"log": "",
"state": "passed"
},
"crosslinkermover_tetrahedral_metal": {
"log": "",
"state": "passed"
},
"crosslinkermover_tetrahedral_metal_asp": {
"log": "",
"state": "passed"
},
"crosslinkermover_tetrahedral_metal_c2_symmetry": {
"log": "",
"state": "passed"
},
"crosslinkermover_tetrahedral_metal_d2_symmetry": {
"log": "",
"state": "passed"
},
"crosslinkermover_thioether": {
"log": "",
"state": "passed"
},
"crosslinkermover_tma": {
"log": "",
"state": "passed"
},
"crosslinkermover_tma_symm": {
"log": "",
"state": "passed"
},
"crosslinkermover_trigonal_planar": {
"log": "",
"state": "passed"
},
"crosslinkermover_trigonal_planar_c3_symm": {
"log": "",
"state": "passed"
},
"crosslinkermover_trigonal_pyramidal": {
"log": "",
"state": "passed"
},
"crosslinkermover_trigonal_pyramidal_c3_symm": {
"log": "",
"state": "passed"
},
"cs_rosetta_rna": {
"log": "",
"state": "passed"
},
"cst_info": {
"log": "",
"state": "passed"
},
"cstfile_to_theozyme_pdb": {
"log": "",
"state": "passed"
},
"custom_basetype_packer_palette": {
"log": "",
"state": "passed"
},
"cyclization": {
"log": "",
"state": "passed"
},
"cycpep_design_pipeline": {
"log": "",
"state": "passed"
},
"cycpep_rdkit_metric": {
"log": "",
"state": "passed"
},
"cycpep_rigid_body_permutation_mover": {
"log": "",
"state": "passed"
},
"cycpep_symmetry_filter": {
"log": "",
"state": "passed"
},
"d_workflow": {
"log": "",
"state": "passed"
},
"database_jd2_compact_io": {
"log": "",
"state": "passed"
},
"database_jd2_io": {
"log": "",
"state": "passed"
},
"database_md5": {
"log": "",
"state": "passed"
},
"database_session_resource": {
"log": "",
"state": "passed"
},
"ddG_ensemble": {
"log": "",
"state": "passed"
},
"ddG_of_mutation": {
"log": "Brief Diff:\nOnly in /home/benchmark/working_dir/master:62041/ddG_of_mutation: ddg_predictions.out\r\nFiles /home/benchmark/working_dir/master:62040/ddG_of_mutation/log and /home/benchmark/working_dir/master:62041/ddG_of_mutation/log differ\r\nFiles /home/benchmark/working_dir/master:62040/ddG_of_mutation/mut_V61G.out and /home/benchmark/working_dir/master:62041/ddG_of_mutation/mut_V61G.out differ\r\nOnly in /home/benchmark/working_dir/master:62040/ddG_of_mutation: .test_got_timeout_kill.log\r\n\n\nFull Diff:\nOnly in /home/benchmark/working_dir/master:62041/ddG_of_mutation: ddg_predictions.out\r\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/master:62040/ddG_of_mutation/log /home/benchmark/working_dir/master:62041/ddG_of_mutation/log\r\n55013c55013,55766\r\n< core.kinematics.AtomTree: atom1->raw_input_stub_atom1() \r\n---\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 51-11) == ( atom2 ~ 51-8 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 51-9) == ( atom3 ~ 51-6 ) = 0\r\n> core.scoring.elec.FA_ElecEnergy: Warning! Unable to find atompair N,H for ASN (ASN:NtermProteinFull)\r\n> core.scoring.elec.FA_ElecEnergy: Warning! Unable to find atompair N1H,1H1H for ARG (ARG)\r\n> core.scoring.elec.FA_ElecEnergy: Warning! Unable to find atompair N2H,1H2H for ARG (ARG)\r\n> core.scoring.NeighborList: Minimization stats: 198 score/deriv cals, 76 narrow-from-wide updates, 2 full updates.\r\n> core.scoring.NeighborList: Minimization stats: 298 score/deriv cals, 77 narrow-from-wide updates, 2 full updates.\r\n> core.scoring.NeighborList: Minimization stats: 298 score/deriv cals, 77 narrow-from-wide updates, 2 full updates.\r\n> core.optimize: AtomTreeMinimizer::run: nangles= 334 start_score: -259.367 start_func: -259.367 end_score: -273.705 end_func: -273.705\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: CNH2 2.72863 3.3683\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: COO 2.66463 3.31666\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: CH0 2.7821 3.41176\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: CH1 2.7821 3.41176\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: CH2 2.7821 3.41176\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: CH3 2.7821 3.41176\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: aroC 2.78784 3.41644\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ntrp 2.52105 3.20245\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Nhis 2.52105 3.20245\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: NtrR 2.52105 3.20245\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: NH2O 2.52105 3.20245\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Nlys 2.52105 3.20245\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Narg 2.52105 3.20245\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Npro 2.52105 3.20245\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: OH 2.18168 2.94274\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: OW 2.18168 2.94274\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: ONH2 2.18966 2.94866\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: OOC 2.11393 2.89287\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Oaro 2.19146 2.95\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Oet2 2.19146 2.95\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Oet3 2.19146 2.95\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: S 2.73809 3.37597\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: SH1 2.73809 3.37597\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Nbb 2.52105 3.20245\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: CAbb 2.7821 3.41176\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: CObb 2.66463 3.31666\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: OCbb 2.17876 2.94058\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Phos 2.95 3.55\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Pbb 2.95 3.55\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Hpol 1.18226 2.30168\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: HS 0 1.76389\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Hapo 2.01484 2.82127\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Haro 1.9494 2.77491\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: HNbb 1.18226 2.30168\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Hwat 1.36382 2.4\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Owat 2.19146 2.95\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Opoint 2.19146 2.95\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: HOH 1.98494 2.8\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Bsp2 2.74306 3.38\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: F 2.40252 3.11\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Cl 2.85323 3.47\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Br 3.03388 3.62\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: I 3.19962 3.76\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Zn2p 1.51661 2.49\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Co2p 2.21563 2.968\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Cu2p 1.52938 2.4978\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Fe2p 0.923255 2.18\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Fe3p 0.55 2.05\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Mg2p 1.668 2.585\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ca2p 1.93811 2.767\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Pha 2.95 3.55\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: OPha 2.38956 3.1\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: OHha 2.4797 3.17\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Hha 0 1.6245\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: CO3 2.38956 3.1\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: OC3 2.25832 3\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Si 2.58521 3.2532\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: OSi 2.48813 3.1766\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Oice 2.25832 3\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Hice 0.969536 2.2\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Na1p 1.93354 2.7638\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: K1p 2.47177 3.1638\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: He 1.66179 2.581\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Li 1.7301 2.6255\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Be 1.94596 2.7725\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ne 2.2868 3.0215\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Al 3.06901 3.6495\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ar 2.68618 3.334\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Sc 2.32105 3.0475\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ti 2.24169 2.9875\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: V 2.22099 2.972\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Cr 2.13935 2.9115\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Mn 2.09697 2.8805\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ni 2.00885 2.817\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ga 2.99981 3.5915\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ge 2.93796 3.54\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: As 2.90779 3.515\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Se 2.89266 3.5025\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Kr 2.85383 3.4705\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Rb 2.8374 3.457\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Sr 2.54394 3.2205\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Y 2.35377 3.0725\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Zr 2.20759 2.962\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Nb 2.23502 2.9825\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Mo 2.15905 2.926\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Tc 2.12231 2.899\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ru 2.09834 2.8815\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Rh 2.07494 2.8645\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Pd 2.05418 2.8495\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ag 2.22366 2.974\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Cd 2.01866 2.824\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: In 3.04759 3.6315\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Sn 3.0052 3.596\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Sb 3.02194 3.61\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Te 3.05176 3.635\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Xe 3.01238 3.602\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Cs 3.07971 3.6585\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ba 2.58307 3.2515\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: La 2.46818 3.161\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ce 2.48992 3.178\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Pr 2.52175 3.203\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Nd 2.50203 3.1875\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Pm 2.48417 3.1735\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Sm 2.4669 3.16\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Eu 2.44958 3.1465\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Gd 2.36877 3.084\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Tb 2.42255 3.1255\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Dy 2.4077 3.114\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ho 2.3954 3.1045\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Er 2.38372 3.0955\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Tm 2.37267 3.087\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Yb 2.3603 3.0775\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Lu 2.5433 3.22\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Hf 2.21898 2.9705\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ta 2.23835 2.985\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: W 2.17055 2.9345\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Re 2.09216 2.877\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Os 2.2049 2.96\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ir 2.01306 2.82\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Pt 1.95236 2.777\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Au 2.31973 3.0465\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Hg 1.91736 2.7525\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Tl 2.97824 3.5735\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Pb 2.94819 3.5485\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Bi 2.99203 3.585\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Po 3.19316 3.7545\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: At 3.21724 3.775\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Rn 3.22604 3.7825\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Fr 3.30492 3.85\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ra 2.56669 3.2385\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Ac 2.43994 3.139\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Th 2.38697 3.098\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Pa 2.40511 3.112\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: U 2.38632 3.0975\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Np 2.40511 3.112\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Pu 2.40511 3.112\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Am 2.37722 3.0905\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Cm 2.34136 3.063\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Bk 2.34986 3.0695\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Cf 2.33285 3.0565\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Es 2.32367 3.0495\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Fm 2.31513 3.043\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Md 2.30724 3.037\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: No 2.2901 3.024\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: Lr 2.28218 3.018\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: SUCK 0 1.4\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: REPL 2.12368 2.9\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: REPLS 2.19146 2.95\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: HREPS 1.36382 2.4\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: VIRT 0 1.4\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: MPct 0 1.4\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: MPnm 0 1.4\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: MPdp 0 1.4\r\n> core.scoring.methods.LK_BallEnergy: d2_low_high: MPtk 0 1.4\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: CNH2 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: COO 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: CH0 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: CH1 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: CH2 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: CH3 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: aroC 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ntrp 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Nhis 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: NtrR 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: NH2O 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Nlys 1\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Narg 1\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Npro 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: OH 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: OW 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: ONH2 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: OOC 1\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Oaro 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Oet2 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Oet3 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: S 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: SH1 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Nbb 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: CAbb 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: CObb 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: OCbb 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Phos 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Pbb 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Hpol 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: HS 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Hapo 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Haro 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: HNbb 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Hwat 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Owat 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Opoint 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: HOH 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Bsp2 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: F 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Cl 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Br 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: I 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Zn2p 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Co2p 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Cu2p 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Fe2p 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Fe3p 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Mg2p 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ca2p 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Pha 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: OPha 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: OHha 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Hha 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: CO3 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: OC3 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Si 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: OSi 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Oice 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Hice 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Na1p 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: K1p 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: He 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Li 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Be 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ne 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Al 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ar 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Sc 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ti 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: V 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Cr 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Mn 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ni 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ga 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ge 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: As 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Se 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Kr 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Rb 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Sr 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Y 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Zr 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Nb 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Mo 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Tc 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ru 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Rh 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Pd 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ag 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Cd 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: In 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Sn 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Sb 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Te 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Xe 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Cs 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ba 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: La 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ce 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Pr 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Nd 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Pm 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Sm 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Eu 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Gd 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Tb 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Dy 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ho 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Er 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Tm 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Yb 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Lu 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Hf 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ta 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: W 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Re 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Os 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ir 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Pt 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Au 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Hg 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Tl 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Pb 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Bi 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Po 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: At 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Rn 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Fr 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ra 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Ac 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Th 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Pa 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: U 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Np 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Pu 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Am 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Cm 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Bk 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Cf 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Es 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Fm 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Md 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: No 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: Lr 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: SUCK 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: REPL 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: REPLS 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: HREPS 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: VIRT 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: MPct 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: MPnm 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: MPdp 0\r\n> core.scoring.methods.LK_BallEnergy: atom_type_is_charged_: MPtk 0\r\n> core.optimization.AtomTreeMinimizer: start_score:-250.179\r\n> core.optimization.AtomTreeMinimizer: E fa_atr fa_rep fa_sol fa_intra_repfa_intra_sol_x lk_ball_wtd fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13atom_pair_cons omega fa_dun p_aa_pp yhh_planarity ref rama_prepro\r\n> core.optimization.AtomTreeMinimizer: E(i) 1 -0.81 0.22 0.57 0.99 0.33 -0.15 -0.19 0.00 0.00 0.00 0.00 0.00 0.00 0.03 0.01 4.97 0.00 0.00 -1.34 0.00\r\n> core.optimization.AtomTreeMinimizer: E(i) 2 -4.79 2.85 0.90 2.64 0.07 -0.31 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.19 0.47 0.35 -0.22 0.00 1.66 0.48\r\n> core.optimization.AtomTreeMinimizer: E(i) 3 -7.45 2.18 7.38 2.05 0.30 -0.89 -4.40 0.00 0.00 0.00 0.00 -0.43 0.00 0.17 0.00 1.51 0.44 0.00 -0.71 0.67\r\n> core.optimization.AtomTreeMinimizer: E(i) 4 -6.39 4.59 2.62 1.51 0.08 -0.27 -1.09 0.00 0.00 0.00 0.00 0.00 0.00 0.35 -0.06 0.02 -0.99 0.00 1.15 -0.12\r\n> core.optimization.AtomTreeMinimizer: E(i) 5 -6.40 1.49 3.95 2.10 0.56 -0.42 -0.89 0.00 0.00 0.00 0.00 0.00 0.00 0.03 0.16 4.21 -0.15 0.00 -2.72 -0.24\r\n> core.optimization.AtomTreeMinimizer: E(i) 6 -19.00 14.92 5.53 4.06 0.59 -0.74 -2.23 0.00 0.00 0.00 0.00 -0.80 0.00 0.39 0.72 2.43 0.01 0.00 2.26 0.51\r\n> core.optimization.AtomTreeMinimizer: E(i) 7 -4.97 2.48 2.43 0.53 0.04 -0.38 -0.08 0.01 0.00 0.00 0.00 0.00 0.00 0.13 -0.16 0.96 -0.46 0.00 -1.64 0.02\r\n> core.optimization.AtomTreeMinimizer: E(i) 8 -5.39 0.93 5.02 1.84 0.52 -0.64 -1.72 0.00 0.00 0.00 0.00 0.00 0.00 0.06 0.02 5.22 -0.31 0.00 -2.72 -0.88\r\n> core.optimization.AtomTreeMinimizer: E(i) 9 -12.71 9.02 2.57 3.96 0.12 -0.41 -1.39 0.00 0.00 0.00 0.00 0.00 0.00 0.44 0.31 0.20 -0.30 0.00 1.66 -0.91\r\n> core.optimization.AtomTreeMinimizer: E(i) 10 -6.73 1.04 1.95 2.33 0.04 -0.46 -0.09 0.00 0.00 0.00 0.00 0.00 0.00 0.11 -0.06 0.04 -0.51 0.00 2.64 -0.88\r\n> core.optimization.AtomTreeMinimizer: E(i) 11 -3.06 0.15 2.57 0.03 0.00 -0.13 -0.89 0.00 0.00 0.00 0.00 0.00 0.00 0.05 -0.33 0.00 -2.49 0.00 0.80 -1.24\r\n> core.optimization.AtomTreeMinimizer: E(i) 12 -8.76 2.28 7.77 1.44 0.25 -0.68 -3.33 0.00 0.00 0.00 0.00 0.00 0.00 0.15 -0.02 1.29 -0.07 0.00 -0.71 -0.91\r\n> core.optimization.AtomTreeMinimizer: E(i) 13 -6.73 1.89 6.67 0.32 0.07 -0.01 -3.55 0.00 0.00 0.00 -1.69 0.00 0.00 0.17 -0.02 0.23 -0.46 0.00 -0.29 -0.77\r\n> core.optimization.AtomTreeMinimizer: E(i) 14 -9.22 8.88 2.13 2.71 0.05 -0.30 -1.09 0.00 0.00 0.00 0.00 0.00 0.00 0.48 -0.06 -0.01 -0.37 0.00 2.64 -0.86\r\n> core.optimization.AtomTreeMinimizer: E(i) 15 -5.43 0.33 6.28 0.67 0.67 -0.39 -3.15 0.00 0.00 0.00 0.00 -0.64 0.00 0.12 0.59 5.37 -0.37 0.00 -2.72 -0.67\r\n> core.optimization.AtomTreeMinimizer: E(i) 16 -7.16 2.58 7.50 0.78 0.33 -0.22 -3.14 0.00 0.00 0.00 -1.69 0.00 0.00 0.13 0.31 5.21 -0.17 0.00 -2.72 -0.59\r\n> core.optimization.AtomTreeMinimizer: E(i) 17 -8.57 3.76 2.67 0.33 0.00 -0.24 -1.91 0.00 0.00 0.00 0.00 0.00 0.00 0.43 -0.11 0.00 -0.45 0.00 1.32 -0.62\r\n> core.optimization.AtomTreeMinimizer: E(i) 18 -9.58 4.67 7.36 1.47 0.25 -0.15 -4.34 0.00 0.00 0.00 0.00 -0.64 0.00 0.16 0.32 1.88 0.08 0.00 -0.71 -0.68\r\n> core.optimization.AtomTreeMinimizer: E(i) 19 -5.96 1.16 5.55 6.11 0.86 -0.55 -1.67 0.00 0.00 0.00 0.00 0.00 0.00 0.15 0.03 5.75 0.11 0.00 -0.71 -0.11\r\n> core.optimization.AtomTreeMinimizer: E(i) 20 -8.44 2.70 4.47 2.47 0.05 -0.69 -1.06 0.00 0.00 0.00 0.00 0.00 0.00 0.38 -0.08 0.00 -0.59 0.00 2.64 0.19\r\n> core.optimization.AtomTreeMinimizer: E(i) 21 -14.07 5.34 2.15 5.53 0.09 -0.55 -1.82 0.00 0.00 0.00 0.00 0.00 0.00 0.21 -0.08 0.15 -0.64 0.00 2.30 0.13\r\n> core.optimization.AtomTreeMinimizer: E(i) 22 -9.24 1.24 3.99 2.90 0.09 -0.30 -0.99 0.00 0.00 0.00 0.00 0.00 0.00 0.30 0.32 0.13 -0.47 0.00 1.66 -0.35\r\n> core.optimization.AtomTreeMinimizer: E(i) 23 -5.09 2.49 4.65 1.27 0.31 -0.39 -0.59 0.00 0.00 0.00 0.00 0.00 0.00 0.06 0.18 3.86 0.31 0.00 -1.45 -0.16\r\n> core.optimization.AtomTreeMinimizer: E(i) 24 -6.32 1.31 7.19 0.94 0.32 -0.37 -3.98 0.00 0.00 0.00 0.00 -1.23 0.00 0.08 0.09 2.92 -0.45 0.00 -2.15 -0.11\r\n> core.optimization.AtomTreeMinimizer: E(i) 25 -12.90 4.91 11.24 2.05 0.53 -0.54 -5.34 0.00 0.00 0.00 -0.26 -0.80 0.00 0.14 0.16 3.17 0.26 0.00 -0.71 -0.19\r\n> core.optimization.AtomTreeMinimizer: E(i) 26 -4.77 2.05 2.48 0.45 0.04 -0.31 0.10 0.09 0.00 0.00 0.00 0.00 0.00 0.13 0.08 0.29 -0.95 0.00 -1.64 0.14\r\n> core.optimization.AtomTreeMinimizer: E(i) 27 -5.77 0.92 6.33 2.20 1.18 -0.28 -2.81 0.00 0.00 0.00 -0.45 -0.80 0.00 0.03 0.87 5.00 -0.18 0.00 -2.72 -0.57\r\n> core.optimization.AtomTreeMinimizer: E(i) 28 -7.13 5.30 2.03 0.22 0.00 -0.52 -0.84 0.00 0.00 0.00 0.00 0.00 0.00 0.17 0.08 0.00 0.04 0.00 1.32 -1.42\r\n> core.optimization.AtomTreeMinimizer: E(i) 29 -6.22 0.31 5.60 1.31 0.66 -0.12 -2.81 0.00 0.00 0.00 -0.45 0.00 0.00 0.03 0.13 3.61 0.16 0.00 -1.45 -0.18\r\n> core.optimization.AtomTreeMinimizer: E(i) 30 -9.06 3.50 -0.29 4.05 0.08 -0.37 -0.44 0.00 0.00 0.00 0.00 0.00 0.00 0.33 -0.13 0.43 -0.86 0.00 2.30 0.14\r\n> core.optimization.AtomTreeMinimizer: E(i) 31 -7.73 2.17 3.60 2.97 0.09 -0.16 -2.10 0.00 0.00 0.00 0.00 0.00 0.00 0.07 0.00 1.58 -1.28 0.00 2.30 -1.01\r\n> core.optimization.AtomTreeMinimizer: E(i) 32 -6.39 1.31 -0.48 2.73 0.05 -0.21 -0.20 0.00 0.00 0.00 0.00 0.00 0.00 0.50 -0.12 0.01 -0.96 0.00 2.64 -0.82\r\n> core.optimization.AtomTreeMinimizer: E(i) 33 -9.81 9.63 2.55 2.42 0.07 -0.02 -2.02 0.00 0.00 0.00 0.00 0.00 0.00 0.29 0.29 0.25 0.23 0.00 1.66 -0.42\r\n> core.optimization.AtomTreeMinimizer: E(i) 34 -5.48 2.36 2.89 0.66 0.09 -0.03 -2.58 0.15 0.00 0.00 0.00 0.00 0.00 0.27 -0.15 0.86 -1.39 0.00 -1.64 -0.82\r\n> core.optimization.AtomTreeMinimizer: E(i) 35 -5.54 3.45 1.74 2.52 0.04 -0.40 -0.52 0.00 0.00 0.00 0.00 0.00 0.00 0.15 -0.03 0.19 -0.21 0.00 2.64 -1.35\r\n> core.optimization.AtomTreeMinimizer: E(i) 36 -1.70 0.18 1.39 0.02 0.00 -0.07 -0.16 0.00 0.00 0.00 0.00 0.00 0.00 0.12 -0.31 0.00 -2.51 0.00 0.80 -1.12\r\n> core.optimization.AtomTreeMinimizer: E(i) 37 -5.78 1.25 2.67 0.54 0.04 -0.32 -1.51 0.00 0.00 0.00 0.00 0.00 0.00 0.33 0.75 0.12 0.09 0.00 1.15 -0.93\r\n> core.optimization.AtomTreeMinimizer: E(i) 38 -2.61 0.19 0.97 3.18 0.07 -0.25 -0.04 0.00 0.00 0.00 0.00 0.00 0.00 0.02 -0.15 0.40 -0.86 0.00 2.30 -0.94\r\n> core.optimization.AtomTreeMinimizer: E(i) 39 -5.46 1.61 0.72 2.28 0.04 -0.58 0.02 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.02 0.02 -0.70 0.00 2.64 -0.73\r\n> core.optimization.AtomTreeMinimizer: E(i) 40 -3.37 0.32 2.51 0.87 0.05 -0.54 -0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.16 -0.08 0.10 0.10 0.00 1.15 -0.55\r\n> core.optimization.AtomTreeMinimizer: E(i) 41 -1.65 0.08 1.07 5.74 0.20 -0.11 0.22 0.00 0.00 0.00 0.00 0.00 0.00 0.89 -0.05 2.92 0.18 0.00 1.66 1.30\r\n> core.optimization.AtomTreeMinimizer: E(i) 42 -4.76 0.40 4.96 1.43 0.54 -0.09 -2.04 0.00 0.00 0.00 0.00 -0.83 0.00 0.18 0.15 3.84 0.00 0.00 -2.72 1.69\r\n> core.optimization.AtomTreeMinimizer: E(i) 43 -6.44 0.98 3.03 4.78 0.35 -0.42 -0.49 0.00 0.00 0.00 0.00 0.00 0.00 0.97 0.60 2.87 -0.02 0.01 0.58 0.07\r\n> core.optimization.AtomTreeMinimizer: E(i) 44 -8.37 0.52 8.15 4.29 0.63 -0.56 -3.10 0.00 0.00 0.00 0.00 -0.98 0.00 0.18 -0.10 6.02 0.06 0.00 -0.09 0.61\r\n> core.optimization.AtomTreeMinimizer: E(i) 45 -5.92 1.07 3.55 2.79 0.12 0.04 -1.53 0.00 0.00 0.00 -0.26 0.00 0.00 0.11 -0.07 1.04 0.58 0.00 2.30 0.39\r\n> core.optimization.AtomTreeMinimizer: E(i) 46 -6.91 3.23 7.52 0.81 0.59 -0.19 -3.82 0.00 0.00 0.00 0.00 -0.98 0.00 0.07 0.44 4.66 -0.36 0.00 -2.15 -0.59\r\n> core.optimization.AtomTreeMinimizer: E(i) 47 -13.30 1.12 12.93 2.45 0.65 -0.60 -4.75 0.00 0.00 0.00 0.00 -0.83 0.00 0.13 0.29 3.62 0.00 0.00 -0.09 -0.49\r\n> core.optimization.AtomTreeMinimizer: E(i) 48 -11.23 5.36 1.62 2.55 0.05 -0.34 -2.09 0.00 0.00 0.00 0.00 0.00 0.00 0.43 0.05 0.05 -1.03 0.00 2.64 -0.36\r\n> core.optimization.AtomTreeMinimizer: E(i) 49 -11.70 3.92 7.04 2.90 0.52 -1.13 -0.80 0.00 0.00 0.00 0.00 0.00 0.00 0.36 0.62 2.97 -0.04 0.00 -0.09 -0.40\r\n> core.optimization.AtomTreeMinimizer: E(i) 50 -11.65 3.68 0.68 4.11 0.08 0.07 -1.76 0.00 0.00 0.00 0.00 0.00 0.00 0.61 -0.09 1.19 -0.38 0.00 1.66 0.02\r\n> core.optimization.AtomTreeMinimizer: E(i) 51 -12.70 6.52 3.99 3.70 0.23 -0.74 -2.22 0.00 0.00 0.00 0.00 0.00 0.00 0.35 0.70 2.62 -0.30 0.00 1.22 0.20\r\n> core.optimization.AtomTreeMinimizer: E(i) 52 -10.64 6.86 2.48 1.79 0.04 -0.35 -2.38 0.00 0.00 0.00 0.00 0.00 0.00 0.39 -0.02 -0.01 -0.46 0.00 2.64 -0.13\r\n> core.optimization.AtomTreeMinimizer: E(i) 53 -6.68 0.62 8.22 1.62 0.73 -0.15 -4.43 0.00 0.00 0.00 -1.01 0.00 0.00 0.06 -0.09 1.74 -0.89 0.00 -2.15 -0.35\r\n> core.optimization.AtomTreeMinimizer: E(i) 54 -2.43 0.14 2.01 2.58 0.39 -0.18 0.59 0.00 0.00 0.00 0.00 0.00 0.00 0.02 -0.24 3.21 -0.04 0.00 -0.71 -0.71\r\n> core.optimization.AtomTreeMinimizer: E(i) 55 -4.24 0.82 3.93 3.07 0.11 -0.56 -1.26 0.00 0.00 0.00 -0.41 0.00 0.00 0.07 -0.04 0.07 0.01 0.00 1.66 -0.91\r\n> core.optimization.AtomTreeMinimizer: E(i) 56 -5.62 1.92 4.57 2.36 0.37 -0.54 -1.86 0.00 0.00 0.00 0.00 0.00 0.00 0.13 0.04 2.99 -0.64 0.00 -2.15 -0.52\r\n> core.optimization.AtomTreeMinimizer: E(i) 57 -8.68 2.02 7.54 1.45 0.29 -0.70 -2.86 0.00 0.00 0.00 -0.60 0.00 0.00 0.11 0.01 1.98 0.13 0.00 -1.34 0.01\r\n> core.optimization.AtomTreeMinimizer: E(i) 58 -13.34 5.79 2.71 3.35 0.11 -0.43 -2.30 0.00 0.00 0.00 0.00 0.00 0.00 0.19 -0.18 4.97 -0.68 0.00 2.30 -0.26\r\n> core.optimization.AtomTreeMinimizer: E(i) 59 -4.77 2.12 1.49 0.29 0.00 -0.13 -0.97 0.00 0.00 0.00 0.00 0.00 0.00 0.14 -0.08 0.00 0.48 0.00 1.32 -0.26\r\n> core.optimization.AtomTreeMinimizer: E(i) 60 -6.39 3.45 4.27 1.66 0.55 -0.61 -0.37 0.00 0.00 0.00 0.00 0.00 0.00 0.15 0.95 4.54 -0.01 0.00 -2.72 0.16\r\n> core.optimization.AtomTreeMinimizer: E(i) 61 -3.09 1.32 1.69 0.01 0.00 -0.26 0.16 0.00 0.00 0.00 0.00 0.00 0.00 0.14 0.28 0.00 1.95 0.00 0.80 2.95\r\n> core.optimization.AtomTreeMinimizer: E(i) 62 -9.80 8.73 2.97 0.63 0.08 -0.01 -1.60 0.02 0.00 0.00 0.00 0.00 0.00 0.20 -0.09 0.31 -1.75 0.00 -1.64 2.08\r\n> core.optimization.AtomTreeMinimizer: E(i) 63 -5.91 1.28 3.75 2.88 0.51 -0.32 -1.09 0.00 0.00 0.00 0.00 0.00 0.00 0.19 -0.02 2.10 -0.16 0.00 -0.09 -0.93\r\n> core.optimization.AtomTreeMinimizer: E(i) 64 -9.51 2.69 1.45 3.38 0.04 -0.36 -1.82 0.00 0.00 0.00 0.00 0.00 0.00 0.26 -0.10 0.04 -0.74 0.00 2.64 -0.58\r\n> core.optimization.AtomTreeMinimizer: E(i) 65 -5.66 0.76 7.14 0.04 0.00 -0.02 -4.27 0.00 0.00 0.00 0.00 0.00 0.00 0.17 0.00 0.00 0.00 0.00 0.80 -0.49\r\n> core.optimization.AtomTreeMinimizer: total_energy fa_atr -473.356\r\n> core.optimization.AtomTreeMinimizer: total_energy fa_rep 183.347\r\n> core.optimization.AtomTreeMinimizer: total_energy fa_sol 258.612\r\n> core.optimization.AtomTreeMinimizer: total_energy fa_intra_rep 138.133\r\n> core.optimization.AtomTreeMinimizer: total_energyfa_intra_sol_x 16.172\r\n> core.optimization.AtomTreeMinimizer: total_energy lk_ball_wtd -23.045\r\n> core.optimization.AtomTreeMinimizer: total_energy fa_elec -112.210\r\n> core.optimization.AtomTreeMinimizer: total_energy pro_close 0.273\r\n> core.optimization.AtomTreeMinimizer: total_energy hbond_sr_bb -16.499\r\n> core.optimization.AtomTreeMinimizer: total_energy hbond_lr_bb -15.909\r\n> core.optimization.AtomTreeMinimizer: total_energy hbond_bb_sc -6.837\r\n> core.optimization.AtomTreeMinimizer: total_energy hbond_sc -8.931\r\n> core.optimization.AtomTreeMinimizer: total_energy dslf_fa13 0.000\r\n> core.optimization.AtomTreeMinimizer: total_energyatom_pair_cons 14.018\r\n> core.optimization.AtomTreeMinimizer: total_energy omega 6.951\r\n> core.optimization.AtomTreeMinimizer: total_energy fa_dun 116.510\r\n> core.optimization.AtomTreeMinimizer: total_energy p_aa_pp -21.618\r\n> core.optimization.AtomTreeMinimizer: total_energy yhh_planarity 0.013\r\n> core.optimization.AtomTreeMinimizer: total_energy ref 19.150\r\n> core.optimization.AtomTreeMinimizer: total_energy rama_prepro -16.356\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 6-7, 6-9, 6-10, 6-8!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 6-11) == ( atom3 ~ 6-10 ) = 0\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 6-13) == ( atom2 ~ 6-9 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 6-6) == ( atom2 ~ 6-9 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 6-5) == ( atom3 ~ 6-10 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 6-9, 6-10, 6-8, 6-6!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 6-5) == ( atom3 ~ 6-8 ) = 0\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 6-2) == ( atom2 ~ 6-10 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 6-7) == ( atom2 ~ 6-10 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 6-6) == ( atom3 ~ 6-8 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 6-10, 6-8, 6-6, 6-7!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 6-6) == ( atom3 ~ 6-6 ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 6-5) == ( atom2 ~ 6-8 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 6-9) == ( atom2 ~ 6-8 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 6-7) == ( atom3 ~ 6-6 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 6-12, 6-10, 6-8, 6-11!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 6-13) == ( atom3 ~ 6-8 ) = 0\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 6-14) == ( atom2 ~ 6-10 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 6-10) == ( atom2 ~ 6-10 ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 6-9) == ( atom3 ~ 6-8 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 6-10, 6-8, 6-11, 6-13!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 6-14) == ( atom3 ~ 6-11 ) = 0\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 6-12) == ( atom2 ~ 6-8 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 6-9) == ( atom2 ~ 6-8 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 6-7) == ( atom3 ~ 6-11 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 43-6, 43-7, 43-9, 43-11!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 43-10) == ( atom3 ~ 43-9 ) = 0\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 43-8) == ( atom2 ~ 43-7 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 43-5) == ( atom2 ~ 43-7 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 43-2) == ( atom3 ~ 43-9 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 43-7, 43-9, 43-11, 43-10!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 43-8) == ( atom3 ~ 43-11 ) = 0\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 43-6) == ( atom2 ~ 43-9 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 43-6) == ( atom2 ~ 43-9 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 43-5) == ( atom3 ~ 43-11 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 43-9, 43-11, 43-10, 43-8!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 43-6) == ( atom3 ~ 43-10 ) = 0\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 43-5) == ( atom2 ~ 43-11 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 43-7) == ( atom2 ~ 43-11 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 43-6) == ( atom3 ~ 43-10 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 51-11, 51-10, 51-8, 51-6!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 51-5) == ( atom3 ~ 51-8 ) = 0\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 51-2) == ( atom2 ~ 51-10 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 51-9) == ( atom2 ~ 51-10 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 51-7) == ( atom3 ~ 51-8 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 51-10, 51-8, 51-6, 51-7!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 51-6) == ( atom3 ~ 51-6 ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 51-5) == ( atom2 ~ 51-8 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 51-11) == ( atom2 ~ 51-8 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 51-9) == ( atom3 ~ 51-6 ) = 0\r\n> core.scoring.elec.FA_ElecEnergy: Warning! Unable to find atompair N,H for ASN (ASN:NtermProteinFull)\r\n> core.scoring.elec.FA_ElecEnergy: Warning! Unable to find atompair N1H,1H1H for ARG (ARG)\r\n> core.scoring.elec.FA_ElecEnergy: Warning! Unable to find atompair N2H,1H2H for ARG (ARG)\r\n> core.scoring.NeighborList: Minimization stats: 159 score/deriv cals, 32 narrow-from-wide updates, 1 full updates.\r\n> core.scoring.NeighborList: Minimization stats: 241 score/deriv cals, 32 narrow-from-wide updates, 1 full updates.\r\n> core.scoring.NeighborList: Minimization stats: 241 score/deriv cals, 32 narrow-from-wide updates, 1 full updates.\r\n> core.optimize: AtomTreeMinimizer::run: nangles= 334 start_score: -250.179 start_func: -250.179 end_score: -256.080 end_func: -256.080\r\n> core.optimization.AtomTreeMinimizer: start_score:-215.387\r\n> core.optimization.AtomTreeMinimizer: E fa_atr fa_rep fa_sol fa_intra_repfa_intra_sol_x lk_ball_wtd fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13atom_pair_cons omega fa_dun p_aa_pp yhh_planarity ref rama_prepro\r\n> core.optimization.AtomTreeMinimizer: E(i) 1 -0.81 0.22 0.57 0.99 0.33 -0.15 -0.19 0.00 0.00 0.00 0.00 0.00 0.00 0.03 0.02 4.97 0.00 0.00 -1.34 0.00\r\n> core.optimization.AtomTreeMinimizer: E(i) 2 -4.77 1.40 0.95 2.62 0.07 -0.29 0.01 0.00 0.00 0.00 0.00 0.00 0.00 0.19 0.20 0.34 -0.19 0.00 1.66 0.50\r\n> core.optimization.AtomTreeMinimizer: E(i) 3 -7.23 1.22 7.00 2.00 0.29 -0.82 -4.10 0.00 0.00 0.00 0.00 -0.48 0.00 0.16 0.16 1.48 0.44 0.00 -0.71 0.70\r\n> core.optimization.AtomTreeMinimizer: E(i) 4 -6.31 2.72 2.64 1.47 0.07 -0.27 -1.09 0.00 0.00 0.00 0.00 0.00 0.00 0.30 -0.09 0.03 -1.00 0.00 1.15 -0.12\r\n> core.optimization.AtomTreeMinimizer: E(i) 5 -6.31 1.20 3.87 2.05 0.56 -0.42 -0.83 0.00 0.00 0.00 0.00 0.00 0.00 0.03 0.28 4.17 -0.15 0.00 -2.72 -0.22\r\n> core.optimization.AtomTreeMinimizer: E(i) 6 -18.30 7.97 5.48 4.09 0.60 -0.69 -2.17 0.00 0.00 0.00 0.00 -0.78 0.00 0.24 0.50 2.45 0.02 0.00 2.26 0.56\r\n> core.optimization.AtomTreeMinimizer: E(i) 7 -4.88 2.25 2.39 0.53 0.04 -0.37 -0.09 0.02 0.00 0.00 0.00 0.00 0.00 0.11 -0.25 1.02 -0.53 0.00 -1.64 0.04\r\n> core.optimization.AtomTreeMinimizer: E(i) 8 -5.25 0.62 4.74 1.82 0.52 -0.63 -1.43 0.00 0.00 0.00 0.00 0.00 0.00 0.03 0.06 5.30 -0.32 0.00 -2.72 -0.94\r\n> core.optimization.AtomTreeMinimizer: E(i) 9 -12.20 4.93 2.57 4.11 0.12 -0.40 -1.35 0.00 0.00 0.00 0.00 0.00 0.00 0.37 0.14 0.29 -0.29 0.00 1.66 -1.00\r\n> core.optimization.AtomTreeMinimizer: E(i) 10 -6.65 0.88 1.94 2.34 0.04 -0.47 -0.11 0.00 0.00 0.00 0.00 0.00 0.00 0.07 -0.13 0.04 -0.50 0.00 2.64 -0.93\r\n> core.optimization.AtomTreeMinimizer: E(i) 11 -3.04 0.15 2.56 0.03 0.00 -0.13 -0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.05 -0.34 0.00 -2.49 0.00 0.80 -1.23\r\n> core.optimization.AtomTreeMinimizer: E(i) 12 -8.48 1.29 7.57 1.42 0.25 -0.64 -3.18 0.00 0.00 0.00 0.00 0.00 0.00 0.15 -0.03 1.28 -0.08 0.00 -0.71 -0.87\r\n> core.optimization.AtomTreeMinimizer: E(i) 13 -6.63 0.92 6.58 0.32 0.07 -0.01 -3.46 0.00 0.00 0.00 -1.69 0.00 0.00 0.14 -0.02 0.20 -0.51 0.00 -0.29 -0.75\r\n> core.optimization.AtomTreeMinimizer: E(i) 14 -8.95 4.36 2.05 2.78 0.05 -0.30 -1.07 0.00 0.00 0.00 0.00 0.00 0.00 0.29 0.05 0.00 -0.37 0.00 2.64 -0.84\r\n> core.optimization.AtomTreeMinimizer: E(i) 15 -5.41 0.36 6.24 0.66 0.66 -0.37 -3.14 0.00 0.00 0.00 0.00 -0.66 0.00 0.12 0.58 5.29 -0.37 0.00 -2.72 -0.65\r\n> core.optimization.AtomTreeMinimizer: E(i) 16 -7.11 1.29 7.44 0.80 0.33 -0.27 -3.05 0.00 0.00 0.00 -1.69 0.00 0.00 0.15 0.39 5.24 -0.20 0.00 -2.72 -0.65\r\n> core.optimization.AtomTreeMinimizer: E(i) 17 -8.37 1.88 2.66 0.33 0.00 -0.23 -1.88 0.00 0.00 0.00 0.00 0.00 0.00 0.32 -0.09 0.00 -0.44 0.00 1.32 -0.66\r\n> core.optimization.AtomTreeMinimizer: E(i) 18 -9.31 2.47 7.30 1.48 0.24 -0.11 -4.38 0.00 0.00 0.00 0.00 -0.66 0.00 0.14 0.11 2.10 0.10 0.00 -0.71 -0.46\r\n> core.optimization.AtomTreeMinimizer: E(i) 19 -5.85 0.79 5.47 6.42 0.87 -0.56 -1.66 0.00 0.00 0.00 0.00 0.00 0.00 0.14 0.01 5.69 0.09 0.00 -0.71 0.10\r\n> core.optimization.AtomTreeMinimizer: E(i) 20 -8.28 1.57 4.35 2.48 0.05 -0.67 -1.03 0.00 0.00 0.00 0.00 0.00 0.00 0.31 -0.08 0.00 -0.60 0.00 2.64 0.17\r\n> core.optimization.AtomTreeMinimizer: E(i) 21 -13.63 2.91 2.22 5.48 0.09 -0.52 -1.76 0.00 0.00 0.00 0.00 0.00 0.00 0.15 -0.06 0.19 -0.65 0.00 2.30 0.10\r\n> core.optimization.AtomTreeMinimizer: E(i) 22 -9.05 1.00 3.99 2.87 0.09 -0.31 -1.01 0.00 0.00 0.00 0.00 0.00 0.00 0.22 0.18 0.15 -0.50 0.00 1.66 -0.37\r\n> core.optimization.AtomTreeMinimizer: E(i) 23 -4.96 1.42 4.57 1.26 0.31 -0.38 -0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.04 0.16 3.84 0.33 0.00 -1.45 -0.13\r\n> core.optimization.AtomTreeMinimizer: E(i) 24 -6.30 0.96 7.14 0.96 0.32 -0.34 -3.97 0.00 0.00 0.00 0.00 -1.26 0.00 0.07 0.03 2.81 -0.42 0.00 -2.15 -0.07\r\n> core.optimization.AtomTreeMinimizer: E(i) 25 -12.61 3.17 11.02 2.01 0.53 -0.46 -5.20 0.00 0.00 0.00 -0.24 -0.79 0.00 0.11 0.13 3.18 0.26 0.00 -0.71 -0.14\r\n> core.optimization.AtomTreeMinimizer: E(i) 26 -4.70 1.66 2.47 0.45 0.04 -0.32 0.12 0.11 0.00 0.00 0.00 0.00 0.00 0.09 -0.13 0.27 -0.92 0.00 -1.64 0.19\r\n> core.optimization.AtomTreeMinimizer: E(i) 27 -5.72 0.68 6.28 2.18 1.17 -0.26 -2.76 0.00 0.00 0.00 -0.46 -0.79 0.00 0.03 0.64 5.10 -0.17 0.00 -2.72 -0.57\r\n> core.optimization.AtomTreeMinimizer: E(i) 28 -6.98 2.59 1.97 0.22 0.00 -0.52 -0.79 0.00 0.00 0.00 0.00 0.00 0.00 0.19 0.12 0.00 0.07 0.00 1.32 -1.36\r\n> core.optimization.AtomTreeMinimizer: E(i) 29 -6.22 0.26 5.59 1.31 0.66 -0.12 -2.83 0.00 0.00 0.00 -0.46 0.00 0.00 0.03 0.23 3.58 0.16 0.00 -1.45 -0.12\r\n> core.optimization.AtomTreeMinimizer: E(i) 30 -8.77 2.16 -0.31 4.08 0.08 -0.38 -0.40 0.00 0.00 0.00 0.00 0.00 0.00 0.15 -0.12 0.44 -0.85 0.00 2.30 0.16\r\n> core.optimization.AtomTreeMinimizer: E(i) 31 -7.58 1.38 3.51 2.97 0.09 -0.16 -2.02 0.00 0.00 0.00 0.00 0.00 0.00 0.09 0.05 1.52 -1.29 0.00 2.30 -1.01\r\n> core.optimization.AtomTreeMinimizer: E(i) 32 -6.27 0.94 -0.54 2.74 0.05 -0.22 -0.20 0.00 0.00 0.00 0.00 0.00 0.00 0.32 -0.10 0.02 -1.00 0.00 2.64 -0.83\r\n> core.optimization.AtomTreeMinimizer: E(i) 33 -9.40 5.45 2.57 2.44 0.07 -0.01 -2.04 0.01 0.00 0.00 0.00 0.00 0.00 0.22 0.40 0.27 0.27 0.00 1.66 -0.39\r\n> core.optimization.AtomTreeMinimizer: E(i) 34 -5.38 2.07 2.85 0.66 0.09 -0.02 -2.54 0.20 0.00 0.00 0.00 0.00 0.00 0.21 -0.10 0.79 -1.44 0.00 -1.64 -0.85\r\n> core.optimization.AtomTreeMinimizer: E(i) 35 -5.48 2.23 1.73 2.54 0.04 -0.41 -0.49 0.00 0.00 0.00 0.00 0.00 0.00 0.16 -0.12 0.20 -0.18 0.00 2.64 -1.38\r\n> core.optimization.AtomTreeMinimizer: E(i) 36 -1.70 0.19 1.39 0.02 0.00 -0.07 -0.14 0.00 0.00 0.00 0.00 0.00 0.00 0.12 -0.32 0.00 -2.51 0.00 0.80 -1.10\r\n> core.optimization.AtomTreeMinimizer: E(i) 37 -5.64 0.78 2.65 0.53 0.04 -0.32 -1.50 0.00 0.00 0.00 0.00 0.00 0.00 0.24 0.56 0.11 0.08 0.00 1.15 -0.92\r\n> core.optimization.AtomTreeMinimizer: E(i) 38 -2.58 0.19 0.97 3.18 0.07 -0.25 -0.04 0.00 0.00 0.00 0.00 0.00 0.00 0.02 -0.15 0.39 -0.85 0.00 2.30 -0.96\r\n> core.optimization.AtomTreeMinimizer: E(i) 39 -5.29 0.72 0.74 2.29 0.04 -0.57 0.02 0.00 0.00 0.00 0.00 0.00 0.00 0.05 -0.01 0.03 -0.69 0.00 2.64 -0.78\r\n> core.optimization.AtomTreeMinimizer: E(i) 40 -3.32 0.27 2.46 0.86 0.05 -0.53 -0.56 0.00 0.00 0.00 0.00 0.00 0.00 0.17 -0.06 0.11 0.11 0.00 1.15 -0.61\r\n> core.optimization.AtomTreeMinimizer: E(i) 41 -1.65 0.08 1.06 5.68 0.19 -0.11 0.21 0.00 0.00 0.00 0.00 0.00 0.00 0.86 -0.05 2.91 0.17 0.00 1.66 1.24\r\n> core.optimization.AtomTreeMinimizer: E(i) 42 -4.73 0.34 4.94 1.45 0.54 -0.09 -2.04 0.00 0.00 0.00 0.00 -0.83 0.00 0.19 0.08 3.94 -0.03 0.00 -2.72 1.64\r\n> core.optimization.AtomTreeMinimizer: E(i) 43 -6.29 0.70 2.94 4.80 0.36 -0.42 -0.46 0.00 0.00 0.00 0.00 0.00 0.00 0.94 0.49 2.88 -0.02 0.01 0.58 0.07\r\n> core.optimization.AtomTreeMinimizer: E(i) 44 -8.34 0.50 8.12 4.28 0.63 -0.57 -3.08 0.00 0.00 0.00 0.00 -0.97 0.00 0.16 -0.09 5.98 0.07 0.00 -0.09 0.62\r\n> core.optimization.AtomTreeMinimizer: E(i) 45 -5.90 0.88 3.50 2.79 0.12 0.04 -1.50 0.00 0.00 0.00 -0.24 0.00 0.00 0.10 -0.17 1.06 0.59 0.00 2.30 0.39\r\n> core.optimization.AtomTreeMinimizer: E(i) 46 -6.81 1.67 7.40 0.83 0.61 -0.15 -3.75 0.00 0.00 0.00 0.00 -0.97 0.00 0.12 0.35 4.77 -0.33 0.00 -2.15 -0.65\r\n> core.optimization.AtomTreeMinimizer: E(i) 47 -13.14 1.04 12.85 2.46 0.65 -0.61 -4.70 0.00 0.00 0.00 0.00 -0.83 0.00 0.09 0.26 3.60 0.04 0.00 -0.09 -0.52\r\n> core.optimization.AtomTreeMinimizer: E(i) 48 -10.86 2.75 1.61 2.54 0.05 -0.34 -2.01 0.00 0.00 0.00 0.00 0.00 0.00 0.34 -0.01 0.06 -1.02 0.00 2.64 -0.31\r\n> core.optimization.AtomTreeMinimizer: E(i) 49 -11.36 2.08 6.91 2.90 0.52 -1.12 -0.77 0.00 0.00 0.00 0.00 0.00 0.00 0.29 0.68 3.10 -0.01 0.00 -0.09 -0.37\r\n> core.optimization.AtomTreeMinimizer: E(i) 50 -11.44 2.65 0.69 4.34 0.08 0.05 -1.78 0.00 0.00 0.00 0.00 0.00 0.00 0.39 -0.07 1.14 -0.44 0.00 1.66 -0.04\r\n> core.optimization.AtomTreeMinimizer: E(i) 51 -12.17 3.49 3.85 3.69 0.23 -0.67 -2.14 0.00 0.00 0.00 0.00 0.00 0.00 0.24 0.79 2.62 -0.33 0.00 1.22 0.17\r\n> core.optimization.AtomTreeMinimizer: E(i) 52 -10.46 3.92 2.42 1.81 0.04 -0.38 -2.34 0.00 0.00 0.00 0.00 0.00 0.00 0.25 -0.02 0.04 -0.47 0.00 2.64 -0.05\r\n> core.optimization.AtomTreeMinimizer: E(i) 53 -6.63 0.58 8.19 1.64 0.73 -0.15 -4.36 0.00 0.00 0.00 -1.02 0.00 0.00 0.06 -0.09 1.73 -0.88 0.00 -2.15 -0.33\r\n> core.optimization.AtomTreeMinimizer: E(i) 54 -2.43 0.14 2.01 2.58 0.39 -0.18 0.59 0.00 0.00 0.00 0.00 0.00 0.00 0.02 -0.23 3.21 -0.04 0.00 -0.71 -0.75\r\n> core.optimization.AtomTreeMinimizer: E(i) 55 -4.23 0.78 3.92 3.07 0.11 -0.56 -1.25 0.00 0.00 0.00 -0.41 0.00 0.00 0.06 -0.03 0.07 0.02 0.00 1.66 -0.91\r\n> core.optimization.AtomTreeMinimizer: E(i) 56 -5.50 1.25 4.54 2.33 0.37 -0.55 -1.79 0.00 0.00 0.00 0.00 0.00 0.00 0.10 0.09 3.01 -0.68 0.00 -2.15 -0.55\r\n> core.optimization.AtomTreeMinimizer: E(i) 57 -8.59 1.36 7.50 1.44 0.29 -0.73 -2.78 0.00 0.00 0.00 -0.61 0.00 0.00 0.09 0.04 1.98 0.18 0.00 -1.34 -0.01\r\n> core.optimization.AtomTreeMinimizer: E(i) 58 -13.05 3.54 2.62 3.54 0.11 -0.39 -2.30 0.00 0.00 0.00 0.00 0.00 0.00 0.14 -0.18 5.43 -0.69 0.00 2.30 -0.26\r\n> core.optimization.AtomTreeMinimizer: E(i) 59 -4.74 1.27 1.51 0.29 0.00 -0.13 -0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.08 -0.08 0.00 0.44 0.00 1.32 -0.23\r\n> core.optimization.AtomTreeMinimizer: E(i) 60 -6.17 2.19 4.03 1.64 0.55 -0.58 -0.32 0.00 0.00 0.00 0.00 0.00 0.00 0.13 1.63 4.71 -0.04 0.00 -2.72 0.19\r\n> core.optimization.AtomTreeMinimizer: E(i) 61 -3.03 1.23 1.68 0.01 0.00 -0.26 0.16 0.01 0.00 0.00 0.00 0.00 0.00 0.08 0.36 0.00 1.92 0.00 0.80 2.98\r\n> core.optimization.AtomTreeMinimizer: E(i) 62 -9.41 5.18 2.90 0.62 0.08 -0.05 -1.49 0.02 0.00 0.00 0.00 0.00 0.00 0.16 -0.09 0.26 -1.77 0.00 -1.64 2.14\r\n> core.optimization.AtomTreeMinimizer: E(i) 63 -5.83 1.03 3.69 2.88 0.51 -0.32 -1.06 0.00 0.00 0.00 0.00 0.00 0.00 0.14 -0.02 2.10 -0.16 0.00 -0.09 -0.92\r\n> core.optimization.AtomTreeMinimizer: E(i) 64 -9.34 2.17 1.41 3.43 0.04 -0.36 -1.79 0.00 0.00 0.00 0.00 0.00 0.00 0.21 -0.04 0.05 -0.71 0.00 2.64 -0.59\r\n> core.optimization.AtomTreeMinimizer: E(i) 65 -5.62 0.63 7.10 0.04 0.00 -0.01 -4.23 0.00 0.00 0.00 0.00 0.00 0.00 0.14 0.00 0.00 0.00 0.00 0.80 -0.50\r\n> core.optimization.AtomTreeMinimizer: total_energy fa_atr -463.454\r\n> core.optimization.AtomTreeMinimizer: total_energy fa_rep 110.976\r\n> core.optimization.AtomTreeMinimizer: total_energy fa_sol 255.055\r\n> core.optimization.AtomTreeMinimizer: total_energy fa_intra_rep 138.850\r\n> core.optimization.AtomTreeMinimizer: total_energyfa_intra_sol_x 16.183\r\n> core.optimization.AtomTreeMinimizer: total_energy lk_ball_wtd -22.602\r\n> core.optimization.AtomTreeMinimizer: total_energy fa_elec -109.703\r\n> core.optimization.AtomTreeMinimizer: total_energy pro_close 0.383\r\n> core.optimization.AtomTreeMinimizer: total_energy hbond_sr_bb -16.596\r\n> core.optimization.AtomTreeMinimizer: total_energy hbond_lr_bb -15.759\r\n> core.optimization.AtomTreeMinimizer: total_energy hbond_bb_sc -6.816\r\n> core.optimization.AtomTreeMinimizer: total_energy hbond_sc -9.025\r\n> core.optimization.AtomTreeMinimizer: total_energy dslf_fa13 0.000\r\n> core.optimization.AtomTreeMinimizer: total_energyatom_pair_cons 11.405\r\n> core.optimization.AtomTreeMinimizer: total_energy omega 6.375\r\n> core.optimization.AtomTreeMinimizer: total_energy fa_dun 117.539\r\n> core.optimization.AtomTreeMinimizer: total_energy p_aa_pp -21.777\r\n> core.optimization.AtomTreeMinimizer: total_energy yhh_planarity 0.009\r\n> core.optimization.AtomTreeMinimizer: total_energy ref 19.150\r\n> core.optimization.AtomTreeMinimizer: total_energy rama_prepro -16.004\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 6-7, 6-9, 6-10, 6-8!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 6-11) == ( atom3 ~ 6-10 ) = 0\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 6-13) == ( atom2 ~ 6-9 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 6-6) == ( atom2 ~ 6-9 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 6-5) == ( atom3 ~ 6-10 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 6-9, 6-10, 6-8, 6-6!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 6-5) == ( atom3 ~ 6-8 ) = 0\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 6-2) == ( atom2 ~ 6-10 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 6-7) == ( atom2 ~ 6-10 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 6-6) == ( atom3 ~ 6-8 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 6-10, 6-8, 6-6, 6-7!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 6-6) == ( atom3 ~ 6-6 ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 6-5) == ( atom2 ~ 6-8 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 6-9) == ( atom2 ~ 6-8 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 6-7) == ( atom3 ~ 6-6 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 6-12, 6-10, 6-8, 6-11!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 6-13) == ( atom3 ~ 6-8 ) = 0\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 6-14) == ( atom2 ~ 6-10 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 6-10) == ( atom2 ~ 6-10 ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 6-9) == ( atom3 ~ 6-8 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 6-10, 6-8, 6-11, 6-13!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 6-14) == ( atom3 ~ 6-11 ) = 0\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 6-12) == ( atom2 ~ 6-8 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 6-9) == ( atom2 ~ 6-8 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 6-7) == ( atom3 ~ 6-11 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 43-6, 43-7, 43-9, 43-11!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 43-10) == ( atom3 ~ 43-9 ) = 0\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 43-8) == ( atom2 ~ 43-7 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 43-5) == ( atom2 ~ 43-7 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 43-2) == ( atom3 ~ 43-9 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 43-7, 43-9, 43-11, 43-10!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 43-8) == ( atom3 ~ 43-11 ) = 0\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 43-6) == ( atom2 ~ 43-9 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 43-6) == ( atom2 ~ 43-9 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 43-5) == ( atom3 ~ 43-11 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 43-9, 43-11, 43-10, 43-8!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 43-6) == ( atom3 ~ 43-10 ) = 0\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 43-5) == ( atom2 ~ 43-11 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 43-7) == ( atom2 ~ 43-11 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 43-6) == ( atom3 ~ 43-10 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 51-11, 51-10, 51-8, 51-6!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 51-5) == ( atom3 ~ 51-8 ) = 0\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 51-2) == ( atom2 ~ 51-10 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 51-9) == ( atom2 ~ 51-10 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 51-7) == ( atom3 ~ 51-8 ) = 0\r\n> core.kinematics.AtomTree: No proper DoF can be found for these four atoms: 51-10, 51-8, 51-6, 51-7!\r\n> core.kinematics.AtomTree: What condition failed?\r\n> core.kinematics.AtomTree: !atom4->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom4->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom1() ~ 51-6) == ( atom3 ~ 51-6 ) = 1\r\n> core.kinematics.AtomTree: (atom4->raw_input_stub_atom2() ~ 51-5) == ( atom2 ~ 51-8 ) = 0\r\n> core.kinematics.AtomTree: or... \r\n> core.kinematics.AtomTree: !atom1->is_jump() = 1\r\n> core.kinematics.AtomTree: !atom1->keep_dof_fixed( id::PHI ) = 1\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom1() ~ 51-11) == ( atom2 ~ 51-8 ) = 0\r\n> core.kinematics.AtomTree: atom1->raw_input_stub_atom2() ~ 51-9) == ( atom3 ~ 51-6 ) = 0\r\n> core.scoring.NeighborList: Minimization stats: 177 score/deriv cals, 64 narrow-from-wide updates, 0 full updates.\r\n> core.scoring.NeighborList: Minimization stats: 265 score/deriv cals, 65 narrow-from-wide updates, 0 full updates.\r\n> core.scoring.NeighborList: Minimization stats: 265 score/deriv cals, 65 narrow-from-wide updates, 0 full updates.\r\n> core.optimize: AtomTreeMinimizer::run: nangles= 334 start_score: -215.387 start_func: -215.387 end_score: -224.996 end_func: -224.996\r\n> \r\n> ------------------------------------------------------------\r\n> Scores Weight Raw Score Wghtd.Score\r\n> ------------------------------------------------------------\r\n> fa_atr 1.000 -450.959 -450.959\r\n> fa_rep 0.550 69.418 38.180\r\n> fa_sol 1.000 250.173 250.173\r\n> fa_intra_rep 0.005 139.586 0.698\r\n> fa_intra_sol_xover4 1.000 16.212 16.212\r\n> lk_ball_wtd 1.000 -22.306 -22.306\r\n> fa_elec 1.000 -105.834 -105.834\r\n> pro_close 1.250 0.715 0.893\r\n> hbond_sr_bb 1.000 -16.502 -16.502\r\n> hbond_lr_bb 1.000 -15.630 -15.630\r\n> hbond_bb_sc 1.000 -6.733 -6.733\r\n> hbond_sc 1.000 -9.200 -9.200\r\n> dslf_fa13 1.250 0.000 0.000\r\n> atom_pair_constraint 1.000 10.802 10.802\r\n> omega 0.400 6.607 2.643\r\n> fa_dun 0.700 119.661 83.763\r\n> p_aa_pp 0.600 -21.901 -13.141\r\n> yhh_planarity 0.625 0.004 0.003\r\n> ref 1.000 19.150 19.150\r\n> rama_prepro 0.450 -16.019 -7.208\r\n> ---------------------------------------------------\r\n> Total weighted score: -224.996\r\n> protocols.moves.ddGMover: 2 score after mutation: residue V61G -235.798 fa_atr: -450.959 fa_rep: 38.180 fa_sol: 250.173 fa_intra_rep: 0.698 fa_intra_sol_xover4: 16.212 lk_ball_wtd: -22.306 fa_elec: -105.834 pro_close: 0.893 hbond_sr_bb: -16.502 hbond_lr_bb: -15.630 hbond_bb_sc: -6.733 hbond_sc: -9.200 dslf_fa13: 0.000 omega: 2.643 fa_dun: 83.763 p_aa_pp: -13.141 yhh_planarity: 0.003 ref: 19.150 rama_prepro: -7.208\r\n> protocols.moves.ddGMover: round 2 mutate V61G -235.798\r\n> core.io.silent.SilentStruct: get energies from pose...\r\n> core.io.silent: read coords...\r\n> protocols.moves.ddGMover: mutate V61G wildtype_dG is: -245.223 and mutant_dG is: -235.798 ddG is: 9.42552\r\n> apps.public.ddg.ddg_monomer: mutation label for this round is V61G\r\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/master:62040/ddG_of_mutation/mut_V61G.out /home/benchmark/working_dir/master:62041/ddG_of_mutation/mut_V61G.out\r\n70a71,137\r\n> SCORE: -235.798 -450.959 38.180 250.173 0.698 16.212 -22.306 -105.834 0.893 -16.502 -15.630 -6.733 -9.200 0.000 2.643 83.763 -13.141 0.003 19.150 -7.208 mut_V61G_round_2\r\n> ANNOTATED_SEQUENCE: N[ASN:NtermProteinFull]LKTEWPELVGKSVEEAKKVILQDKPEAQIIVLPVGTIVTMEYRIDRVRLFVDKLDNIAEGPRVG[GLY:CtermProteinFull] mut_V61G_round_2\r\n> LsHFVB1jCWI8d+eIQNepPBZ5QUIc0iMJQgqxPBNIQOIMCsyJQrEsQBZT9KIMdI+HQuzXNBhrnXIs78dLQhYKMBFNWdIMIirKQLxxOBt9GhIciRoLQlaMIBllGeI8+h8IQLH6WBBB2YIsrHlJQgqxVB5QrXIc3kYFQ14FYBNHaTIslDdIQnv/MBZktUI8xL9GQzNOPBp7kXIsLXcNQ/hoJBtBYVI8v4hLQ5dPHBB4zhIMDQXIQG7KGBhH+aI8qbOIQ mut_V61G_round_2\r\n> 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LYMoPBtc45HM1f0VQFRdQBNfw2H8WpOXQW8MWBh5pzHMnlfXQtx1ZBphf3H8LUzWQvb3OBNW3/HcQeFYQcMNSB9G/EI8RlAYQaFiQBldXJIMtseYQZJuMBNsmIIM9o1YQXdETBJ0eNIc0weYQmMrSB1ZR9HMfxTVQC7SOBd0XvHcxJcXQMyNPB9eL9HM3imYQDXsKBpv/AIcmAAYQvw1RBdwbGIsQp/WQdCZWBdYAEI8bQGYQ mut_V61G_round_2\r\n> L4gyWBtQbsHcjJOYQj59bB5T+nH8I4aYQKXtcBNUvnHs+hLZQKJSdBp0DfH8pOeZQ2C1cBpq6cHsMsGYQhaEdBtVfcH84RuWQ5mwgBhwUdHctT7VQh/nYB5fXbH8Ef0VQCCEgBtgzcHMdlmUQwxtaBZZqbHsVbgUQzIJTB54faH8kSAWQSWfXBhluaHcseYTQLz4PBNgoZH8RU5UQvUBSBd4yZHMQ7mTQ/NcTB9m5pHcDLdYQqhLfBdBPtHM+RQYQrgkZBdAjXHsfcPYQJmTgBlFiZHMUcRYQUEriB9mPeHMUnbWQ87VhBNbMdH8Zr0TQ7eRRBp9eaHsLU/WQ42WZB1myaHcnbZSQEylLBZF0YHcaVDVQRyTPBBKKZHMTjwSQ mut_V61G_round_2\r\n> LE15cBBnNxH81UeZQiardBFnoyHsPZMaQTrbhBZIztHccocaQwIohBdiWrHsMBDbQiDqdBBWv+HslSTaQW2veBperBIcOjnZQYj/bBZ4n7H8j7IZQGT3cBlZKxHsNqdZQe4jaBNeruHsYkfaQotXgBBZmAI8pZqaQLhyZB55wAI8c2faQsOihBxK8BIs3RhZQ3JIdBVcwFIcXrkZQQbwdBpF17Hs1qoYQo+sXBVIY9HsGSFZQ mut_V61G_round_2\r\n> 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mut_V61G_round_2\r\n> L795kBd4HuGMax9bQ7+UmBVdomGsXthbQGsjkBtBJdGMffVbQEmGiB9xgdG854ZbQ41TnB56VsGM+X5aQ51YpBlzA1GspiBbQ3RbqBp5s5GcKzXaQwxasBFTrCHMD7faQkgZtB91hHH8VX3ZQqe3jBBKO0GMClwbQNAEoBVBYjGMlZybQoinlBRECwGcRDpaQYyLoBJIhmGc3fjaQ++DrBppoxGMHYTbQu8foBB6Y7GchlUbQqSwoBRi18GM4MFaQx1ZrBpkczG84MFaQe1HuBpDk/GsnsxaQRSerBtN5IHs3IzaQ6htuB51bNHs3H+ZQ7i1rB9JlKHcp3mZQBEUuBly3BHs8hlZQ mut_V61G_round_2\r\n> LaE3lBZSuUGst3GbQu9fkBZd1KG8r35aQQ3+iBph8MG84IQaQlqejBNzvUGsQE5ZQeTdmBhlnBGsNU1aQNzKoBxoUDGsW2RaQV03nB50JVGc2lEbQ2/JjBNiqHG8ZVSbQ2HVlBZKf0F8D2waQexonB9/CBG8RjSbQt23pBth1FGs/ybaQ mut_V61G_round_2\r\n> LmoFhBNrzFGMQeIaQa88eBlhrFG8HWhZQOSXhBR8REGMrG7YQsQEhBBVBKG8vcbYQpYfaBFvi6FcEviZQ4O8XBFpA4FstY2YQ3iIWBRJc/Fc0ZDaQyewgBdPMAGc1GfaQicHdBhYdNG8mabZQDbMcBVGRrFcIrsZQf3xUBBQBsF8V33YQXh+aBVh8yF8sffYQB0PWBRboDGc2QsYQ9yHTBtD3yFMymCaQI2RUBRuXHGsYr7ZQ5A5XBJBIAGMlSjaQ mut_V61G_round_2\r\n> LDnRjBBlP6Fsi8+YQBGHlBBIR0FMLacYQ/L3mBVirDGcjcQYQvXUnBlPNGG8F1UXQlyxmBJX9gFMieoYQW0glBxwYLFMaYwYQfG4jB9fM/Es+BRYQIpmiBVt3uE8U3YYQJ+5jBViaGFsuPXXQAWdjBx1GzFMXxbZQLi+jBJOVwFsKR/XQqV1nBBbAlFcT7FZQ+JOoBNfgeFclzOYQCpMkBRQGLF8wMMZQf3NnBZM6AF8ED2YQ mut_V61G_round_2\r\n> LdYunB5cYJGsIbxYQcDSpBdbLTGsCjsYQJlfnBtQwbGcBjYYQN8aoBtWShG86D2XQJtdqBVBiXGc3qVZQM3ysBVPMSGc2PsZQ+EXtBBDbVGsWtZaQRfprBhgNWGs0k1aQ9MyvBJFWXGMz+gaQ4cRnBpoxGGcAIPZQBm9qBxWwRGcx/WYQ5m2oBZcuXGsaKtZQdYIrB5mqfGseAPZQyIsuB9NETGMLWbZQmvOsB9xxJGsV+sZQ mut_V61G_round_2\r\n> L/2ClBpKzcGMugnYQ57EjBFHQkG8rvVYQIjSiB5qZiGMtxOXQdEBiBtEPqGM9leWQOcrgBZI0kG8YnzYQmdhkB5EJYGMkjAZQ7R/jBhzJsGMLaTYQFVaeBxuWqGcgmmYQxpUhBRPmnGMXATZQ0wkfBVU5cG8ym2YQ mut_V61G_round_2\r\n> 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"state": "failed"
},
"ddG_scan": {
"log": "",
"state": "passed"
},
"ddG_sym": {
"log": "",
"state": "passed"
},
"density_denovo": {
"log": "",
"state": "passed"
},
"density_refine": {
"log": "",
"state": "passed"
},
"density_refine_symm": {
"log": "",
"state": "passed"
},
"density_tools": {
"log": "",
"state": "passed"
},
"design_glycans": {
"log": "",
"state": "passed"
},
"design_w_custom_palette-CAAs": {
"log": "",
"state": "passed"
},
"design_w_custom_palette-NCAAs": {
"log": "",
"state": "passed"
},
"design_w_custom_palette-RNA": {
"log": "",
"state": "passed"
},
"dgdp_aio": {
"log": "",
"state": "passed"
},
"dgdp_script": {
"log": "Brief Diff:\nOnly in /home/benchmark/working_dir/master:62040/dgdp_script: .test_got_timeout_kill.log\r\n",
"state": "failed"
},
"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": "Brief Diff:\nFiles /home/benchmark/working_dir/master:62040/energy_based_clustering_alpha_aa_scorefile/.test_did_not_run.log and /home/benchmark/working_dir/master:62041/energy_based_clustering_alpha_aa_scorefile/.test_did_not_run.log differ\r\n\n\nFull Diff:\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/master:62040/energy_based_clustering_alpha_aa_scorefile/.test_did_not_run.log /home/benchmark/working_dir/master:62041/energy_based_clustering_alpha_aa_scorefile/.test_did_not_run.log\r\n1c1\r\n< *** Test energy_based_clustering_alpha_aa_scorefile did not run! Check your --mode flag and paths. [2023-08-26 17:56:19.966516]\r\n---\r\n> *** Test energy_based_clustering_alpha_aa_scorefile did not run! Check your --mode flag and paths. [2023-08-30 20:55:12.981117]\r\n\nCompare(...): Marking as \"Script failed\" due to presense of .test_did_not_run.log or .test_got_timeout_kill.log file!\n",
"state": "script failed"
},
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"log": "",
"state": "passed"
},
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"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"
},
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"log": "",
"state": "passed"
},
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"log": "",
"state": "passed"
},
"evolution": {
"log": "",
"state": "passed"
},
"exclusively_shared_jumps": {
"log": "",
"state": "passed"
},
"explicit_membrane": {
"log": "",
"state": "passed"
},
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"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"
},
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"log": "",
"state": "passed"
},
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"log": "",
"state": "passed"
},
"features": {
"log": "",
"state": "passed"
},
"features_database_schema": {
"log": "",
"state": "passed"
},
"features_parallel": {
"log": "",
"state": "passed"
},
"features_pdb": {
"log": "",
"state": "passed"
},
"features_pdb_mpi": {
"log": "",
"state": "passed"
},
"features_postgres": {
"log": "",
"state": "passed"
},
"features_scientific_benchmark": {
"log": "",
"state": "passed"
},
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"log": "",
"state": "passed"
},
"fiber_diffraction_fad": {
"log": "",
"state": "passed"
},
"fit_helixparams": {
"log": "",
"state": "passed"
},
"fit_helixparams_a3b": {
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"state": "passed"
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"fixbb": {
"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"
},
"fold_from_loops": {
"log": "",
"state": "passed"
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"log": "",
"state": "passed"
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"fragmentpicker_integration_demo": {
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},
"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": "Brief Diff:\nOnly in /home/benchmark/working_dir/master:62040/glycan_tree_relax: .test_got_timeout_kill.log\r\n",
"state": "failed"
},
"glycomutagenesis": {
"log": "",
"state": "passed"
},
"glycopeptidedocking": {
"log": "",
"state": "passed"
},
"glycopeptidedocking_diglyco_long": {
"log": "",
"state": "passed"
},
"glycosylation": {
"log": "",
"state": "passed"
},
"grid_scores_features": {
"log": "",
"state": "passed"
},
"hbnet": {
"log": "",
"state": "passed"
},
"hbnet_asymm": {
"log": "",
"state": "passed"
},
"hbnet_energy": {
"log": "",
"state": "passed"
},
"hbnet_energy_rosettascripts_linear": {
"log": "",
"state": "passed"
},
"hbnet_energy_symm": {
"log": "",
"state": "passed"
},
"hbnet_use_input_rot": {
"log": "",
"state": "passed"
},
"hbonds": {
"log": "",
"state": "passed"
},
"hbonds_sp2": {
"log": "",
"state": "passed"
},
"hbondstoresidue_selector": {
"log": "",
"state": "passed"
},
"hbs_design": {
"log": "",
"state": "passed"
},
"header_using_check": {
"log": "",
"state": "passed"
},
"helical_bundle": {
"log": "",
"state": "passed"
},
"helical_bundle_nonideal": {
"log": "",
"state": "passed"
},
"helical_bundle_predict": {
"log": "",
"state": "passed"
},
"helical_bundle_predict_psipred": {
"log": "",
"state": "passed"
},
"helical_bundle_predict_psipred_with_helix_globals": {
"log": "",
"state": "passed"
},
"helical_bundle_predict_sequence": {
"log": "",
"state": "passed"
},
"helical_bundle_predict_skipping_residues": {
"log": "",
"state": "passed"
},
"helix_from_sequence": {
"log": "",
"state": "passed"
},
"hierarchical_clustering": {
"log": "",
"state": "passed"
},
"homodimer_fnd_ref2015_memb": {
"log": "",
"state": "passed"
},
"hotspot_graft": {
"log": "",
"state": "passed"
},
"hotspot_hashing": {
"log": "",
"state": "passed"
},
"hotspot_stub_constraints": {
"log": "",
"state": "passed"
},
"hshash_utils": {
"log": "",
"state": "passed"
},
"hts_io": {
"log": "",
"state": "passed"
},
"hybridization": {
"log": "",
"state": "passed"
},
"hydrate": {
"log": "",
"state": "passed"
},
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"ligand_dock_ensemble": {
"log": "Brief Diff:\nOnly in /home/benchmark/working_dir/master:62041/ligand_dock_ensemble: B_1.pdb\r\nOnly in /home/benchmark/working_dir/master:62041/ligand_dock_ensemble: C_1.pdb\r\nOnly in /home/benchmark/working_dir/master:62041/ligand_dock_ensemble: D_1.pdb\r\nOnly in /home/benchmark/working_dir/master:62041/ligand_dock_ensemble: girk_ligands_0001.pdb\r\nFiles /home/benchmark/working_dir/master:62040/ligand_dock_ensemble/log and /home/benchmark/working_dir/master:62041/ligand_dock_ensemble/log differ\r\nOnly in /home/benchmark/working_dir/master:62041/ligand_dock_ensemble: score.sc\r\nOnly in /home/benchmark/working_dir/master:62040/ligand_dock_ensemble: .test_got_timeout_kill.log\r\n\n\nFull Diff:\nOnly in /home/benchmark/working_dir/master:62041/ligand_dock_ensemble: B_1.pdb\r\nOnly in /home/benchmark/working_dir/master:62041/ligand_dock_ensemble: C_1.pdb\r\nOnly in /home/benchmark/working_dir/master:62041/ligand_dock_ensemble: D_1.pdb\r\nOnly in /home/benchmark/working_dir/master:62041/ligand_dock_ensemble: girk_ligands_0001.pdb\r\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/master:62040/ligand_dock_ensemble/log /home/benchmark/working_dir/master:62041/ligand_dock_ensemble/log\r\n1096c1096,1137\r\n< core.pack.task: Packer task: initialize from \r\n---\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.rotamers.SingleLigandRotamerLibrary: Added 548 rotamers for 00D\r\n> Adjusted Current Score is-3740.86\r\n> Score Delta is-3.23121\r\n> Monte Carlo Accepted\r\n> Beat lowest score\r\n> Correlation For Cycle 5 is -0.5core.pack.task: Packer task: initialize from command line() \r\n> core.pack.rotamers.SingleLigandRotamerLibrary: Added 180 rotamers for 00B\r\n> Adjusted Current Score is-3745.99\r\n> Score Delta is0.984815\r\n> Monte Carlo Accepted\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.rotamers.SingleLigandRotamerLibrary: Added 917 rotamers for 00C\r\n> Adjusted Current Score is-3734.46\r\n> Score Delta is1.19689\r\n> rejected\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.rotamers.SingleLigandRotamerLibrary: Added 548 rotamers for 00D\r\n> Adjusted Current Score is-3740.1\r\n> Score Delta is0.758271\r\n> Monte Carlo Accepted\r\n> Correlation For Cycle 6 is -0.5protocols.ligand_docking.ligand_options.FinalMinimizer: Energy prior to minimizing: -3814.65\r\n> protocols.ligand_docking.ligand_options.FinalMinimizer: Energy after minimizing: -4184.48\r\n> protocols.ligand_docking.ligand_options.FinalMinimizer: Energy prior to minimizing: -3115.55\r\n> protocols.ligand_docking.ligand_options.FinalMinimizer: Energy after minimizing: -4160.08\r\n> protocols.ligand_docking.ligand_options.FinalMinimizer: Energy prior to minimizing: -3162.33\r\n> protocols.ligand_docking.ligand_options.FinalMinimizer: Energy after minimizing: -4176.04\r\n> protocols.rosetta_scripts.ParsedProtocol: setting status to success\r\n> protocols.jd2.JobDistributor: no more batches to process... \r\n> basic.citation_manager.CitationManager: \r\n> The following Rosetta modules were used during this run of Rosetta, and should be cited:\r\n> \r\n> rosetta_scripts Application's citation(s):\r\n> Fleishman SJ, Leaver-Fay A, Corn JE, Strauch E-M, Khare SD, Koga N, Ashworth J, Murphy P, Richter F, Lemmon G, Meiler J, and Baker D. (2011). RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite. PLoS ONE 6(6):e20161. doi: 10.1371/journal.pone.0020161.\r\n> \r\n> TransformEnsemble Mover's citation(s):\r\n> Fu DY, and Meiler J. (2018). RosettaLigandEnsemble: A Small-Molecule Ensemble-Driven Docking Approach. ACS Omega 3(4):3655-64. doi: 10.1021/acsomega.7b02059.\r\n> \r\n> HighResEnsemble Mover's citation(s):\r\n> Fu DY, and Meiler J. (2018). RosettaLigandEnsemble: A Small-Molecule Ensemble-Driven Docking Approach. ACS Omega 3(4):3655-64. doi: 10.1021/acsomega.7b02059.\r\n> \r\n> \r\nOnly in /home/benchmark/working_dir/master:62041/ligand_dock_ensemble: score.sc\r\nOnly in /home/benchmark/working_dir/master:62040/ligand_dock_ensemble: .test_got_timeout_kill.log\r\n",
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"rna_puzzle6_U75G76A77_on_thread1": {
"log": "",
"state": "passed"
},
"rna_puzzle6_j67_into_p6p7rigidbody_thread1": {
"log": "",
"state": "passed"
},
"rna_ribosome_tether": {
"log": "",
"state": "passed"
},
"rna_score": {
"log": "",
"state": "passed"
},
"rna_screen_phosphates": {
"log": "",
"state": "passed"
},
"rna_suitename": {
"log": "",
"state": "passed"
},
"rnp_ddg_calc_mut": {
"log": "",
"state": "passed"
},
"rnp_ddg_calc_setup": {
"log": "",
"state": "passed"
},
"rnp_ddg_calc_wt": {
"log": "",
"state": "passed"
},
"rnp_ddg_finalize": {
"log": "",
"state": "passed"
},
"rnp_ddg_relax_command_1": {
"log": "",
"state": "passed"
},
"rnp_ddg_relax_command_2": {
"log": "",
"state": "passed"
},
"rnp_ddg_relax_finalize": {
"log": "",
"state": "passed"
},
"rnp_ddg_relax_setup": {
"log": "",
"state": "passed"
},
"rollmover": {
"log": "",
"state": "passed"
},
"rosetta_scripts_hbond_options": {
"log": "",
"state": "passed"
},
"rosetta_scripts_include": {
"log": "",
"state": "passed"
},
"rosetta_scripts_info": {
"log": "",
"state": "passed"
},
"rosetta_scripts_jd3": {
"log": "",
"state": "passed"
},
"rosetta_scripts_loops": {
"log": "",
"state": "passed"
},
"rosetta_scripts_setup": {
"log": "",
"state": "passed"
},
"rosie_ligand_docking": {
"log": "",
"state": "passed"
},
"rotamer_probability": {
"log": "",
"state": "passed"
},
"rotamer_recovery": {
"log": "",
"state": "passed"
},
"rotamer_recovery_compare_two_structures": {
"log": "",
"state": "passed"
},
"rs_flexbbmoves": {
"log": "",
"state": "passed"
},
"rs_loophash": {
"log": "",
"state": "passed"
},
"sasa_metric_options": {
"log": "",
"state": "passed"
},
"score12_docking": {
"log": "",
"state": "passed"
},
"score_aln": {
"log": "",
"state": "passed"
},
"score_jd2": {
"log": "",
"state": "passed"
},
"score_only_silence": {
"log": "",
"state": "passed"
},
"sdf_reader": {
"log": "",
"state": "passed"
},
"secondary_structure_output": {
"log": "",
"state": "passed"
},
"seed_ensemble_JD2_JI": {
"log": "",
"state": "passed"
},
"select_best_unique_ligand_poses": {
"log": "",
"state": "passed"
},
"selected_residue_count_metric": {
"log": "",
"state": "passed"
},
"sequence_profile_constraints": {
"log": "",
"state": "passed"
},
"sequence_recovery": {
"log": "",
"state": "passed"
},
"sequence_tolerance": {
"log": "",
"state": "passed"
},
"set_torsion": {
"log": "",
"state": "passed"
},
"shobuns": {
"log": "",
"state": "passed"
},
"silent2frag": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_1_4_bbmb": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_angle": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_anglelength": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_beta_thioether_lariat": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_bondangle_bondlength": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_cartesian": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_cispro": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_cterm_isopeptide_lariat": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_cterm_isopeptide_lariat_tailless": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_design": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_nmethyl": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_nterm_isopeptide_lariat": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_nterm_isopeptide_lariat_tailless": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_octahedral_metal": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_peptoid": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_setting": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_sidechain_isopeptide": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_sidechain_isopeptide_reverse": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_square_planar_metal": {
"log": "",
"state": "passed"
},
"simple_cycpep_predict_square_pyramidal_metal": {
"log": "Brief Diff:\nFiles /home/benchmark/working_dir/master:62040/simple_cycpep_predict_square_pyramidal_metal/log and /home/benchmark/working_dir/master:62041/simple_cycpep_predict_square_pyramidal_metal/log differ\r\nOnly in /home/benchmark/working_dir/master:62041/simple_cycpep_predict_square_pyramidal_metal: S_0001.pdb\r\nOnly in /home/benchmark/working_dir/master:62040/simple_cycpep_predict_square_pyramidal_metal: .test_got_timeout_kill.log\r\n\n\nFull Diff:\ndiff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/master:62040/simple_cycpep_predict_square_pyramidal_metal/log /home/benchmark/working_dir/master:62041/simple_cycpep_predict_square_pyramidal_metal/log\r\n7099c7099,8301\r\n< protocols.rosetta_scripts.ParsedProtocol.REPOR\r\n---\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is not s6 symmetric.\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: Filter reports failure!\r\n> protocols.generalized_kinematic_closure.GeneralizedKIC: Preselection mover failed! Continuing to next solution.\r\n> protocols.generalized_kinematic_closure.GeneralizedKIC: Applying pre-selection mover to solution 1 from attempt 107.\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_1=======================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 1\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is s6 symmetric.\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER CrosslinkerMover - square_pyramidal_metal_link_1=======================\r\n> protocols.cyclic_peptide.CrosslinkerMover: Sidechain distance filter PASSED.\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> protocols.relax.FastRelax: CMD: repeat 2.82206e+06 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 2.82206e+06 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 2.8181e+06 0 0 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 82 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 152370\r\n> protocols.relax.FastRelax: CMD: repack 152350 0 0 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 152364 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: min 6026.79 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 6026.79 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 6537.02 0 0 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 51 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 6550.86\r\n> protocols.relax.FastRelax: CMD: repack 6537.02 0 0 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 6572.79 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: min 6566.56 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 6566.56 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 7214.14 0 0 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 48 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7224.7\r\n> protocols.relax.FastRelax: CMD: repack 7214.14 0 0 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 7265.2 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: min 7251.09 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 7251.09 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 8181.78 0 0 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 46 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 8191.2\r\n> protocols.relax.FastRelax: CMD: repack 8181.78 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: min 8151 0 0 0.55\r\n> protocols.relax.FastRelax: MRP: 0 8151 8151 0 0 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 8151 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 8151 0 0 0.55\r\n> protocols::checkpoint: Deleting checkpoints of FastRelax\r\n> protocols.relax.FastRelax: CMD: repeat 8151 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 8151 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 6152.67 0 0 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 82 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 6171.48\r\n> protocols.relax.FastRelax: CMD: repack 6152.67 0 0 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 6175.56 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: min 6026.79 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 6026.79 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 6537.13 0 0 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 51 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 6550.57\r\n> protocols.relax.FastRelax: CMD: repack 6537.13 0 0 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 6572.9 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: min 6566.56 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 6566.56 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 7214.13 0 0 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 48 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7224.71\r\n> protocols.relax.FastRelax: CMD: repack 7214.13 0 0 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 7265.2 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: min 7251.09 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 7251.09 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 8181.78 0 0 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 46 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 8190.12\r\n> protocols.relax.FastRelax: CMD: repack 8181.78 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: min 8151 0 0 0.55\r\n> protocols.relax.FastRelax: MRP: 0 8151 8151 0 0 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 8151 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 8151 0 0 0.55\r\n> protocols::checkpoint: Deleting checkpoints of FastRelax\r\n> protocols.relax.FastRelax: CMD: repeat 8151 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 8151 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 6152.67 0 0 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 82 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 6168.63\r\n> protocols.relax.FastRelax: CMD: repack 6152.67 0 0 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 6175.56 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: min 6026.79 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 6026.79 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 6537.13 0 0 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 51 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 6551.36\r\n> protocols.relax.FastRelax: CMD: repack 6537.13 0 0 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 6572.9 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: min 6566.56 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 6566.56 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 7214.13 0 0 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 48 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7223.5\r\n> protocols.relax.FastRelax: CMD: repack 7214.13 0 0 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 7265.2 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: min 7251.09 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 7251.09 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 8181.78 0 0 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 46 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 8190.13\r\n> protocols.relax.FastRelax: CMD: repack 8181.78 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: min 8151 0 0 0.55\r\n> protocols.relax.FastRelax: MRP: 0 8151 8151 0 0 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 8151 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 8151 0 0 0.55\r\n> protocols::checkpoint: Deleting checkpoints of FastRelax\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper: Constraint energy for crosslinked pose is 6046.01. Filter passes.\r\n> protocols.cyclic_peptide.CrosslinkerMover: Linker constraints filter PASSED.\r\n> protocols.cyclic_peptide.CrosslinkerMover: CrosslinkerMover reports SUCCESS. Updating pose.\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - High_Hbond_FastRelax=======================\r\n> protocols.relax.FastRelax: CMD: repeat 8151 1.69614 0 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 8151 1.69614 0 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 6152.67 1.69614 0 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 107 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 6150.37\r\n> protocols.relax.FastRelax: CMD: repack 6152.67 1.69614 0 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 6175.56 1.69614 0 0.02805\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 7.45058e-09 Deriv= -91901.1 Finite Diff= 24433.4\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 2.38419e-07 Deriv= -96.9649 Finite Diff= 2.48518\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.4234e-09 Deriv= -21194 Finite Diff= -1203.32\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 7.78951e-09 Deriv= -541.221 Finite Diff= 130.601\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 8.95401e-09 Deriv= -183232 Finite Diff= 4779.12\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 8.66432e-08 Deriv= -7753.74 Finite Diff= 2271.34\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#263\r\n> protocols.relax.FastRelax: CMD: min 53.9948 2.76225 2.12952 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 53.9948 2.76225 2.12952 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 240.414 2.76225 2.12952 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 75 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 226.856\r\n> protocols.relax.FastRelax: CMD: repack 240.414 2.76225 2.12952 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 253.481 2.76225 2.12952 0.154\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 5.96046e-10 Deriv= -490223 Finite Diff= -29093.5\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 6.8235e-08 Deriv= -12501.6 Finite Diff= -322.982\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#5\r\n> protocols.relax.FastRelax: CMD: min 252.258 2.76075 2.129 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 252.258 2.76075 2.129 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 488.913 2.76075 2.129 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 65 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 474.621\r\n> protocols.relax.FastRelax: CMD: repack 488.913 2.76075 2.129 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 507.574 2.76075 2.129 0.31955\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 5.96046e-08 Deriv= -16367.3 Finite Diff= 5571.76\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 4.86392e-09 Deriv= -3474.76 Finite Diff= -175.706\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 7.62639e-09 Deriv= -94129.7 Finite Diff= 6376.62\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 8.737e-09 Deriv= -6962.28 Finite Diff= 739.739\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 2.54012e-09 Deriv= -35949.5 Finite Diff= 1642.99\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 2.78044e-09 Deriv= -66785.2 Finite Diff= 2552.78\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.35949e-07 Deriv= -3149.42 Finite Diff= -158.984\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#71\r\n> protocols.relax.FastRelax: CMD: min 230.017 2.80273 2.31818 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 230.017 2.80273 2.31818 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 322.335 2.80273 2.31818 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 53 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 305.227\r\n> protocols.relax.FastRelax: CMD: repack 322.335 2.80273 2.31818 0.55\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -59126.8 Finite Diff= 3318.85\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 8.54482e-09 Deriv= -80468.3 Finite Diff= 2579.93\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 9.43134e-09 Deriv= -305942 Finite Diff= 7899.79\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 9.80424e-09 Deriv= -425640 Finite Diff= 10144.4\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 2.51368e-09 Deriv= -174045 Finite Diff= 2501.25\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 2.52561e-09 Deriv= -128665 Finite Diff= 1866.88\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 5.09993e-09 Deriv= -179467 Finite Diff= 1743.54\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.64617e-07 Deriv= -2147.97 Finite Diff= -214.262\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#42\r\n> protocols.relax.FastRelax: CMD: min 321.792 2.8005 2.31562 0.55\r\n> protocols.relax.FastRelax: MRP: 0 321.792 321.792 2.8005 2.31562 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 321.792 2.8005 2.31562 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 321.792 2.8005 2.31562 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 321.792 2.8005 2.31562 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 111.895 2.8005 2.31562 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 124 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 94.7402\r\n> protocols.relax.FastRelax: CMD: repack 111.895 2.8005 2.31562 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 114.3 2.8005 2.31562 0.02805\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -5398.56 Finite Diff= 2046.25\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 8.69349e-09 Deriv= -50152.5 Finite Diff= 2534.34\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 4.5691e-09 Deriv= -57859.2 Finite Diff= 2206.43\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 9.4011e-09 Deriv= -29610.1 Finite Diff= 2473.58\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.63259e-10 Deriv= -70265.2 Finite Diff= -1329.84\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.82937e-07 Deriv= -1739.3 Finite Diff= -47.4087\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#32\r\n> protocols.relax.FastRelax: CMD: min 113.121 2.79934 2.31276 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 113.121 2.79934 2.31276 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 160.724 2.79934 2.31276 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 84 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 143.512\r\n> protocols.relax.FastRelax: CMD: repack 160.724 2.79934 2.31276 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 164.061 2.79934 2.31276 0.154\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 4.76837e-09 Deriv= -34111.6 Finite Diff= 984.208\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.70443e-07 Deriv= -2003.66 Finite Diff= -14.3366\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#4\r\n> protocols.relax.FastRelax: CMD: min 163.936 2.79779 2.31141 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 163.936 2.79779 2.31141 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 225.811 2.79779 2.31141 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 76 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 208.627\r\n> protocols.relax.FastRelax: CMD: repack 225.811 2.79779 2.31141 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 230.69 2.79779 2.31141 0.31955\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 4.76837e-09 Deriv= -54134 Finite Diff= 7442.63\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.95053e-07 Deriv= -1529.95 Finite Diff= 64.4142\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#6\r\n> protocols.relax.FastRelax: CMD: min 230.678 2.79779 2.3114 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 230.678 2.79779 2.3114 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 323.585 2.79779 2.3114 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 53 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 306.266\r\n> protocols.relax.FastRelax: CMD: repack 323.585 2.79779 2.3114 0.55\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -66391.4 Finite Diff= 3890.07\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 8.55219e-09 Deriv= -2.07179e+07 Finite Diff= 1.32429e+06\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 2.59417e-09 Deriv= -45542.9 Finite Diff= 1780.64\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.68492e-07 Deriv= -2050.32 Finite Diff= -204.131\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#21\r\n> protocols.relax.FastRelax: CMD: min 322.413 2.79333 2.30646 0.55\r\n> protocols.relax.FastRelax: MRP: 1 322.413 321.792 2.8005 2.31562 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 322.413 2.79333 2.30646 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 322.413 2.79333 2.30646 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 322.413 2.79333 2.30646 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 113.612 2.79333 2.30646 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 124 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 96.416\r\n> protocols.relax.FastRelax: CMD: repack 113.612 2.79333 2.30646 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 116.005 2.79333 2.30646 0.02805\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 7.45058e-11 Deriv= -13731.8 Finite Diff= -832.944\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 5.37475e-09 Deriv= -43573 Finite Diff= 1883.7\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.78988e-09 Deriv= -117591 Finite Diff= 3991.69\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 8.87673e-09 Deriv= -25761.8 Finite Diff= 2054.02\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 2.82336e-09 Deriv= -34350.6 Finite Diff= 803.647\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.55224e-07 Deriv= -2415.81 Finite Diff= 321.374\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#32\r\n> protocols.relax.FastRelax: CMD: min 114.145 2.79265 2.30381 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 114.145 2.79265 2.30381 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 161.594 2.79265 2.30381 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 85 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 144.331\r\n> protocols.relax.FastRelax: CMD: repack 161.594 2.79265 2.30381 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 164.92 2.79265 2.30381 0.154\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -2163.08 Finite Diff= 116.62\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.64042e-07 Deriv= -2163.08 Finite Diff= 116.837\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 164.92 2.79265 2.30381 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 164.92 2.79265 2.30381 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 226.782 2.79265 2.30381 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 77 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 209.641\r\n> protocols.relax.FastRelax: CMD: repack 226.782 2.79265 2.30381 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 231.66 2.79265 2.30381 0.31955\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -48505.5 Finite Diff= 4854.28\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 5.7357e-12 Deriv= -155903 Finite Diff= -1980.87\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.93784e-07 Deriv= -1550.05 Finite Diff= -93.1044\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#10\r\n> protocols.relax.FastRelax: CMD: min 231.603 2.79181 2.30321 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 231.603 2.79181 2.30321 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 324.34 2.79181 2.30321 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 53 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 307.332\r\n> protocols.relax.FastRelax: CMD: repack 324.34 2.79181 2.30321 0.55\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -483332 Finite Diff= 9806.93\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 7.16248e-15 Deriv= -2.56615e+06 Finite Diff= 11023.5\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 2.89927e-09 Deriv= -92210.2 Finite Diff= 1861.16\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.80291e-11 Deriv= -447337 Finite Diff= -2370.16\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.62639e-07 Deriv= -2200.53 Finite Diff= -114.888\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#33\r\n> protocols.relax.FastRelax: CMD: min 323.399 2.78913 2.30077 0.55\r\n> protocols.relax.FastRelax: MRP: 2 323.399 321.792 2.8005 2.31562 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 323.399 2.78913 2.30077 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 323.399 2.78913 2.30077 0.55\r\n> protocols::checkpoint: Deleting checkpoints of FastRelax\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_2=======================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 0\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is not s6 symmetric.\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: Filter reports failure!\r\n> protocols.generalized_kinematic_closure.GeneralizedKIC: Preselection mover failed! Continuing to next solution.\r\n> protocols.generalized_kinematic_closure.GeneralizedKIC: Applying pre-selection mover to solution 2 from attempt 107.\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_1=======================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 0\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is not s6 symmetric.\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: Filter reports failure!\r\n> protocols.generalized_kinematic_closure.GeneralizedKIC: Preselection mover failed! Continuing to next solution.\r\n> protocols.generalized_kinematic_closure.GeneralizedKIC: Applying pre-selection mover to solution 1 from attempt 109.\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_1=======================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 1\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is s6 symmetric.\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER CrosslinkerMover - square_pyramidal_metal_link_1=======================\r\n> protocols.cyclic_peptide.CrosslinkerMover: Sidechain distance filter PASSED.\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> protocols.relax.FastRelax: CMD: repeat 2.62838e+06 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 2.62838e+06 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 2.62593e+06 0 0 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 84 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 306627\r\n> protocols.relax.FastRelax: CMD: repack 306635 0 0 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 306678 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: min 8373.53 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 8373.53 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 8758.07 0 0 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 66 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 8711.56\r\n> protocols.relax.FastRelax: CMD: repack 8758.07 0 0 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 8785.02 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: min 8782.57 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 8782.57 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 9277.98 0 0 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 62 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 9180.1\r\n> protocols.relax.FastRelax: CMD: repack 9277.98 0 0 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 9317.04 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: min 9313.26 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 9313.26 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 10046.9 0 0 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 56 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 9871.43\r\n> protocols.relax.FastRelax: CMD: repack 10046.9 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: min 10040.5 0 0 0.55\r\n> protocols.relax.FastRelax: MRP: 0 10040.5 10040.5 0 0 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 10040.5 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 10040.5 0 0 0.55\r\n> protocols::checkpoint: Deleting checkpoints of FastRelax\r\n> protocols.relax.FastRelax: CMD: repeat 10040.5 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 10040.5 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 8388.17 0 0 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 84 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 8381.05\r\n> protocols.relax.FastRelax: CMD: repack 8388.17 0 0 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 8407.1 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: min 8373.52 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 8373.52 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 8757.87 0 0 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 66 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 8711.93\r\n> protocols.relax.FastRelax: CMD: repack 8757.87 0 0 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 8784.81 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: min 8782.63 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 8782.63 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 9278.02 0 0 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 62 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 9180.49\r\n> protocols.relax.FastRelax: CMD: repack 9278.02 0 0 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 9317.08 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: min 9313.26 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 9313.26 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 10047 0 0 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 56 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 9871.59\r\n> protocols.relax.FastRelax: CMD: repack 10047 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: min 10040.5 0 0 0.55\r\n> protocols.relax.FastRelax: MRP: 0 10040.5 10040.5 0 0 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 10040.5 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 10040.5 0 0 0.55\r\n> protocols::checkpoint: Deleting checkpoints of FastRelax\r\n> protocols.relax.FastRelax: CMD: repeat 10040.5 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 10040.5 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 8388.17 0 0 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 84 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 8381\r\n> protocols.relax.FastRelax: CMD: repack 8388.17 0 0 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 8407.1 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: min 8373.54 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 8373.54 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 8758.08 0 0 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 66 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 8711.53\r\n> protocols.relax.FastRelax: CMD: repack 8758.08 0 0 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 8785.04 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: min 8782.56 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 8782.56 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 9278.03 0 0 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 62 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 9180.19\r\n> protocols.relax.FastRelax: CMD: repack 9278.03 0 0 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 9317.1 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: min 9313.25 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 9313.25 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 10047 0 0 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 56 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 9872.05\r\n> protocols.relax.FastRelax: CMD: repack 10047 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: min 10040.5 0 0 0.55\r\n> protocols.relax.FastRelax: MRP: 0 10040.5 10040.5 0 0 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 10040.5 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 10040.5 0 0 0.55\r\n> protocols::checkpoint: Deleting checkpoints of FastRelax\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper: Constraint energy for crosslinked pose is 8299.95. Filter passes.\r\n> protocols.cyclic_peptide.CrosslinkerMover: Linker constraints filter PASSED.\r\n> protocols.cyclic_peptide.CrosslinkerMover: CrosslinkerMover reports SUCCESS. Updating pose.\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - High_Hbond_FastRelax=======================\r\n> protocols.relax.FastRelax: CMD: repeat 10040.5 2.22394 0 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 10040.5 2.22394 0 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 8388.17 2.22394 0 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 109 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 8388.03\r\n> protocols.relax.FastRelax: CMD: repack 8388.17 2.22394 0 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 8407.1 2.22394 0 0.02805\r\n> protocols.relax.FastRelax: CMD: min 991.856 2.65673 2.14344 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 991.856 2.65673 2.14344 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1120.11 2.65673 2.14344 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 99 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1112.31\r\n> protocols.relax.FastRelax: CMD: repack 1120.11 2.65673 2.14344 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1129.1 2.65673 2.14344 0.154\r\n> protocols.relax.FastRelax: CMD: min 1086.42 2.47913 2.14955 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 1086.42 2.47913 2.14955 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1173.5 2.47913 2.14955 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 102 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1165.4\r\n> protocols.relax.FastRelax: CMD: repack 1173.5 2.47913 2.14955 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1180.37 2.47913 2.14955 0.31955\r\n> protocols.relax.FastRelax: CMD: min 1158.17 2.38315 2.15342 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 1158.17 2.38315 2.15342 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1246.74 2.38315 2.15342 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 102 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1238.48\r\n> protocols.relax.FastRelax: CMD: repack 1246.74 2.38315 2.15342 0.55\r\n> protocols.relax.FastRelax: CMD: min 1235.73 2.34397 2.1443 0.55\r\n> protocols.relax.FastRelax: MRP: 0 1235.73 1235.73 2.34397 2.1443 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 1235.73 2.34397 2.1443 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 1235.73 2.34397 2.1443 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 1235.73 2.34397 2.1443 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1072.08 2.34397 2.1443 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 149 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1064.38\r\n> protocols.relax.FastRelax: CMD: repack 1072.08 2.34397 2.1443 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1073.95 2.34397 2.1443 0.02805\r\n> protocols.relax.FastRelax: CMD: min 991.216 2.68156 2.18826 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 991.216 2.68156 2.18826 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1114.56 2.68156 2.18826 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 105 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1106.72\r\n> protocols.relax.FastRelax: CMD: repack 1114.56 2.68156 2.18826 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1123.21 2.68156 2.18826 0.154\r\n> protocols.relax.FastRelax: CMD: min 1083.2 2.50397 2.21626 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 1083.2 2.50397 2.21626 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1165.5 2.50397 2.21626 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 98 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1156.94\r\n> protocols.relax.FastRelax: CMD: repack 1165.5 2.50397 2.21626 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1171.99 2.50397 2.21626 0.31955\r\n> protocols.relax.FastRelax: CMD: min 1154.57 2.39995 2.1828 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 1154.57 2.39995 2.1828 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1242.74 2.39995 2.1828 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 93 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1234.92\r\n> protocols.relax.FastRelax: CMD: repack 1242.74 2.39995 2.1828 0.55\r\n> protocols.relax.FastRelax: CMD: min 1233.91 2.36707 2.17426 0.55\r\n> protocols.relax.FastRelax: MRP: 1 1233.91 1233.91 2.36707 2.17426 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 1233.91 2.36707 2.17426 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 1233.91 2.36707 2.17426 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 1233.91 2.36707 2.17426 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1068.36 2.36707 2.17426 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 154 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1060.12\r\n> protocols.relax.FastRelax: CMD: repack 1068.36 2.36707 2.17426 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1070.25 2.36707 2.17426 0.02805\r\n> protocols.relax.FastRelax: CMD: min 990.581 2.71258 2.21825 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 990.581 2.71258 2.21825 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1114.75 2.71258 2.21825 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 112 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1105.28\r\n> protocols.relax.FastRelax: CMD: repack 1114.75 2.71258 2.21825 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1123.45 2.71258 2.21825 0.154\r\n> protocols.relax.FastRelax: CMD: min 1082.26 2.47788 2.19263 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 1082.26 2.47788 2.19263 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1162.38 2.47788 2.19263 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 103 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1154.35\r\n> protocols.relax.FastRelax: CMD: repack 1162.38 2.47788 2.19263 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1168.7 2.47788 2.19263 0.31955\r\n> protocols.relax.FastRelax: CMD: min 1154.99 2.41383 2.17993 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 1154.99 2.41383 2.17993 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1243.64 2.41383 2.17993 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 98 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1235.53\r\n> protocols.relax.FastRelax: CMD: repack 1243.64 2.41383 2.17993 0.55\r\n> protocols.relax.FastRelax: CMD: min 1234.02 2.36591 2.16737 0.55\r\n> protocols.relax.FastRelax: MRP: 2 1234.02 1233.91 2.36707 2.17426 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 1234.02 2.36591 2.16737 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 1234.02 2.36591 2.16737 0.55\r\n> protocols::checkpoint: Deleting checkpoints of FastRelax\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_2=======================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 0\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is not s6 symmetric.\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: Filter reports failure!\r\n> protocols.generalized_kinematic_closure.GeneralizedKIC: Preselection mover failed! Continuing to next solution.\r\n> protocols.generalized_kinematic_closure.GeneralizedKIC: Applying pre-selection mover to solution 1 from attempt 111.\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_1=======================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 0\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is not s6 symmetric.\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: Filter reports failure!\r\n> protocols.generalized_kinematic_closure.GeneralizedKIC: Preselection mover failed! Continuing to next solution.\r\n> protocols.generalized_kinematic_closure.GeneralizedKIC: Applying pre-selection mover to solution 2 from attempt 111.\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_1=======================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 0\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is not s6 symmetric.\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: Filter reports failure!\r\n> protocols.generalized_kinematic_closure.GeneralizedKIC: Preselection mover failed! Continuing to next solution.\r\n> protocols.generalized_kinematic_closure.GeneralizedKIC: Applying pre-selection mover to solution 1 from attempt 114.\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_1=======================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 1\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is s6 symmetric.\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER CrosslinkerMover - square_pyramidal_metal_link_1=======================\r\n> protocols.cyclic_peptide.CrosslinkerMover: Sidechain distance filter PASSED.\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> protocols.relax.FastRelax: CMD: repeat 3.00262e+06 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 3.00262e+06 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 3e+06 0 0 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 106 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 223342\r\n> protocols.relax.FastRelax: CMD: repack 223362 0 0 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 223378 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: min 16594.8 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 16594.8 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 16763.2 0 0 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 98 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 16743.4\r\n> protocols.relax.FastRelax: CMD: repack 16763.2 0 0 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 16775 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: min 16774.9 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 16774.9 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 16994.2 0 0 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 96 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 16971.8\r\n> protocols.relax.FastRelax: CMD: repack 16994.2 0 0 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 17011.5 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: min 17009 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 17009 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 17334 0 0 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 82 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 17309.1\r\n> protocols.relax.FastRelax: CMD: repack 17334 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: min 17332.1 0 0 0.55\r\n> protocols.relax.FastRelax: MRP: 0 17332.1 17332.1 0 0 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 17332.1 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 17332.1 0 0 0.55\r\n> protocols::checkpoint: Deleting checkpoints of FastRelax\r\n> protocols.relax.FastRelax: CMD: repeat 17332.1 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 17332.1 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 16596.2 0 0 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 106 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 16579.1\r\n> protocols.relax.FastRelax: CMD: repack 16596.2 0 0 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 16604.6 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: min 16594.9 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 16594.9 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 16763.3 0 0 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 98 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 16743.4\r\n> protocols.relax.FastRelax: CMD: repack 16763.3 0 0 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 16775.1 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: min 16774.7 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 16774.7 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 16993.4 0 0 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 96 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 16971.3\r\n> protocols.relax.FastRelax: CMD: repack 16993.4 0 0 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 17010.6 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: min 17009 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 17009 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 17334 0 0 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 82 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 17307.7\r\n> protocols.relax.FastRelax: CMD: repack 17334 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: min 17332 0 0 0.55\r\n> protocols.relax.FastRelax: MRP: 0 17332 17332 0 0 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 17332 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 17332 0 0 0.55\r\n> protocols::checkpoint: Deleting checkpoints of FastRelax\r\n> protocols.relax.FastRelax: CMD: repeat 17332 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 17332 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 16596.6 0 0 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 106 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 16578.7\r\n> protocols.relax.FastRelax: CMD: repack 16596.6 0 0 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 16605 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: min 16594.8 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 16594.8 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 16763.2 0 0 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 98 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 16743.1\r\n> protocols.relax.FastRelax: CMD: repack 16763.2 0 0 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 16775 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: min 16774.9 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 16774.9 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 16994.3 0 0 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 96 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 16970.9\r\n> protocols.relax.FastRelax: CMD: repack 16994.3 0 0 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 17011.6 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: min 17009 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 17009 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 17334 0 0 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 82 rotamers at 5 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 17308\r\n> protocols.relax.FastRelax: CMD: repack 17334 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: min 17332.1 0 0 0.55\r\n> protocols.relax.FastRelax: MRP: 0 17332.1 17332.1 0 0 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 17332.1 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 17332.1 0 0 0.55\r\n> protocols::checkpoint: Deleting checkpoints of FastRelax\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> core.scoring.constraints.ConstraintsIO: Read in 1 constraints\r\n> protocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper: Constraint energy for crosslinked pose is 16558.1. Filter passes.\r\n> protocols.cyclic_peptide.CrosslinkerMover: Linker constraints filter PASSED.\r\n> protocols.cyclic_peptide.CrosslinkerMover: CrosslinkerMover reports SUCCESS. Updating pose.\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - High_Hbond_FastRelax=======================\r\n> protocols.relax.FastRelax: CMD: repeat 17332.1 1.04652 0 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 17332.1 1.04652 0 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 16596.7 1.04652 0 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 131 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 16596.7\r\n> protocols.relax.FastRelax: CMD: repack 16596.7 1.04652 0 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 16605.1 1.04652 0 0.02805\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 2.38419e-07 Deriv= -1406.55 Finite Diff= 84.7169\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 6.54021e-09 Deriv= -5.00869e+09 Finite Diff= 5.76431e+08\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 7.83508e-09 Deriv= -4.08442e+06 Finite Diff= 4589.49\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 8.94238e-09 Deriv= -249523 Finite Diff= 1198.21\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 9.49466e-09 Deriv= -263346 Finite Diff= 1251.32\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 8.07309e-08 Deriv= -8931.01 Finite Diff= -888.019\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#101\r\n> protocols.relax.FastRelax: CMD: min -10.6087 2.77154 2.3015 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight -10.6087 2.77154 2.3015 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 25.1409 2.77154 2.3015 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 103 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 22.4941\r\n> protocols.relax.FastRelax: CMD: repack 25.1409 2.77154 2.3015 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 27.6467 2.77154 2.3015 0.154\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -9062.11 Finite Diff= -831.141\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 8.01448e-08 Deriv= -9062.11 Finite Diff= -829.136\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 27.6467 2.77154 2.3015 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 27.6467 2.77154 2.3015 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 74.2549 2.77154 2.3015 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 98 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 70.6602\r\n> protocols.relax.FastRelax: CMD: repack 74.2549 2.77154 2.3015 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 77.9301 2.77154 2.3015 0.31955\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 4.54747e-15 Deriv= -249884 Finite Diff= 6553.12\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 8.48963e-08 Deriv= -8076.12 Finite Diff= -296.718\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#30\r\n> protocols.relax.FastRelax: CMD: min 77.6588 2.77045 2.30034 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 77.6588 2.77045 2.30034 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 147.38 2.77045 2.30034 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 93 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 144.781\r\n> protocols.relax.FastRelax: CMD: repack 147.38 2.77045 2.30034 0.55\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -1.02874e+06 Finite Diff= 8291.8\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.04544e-07 Deriv= -5325.74 Finite Diff= -146.807\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#11\r\n> protocols.relax.FastRelax: CMD: min 144.573 2.76132 2.29017 0.55\r\n> protocols.relax.FastRelax: MRP: 0 144.573 144.573 2.76132 2.29017 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 144.573 2.76132 2.29017 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 144.573 2.76132 2.29017 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 144.573 2.76132 2.29017 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep -9.44802 2.76132 2.29017 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 122 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: -12.1504\r\n> protocols.relax.FastRelax: CMD: repack -9.44802 2.76132 2.29017 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep -7.6832 2.76132 2.29017 0.02805\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 4.54747e-15 Deriv= -834501 Finite Diff= 60.1562\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 7.45164e-09 Deriv= -1.64041e+07 Finite Diff= 623666\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 9.56743e-09 Deriv= -156834 Finite Diff= 6289.67\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 8.1573e-08 Deriv= -8747.57 Finite Diff= -812.125\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#31\r\n> protocols.relax.FastRelax: CMD: min -9.72628 2.75848 2.28581 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight -9.72628 2.75848 2.28581 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 25.1832 2.75848 2.28581 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 104 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 21.7158\r\n> protocols.relax.FastRelax: CMD: repack 25.1832 2.75848 2.28581 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 27.6301 2.75848 2.28581 0.154\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -8602.6 Finite Diff= -410.242\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 8.22574e-08 Deriv= -8602.6 Finite Diff= -408.149\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 27.6301 2.75848 2.28581 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 27.6301 2.75848 2.28581 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 73.1429 2.75848 2.28581 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 98 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 69.7695\r\n> protocols.relax.FastRelax: CMD: repack 73.1429 2.75848 2.28581 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 76.7318 2.75848 2.28581 0.31955\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -9184.53 Finite Diff= -651.435\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 7.96089e-08 Deriv= -9184.53 Finite Diff= -649.615\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 76.7318 2.75848 2.28581 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 76.7318 2.75848 2.28581 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 145.083 2.75848 2.28581 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 93 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 142.725\r\n> protocols.relax.FastRelax: CMD: repack 145.083 2.75848 2.28581 0.55\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 2.38419e-07 Deriv= -243.349 Finite Diff= -5.78326\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.78499e-09 Deriv= -2265.6 Finite Diff= 299.482\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.57872e-09 Deriv= -4793.48 Finite Diff= 162.752\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 5.35467e-11 Deriv= -8438.11 Finite Diff= -398.375\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.52358e-09 Deriv= -5254.48 Finite Diff= 98.3818\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 4.08484e-09 Deriv= -11340.9 Finite Diff= 1945.03\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.43049e-07 Deriv= -2844.54 Finite Diff= -274.66\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#84\r\n> protocols.relax.FastRelax: CMD: min 24.1857 2.68923 2.21939 0.55\r\n> protocols.relax.FastRelax: MRP: 1 24.1857 24.1857 2.68923 2.21939 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 24.1857 2.68923 2.21939 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 24.1857 2.68923 2.21939 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 24.1857 2.68923 2.21939 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep -25.8118 2.68923 2.21939 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 118 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: -28.7646\r\n> protocols.relax.FastRelax: CMD: repack -25.8118 2.68923 2.21939 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep -25.2389 2.68923 2.21939 0.02805\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 4.76837e-09 Deriv= -23302.4 Finite Diff= 657.54\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.44637e-07 Deriv= -2782.41 Finite Diff= 84.7345\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#6\r\n> protocols.relax.FastRelax: CMD: min -25.334 2.6887 2.21881 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight -25.334 2.6887 2.21881 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep -14.1895 2.6887 2.21881 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 104 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: -17.125\r\n> protocols.relax.FastRelax: CMD: repack -14.1895 2.6887 2.21881 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep -13.4084 2.6887 2.21881 0.154\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -2565.79 Finite Diff= 236.248\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.50619e-07 Deriv= -2565.79 Finite Diff= 237.237\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min -13.4084 2.6887 2.21881 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight -13.4084 2.6887 2.21881 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 1.12102 2.6887 2.21881 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 100 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: -1.93384\r\n> protocols.relax.FastRelax: CMD: repack 1.12102 2.6887 2.21881 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 2.2667 2.6887 2.21881 0.31955\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -2357.33 Finite Diff= 360.517\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.57137e-07 Deriv= -2357.33 Finite Diff= 361.426\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 2.2667 2.6887 2.21881 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 2.2667 2.6887 2.21881 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 24.0869 2.6887 2.21881 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 97 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 21.0938\r\n> protocols.relax.FastRelax: CMD: repack 24.0869 2.6887 2.21881 0.55\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -2211.37 Finite Diff= 389.296\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.6224e-07 Deriv= -2211.37 Finite Diff= 390.093\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 24.0869 2.6887 2.21881 0.55\r\n> protocols.relax.FastRelax: MRP: 2 24.0869 24.0869 2.6887 2.21881 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 24.0869 2.6887 2.21881 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 24.0869 2.6887 2.21881 0.55\r\n> protocols::checkpoint: Deleting checkpoints of FastRelax\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_2=======================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 1\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is s6 symmetric.\r\n> protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\r\n> protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\r\n> protocols.rosetta_scripts.ParsedProtocol: setting status to success\r\n> protocols.generalized_kinematic_closure.GeneralizedKIC: Storing solution 1 from attempt 114.\r\n> protocols.generalized_kinematic_closure.selector.GeneralizedKICselector: Choosing GeneralizedKIC solution.\r\n> protocols.generalized_kinematic_closure.GeneralizedKIC: Closure successful.\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Closure successful.\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Setting up terminal bond between residue 1, atom N and residue 30, atom C .\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Applying final FastRelax, round 1.\r\n> protocols.relax.FastRelax: CMD: repeat 133.846 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 133.846 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 83.5637 0 0 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 118 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 83.5417\r\n> protocols.relax.FastRelax: CMD: repack 83.5637 0 0 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 84.1398 0 0 0.02805\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -2641.5 Finite Diff= 144.039\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.48445e-07 Deriv= -2641.5 Finite Diff= 144.996\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 84.1398 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 84.1398 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 95.3486 0 0 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 110 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 95.373\r\n> protocols.relax.FastRelax: CMD: repack 95.3486 0 0 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 96.1343 0 0 0.154\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -2411.12 Finite Diff= 311.217\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.55375e-07 Deriv= -2411.12 Finite Diff= 312.085\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 96.1343 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 96.1343 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 110.748 0 0 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 106 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 112.252\r\n> protocols.relax.FastRelax: CMD: repack 110.748 0 0 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 111.9 0 0 0.31955\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -2188.99 Finite Diff= 450.297\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.63068e-07 Deriv= -2188.99 Finite Diff= 451.04\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 111.9 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 111.9 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 133.846 0 0 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 105 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 135.312\r\n> protocols.relax.FastRelax: CMD: repack 133.846 0 0 0.55\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -2032.33 Finite Diff= 491.356\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.69236e-07 Deriv= -2032.33 Finite Diff= 491.934\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 133.846 0 0 0.55\r\n> protocols.relax.FastRelax: MRP: 0 133.846 133.846 0 0 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 133.846 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 133.846 0 0 0.55\r\n> protocols::checkpoint: Deleting checkpoints of FastRelax\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Applying final FastRelax, round 2.\r\n> protocols.relax.FastRelax: CMD: repeat 133.846 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 133.846 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 83.5637 0 0 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 118 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 83.2837\r\n> protocols.relax.FastRelax: CMD: repack 83.5637 0 0 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 84.1398 0 0 0.02805\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -2641.5 Finite Diff= 144.039\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.48445e-07 Deriv= -2641.5 Finite Diff= 144.996\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 84.1398 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 84.1398 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 95.3486 0 0 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 110 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 95.3652\r\n> protocols.relax.FastRelax: CMD: repack 95.3486 0 0 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 96.1343 0 0 0.154\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -2411.12 Finite Diff= 311.217\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.55375e-07 Deriv= -2411.12 Finite Diff= 312.085\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 96.1343 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 96.1343 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 110.748 0 0 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 106 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 110.734\r\n> protocols.relax.FastRelax: CMD: repack 110.748 0 0 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 111.9 0 0 0.31955\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -2188.99 Finite Diff= 450.297\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.63068e-07 Deriv= -2188.99 Finite Diff= 451.04\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 111.9 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 111.9 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 133.846 0 0 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 105 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 134.29\r\n> protocols.relax.FastRelax: CMD: repack 133.846 0 0 0.55\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -2032.33 Finite Diff= 491.356\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.69236e-07 Deriv= -2032.33 Finite Diff= 491.934\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 133.846 0 0 0.55\r\n> protocols.relax.FastRelax: MRP: 0 133.846 133.846 0 0 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 133.846 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 133.846 0 0 0.55\r\n> protocols::checkpoint: Deleting checkpoints of FastRelax\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Applying final FastRelax, round 3.\r\n> protocols.relax.FastRelax: CMD: repeat 133.846 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 133.846 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 83.5637 0 0 0.022\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 118 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 85.6885\r\n> protocols.relax.FastRelax: CMD: repack 83.5637 0 0 0.022\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 84.1398 0 0 0.02805\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -2641.5 Finite Diff= 144.039\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.48445e-07 Deriv= -2641.5 Finite Diff= 144.996\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 84.1398 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 84.1398 0 0 0.02805\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 95.3486 0 0 0.14575\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 110 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 95.3494\r\n> protocols.relax.FastRelax: CMD: repack 95.3486 0 0 0.14575\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 96.1343 0 0 0.154\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -2411.12 Finite Diff= 311.217\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.55375e-07 Deriv= -2411.12 Finite Diff= 312.085\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 96.1343 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 96.1343 0 0 0.154\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 110.748 0 0 0.30745\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 106 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 110.661\r\n> protocols.relax.FastRelax: CMD: repack 110.748 0 0 0.30745\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 111.9 0 0 0.31955\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -2188.99 Finite Diff= 450.297\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.63068e-07 Deriv= -2188.99 Finite Diff= 451.04\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 111.9 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: coord_cst_weight 111.9 0 0 0.31955\r\n> protocols.relax.FastRelax: CMD: scale:fa_rep 133.846 0 0 0.55\r\n> core.pack.task: Packer task: initialize from command line() \r\n> core.pack.pack_rotamers: built 105 rotamers at 30 positions.\r\n> core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\r\n> core.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 133.851\r\n> protocols.relax.FastRelax: CMD: repack 133.846 0 0 0.55\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -2032.33 Finite Diff= 491.356\r\n> core.optimization.LineMinimizer: Inaccurate G in step= 1.69236e-07 Deriv= -2032.33 Finite Diff= 491.934\r\n> core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\r\n> protocols.relax.FastRelax: CMD: min 133.846 0 0 0.55\r\n> protocols.relax.FastRelax: MRP: 0 133.846 133.846 0 0 \r\n> protocols.relax.FastRelax: CMD: accept_to_best 133.846 0 0 0.55\r\n> protocols.relax.FastRelax: CMD: endrepeat 133.846 0 0 0.55\r\n> protocols::checkpoint: Deleting checkpoints of FastRelax\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Final symmetry filter passes. This peptide has s6symmetry.\r\n> protocols.cyclic_peptide.PeptideInternalHbondsMetric: No scorefunction was provided to the PeptideInternalHbondsMetric. Fetching default scorefunction.\r\n> core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\r\n> protocols.cyclic_peptide.PeptideInternalHbondsMetric: Counted 9 hbonds in pose.\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega1=-176.69\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega2=-170.678\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega3=177.83\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega4=-171.056\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega5=-176.853\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega6=166.531\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega7=176.461\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega8=-162.029\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega9=176.824\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega10=148.673\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega11=-169.712\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega12=-178.091\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega13=175.692\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega14=-171.799\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega15=177.622\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega16=168.646\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega17=174.257\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega18=177.36\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega19=166.383\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega20=173.856\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega21=-179.561\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega22=-174.75\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega23=176.914\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega24=-175.113\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega25=-177.944\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega26=163.808\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega27=162.182\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega28=-177.914\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega29=179.739\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: omega30=180\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Result\tRMSD\tEnergy\tHbonds\tCisPepBonds\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: 1\t3.76034\t128.369\t9\t0\r\n> protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: 1 jobs attempted. 1 jobs returned solutions.\r\n> basic.citation_manager.CitationManager: \r\n> The following Rosetta modules were used during this run of Rosetta, and should be cited:\r\n> \r\n> simple_cycpep_predict Application's citation(s):\r\n> *Bhardwaj G, *Mulligan VK, *Bahl G, Gilmore JM, Harvey PJ, Cheneval O, Buchko GW, Pulavarti SVSRK, Kaas Q, Eletsky A, Huang P-S, Johnsen PS, Greisen P Jr., Rocklin GJ, Song Y, Linsky TW, Watkins A, Rettie SA, Xu X, Carter LP, Bonneau R, Olson JM, Coutsias E, Correnti CE, Szyperski T, Craik DJ, and Baker D. (2016). Accurate de novo design of hyperstable constrained peptides. Nature 538(7625):329-35. doi: 10.1038/nature19791. (*Co-primary authors.)\r\n> \r\n> *Hosseinzadeh P, *Bhardwaj G, *Mulligan VK, Shortridge MD, Craven TW, Pardo-Avila F, Rettie SA, Kim DA, Silva D-A, Ibrahim YM, Webb IK, Cort JR, Adkins JN, Varani G, and Baker D. (2017). Comprehensive computational design of ordered peptide macrocycles. Science 358(6369):1461-6. doi: 10.1126/science.aap7577. (*Co-primary authors.)\r\n> \r\n> Mulligan VK, Workman S, Sun T, Rettie S, Li X, Worrall LJ, Craven TW, King DT, Hosseinzadeh P, Watkins AM, Renfrew PD, Guffy S, Labonte JW, Moretti R, Bonneau R, Strynadka NCJ, and Baker D. (2021). Computationally designed peptide macrocycle inhibitors of New Delhi metallo-\u03b2-lactamase 1. Proc Natl Acad Sci USA 118(12). doi: 10.1073/pnas.2012800118.\r\n> \r\n> \r\n> apps.public.cyclic_peptide.simple_cycpep_predict: Finished simple_cycpep_predict.cc. Exiting.\r\nOnly in /home/benchmark/working_dir/master:62041/simple_cycpep_predict_square_pyramidal_metal: S_0001.pdb\r\nOnly in /home/benchmark/working_dir/master:62040/simple_cycpep_predict_square_pyramidal_metal: .test_got_timeout_kill.log\r\n",
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"state": "passed"
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"simple_cycpep_predict_tbmb": {
"log": "",
"state": "passed"
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"simple_cycpep_predict_terminal_disulfide": {
"log": "",
"state": "passed"
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"simple_cycpep_predict_terminal_disulfide_internal_permutations": {
"log": "",
"state": "passed"
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"log": "",
"state": "passed"
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"log": "",
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"simple_cycpep_predict_tetrahedral_metal": {
"log": "",
"state": "passed"
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"simple_cycpep_predict_tetrahedral_metal_asp": {
"log": "",
"state": "passed"
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"log": "",
"state": "passed"
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"simple_cycpep_predict_thioether_lariat": {
"log": "",
"state": "passed"
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"log": "",
"state": "passed"
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"simple_cycpep_predict_trigonal_planar_metal": {
"log": "",
"state": "passed"
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"state": "passed"
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"simple_dna_test": {
"log": "",
"state": "passed"
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"simple_glycosylation": {
"log": "",
"state": "passed"
},
"simple_glycosylation_alternate_AAs": {
"log": "",
"state": "passed"
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"simple_grafting_movers": {
"log": "",
"state": "passed"
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"simple_hbondstoatom": {
"log": "",
"state": "passed"
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"simple_metric_cache": {
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"state": "passed"
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"simple_metric_features": {
"log": "",
"state": "passed"
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"simple_metric_filter": {
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"simple_metrics": {
"log": "",
"state": "passed"
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"simple_metrics_in_protocols": {
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"simple_metrics_per_residue": {
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"state": "passed"
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"site_constraint": {
"log": "",
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"small_molecule_lattice_dock": {
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"state": "passed"
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"smallmover_resselector": {
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"state": "passed"
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"smart_annealer": {
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"splice_in_4loops_longer": {
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"state": "passed"
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"splice_out_H1_H2_longer": {
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"swa_protein_cluster": {
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"swm_rna_nickedhelix": {
"log": "",
"state": "passed"
},
"swm_rna_protonated_adenosine": {
"log": "",
"state": "passed"
},
"swm_rna_singleloop": {
"log": "",
"state": "passed"
},
"swm_rna_srl_triplet": {
"log": "",
"state": "passed"
},
"symm_disulfidize": {
"log": "",
"state": "passed"
},
"symm_rotamer_boltzmann": {
"log": "",
"state": "passed"
},
"symmetric_cycpep_align_and_symmetrize": {
"log": "",
"state": "passed"
},
"symmetric_docking": {
"log": "",
"state": "passed"
},
"symmetrical_residue_selector": {
"log": "",
"state": "passed"
},
"symmetry_data_resource": {
"log": "",
"state": "passed"
},
"symmetry_multicomponent": {
"log": "",
"state": "passed"
},
"target_clash": {
"log": "",
"state": "passed"
},
"task_selector": {
"log": "",
"state": "passed"
},
"tcrmodel": {
"log": "",
"state": "passed"
},
"template_features": {
"log": "",
"state": "passed"
},
"tensorflow_connection_test": {
"log": "",
"state": "passed"
},
"tensorflow_manager": {
"log": "",
"state": "passed"
},
"tensorflow_simple_model_load_and_evaluate": {
"log": "",
"state": "passed"
},
"test1_benchmark": {
"log": "",
"state": "passed"
},
"test_computed_saxs_spectrum": {
"log": "",
"state": "passed"
},
"test_d_l_readin": {
"log": "",
"state": "passed"
},
"test_degreaser": {
"log": "",
"state": "passed"
},
"test_energy_method_options": {
"log": "",
"state": "passed"
},
"test_idealize": {
"log": "",
"state": "passed"
},
"test_rosetta_thread_manager_advanced_API": {
"log": "",
"state": "passed"
},
"test_rosetta_thread_manager_basic_API": {
"log": "",
"state": "passed"
},
"thermal_sampler": {
"log": "",
"state": "passed"
},
"thread_local_tracers_check": {
"log": "",
"state": "passed"
},
"threefold_symm_peptide_design": {
"log": "",
"state": "passed"
},
"threefoldlinkermover_tbmb": {
"log": "",
"state": "passed"
},
"threefoldlinkermover_tbmb_symmetric": {
"log": "",
"state": "passed"
},
"tna_base_pairs": {
"log": "",
"state": "passed"
},
"torsion_restricted_sampling": {
"log": "",
"state": "passed"
},
"trRosetta": {
"log": "",
"state": "passed"
},
"trRosettaConstraintGenerator": {
"log": "",
"state": "passed"
},
"trRosettaConstraintGenerator_rosettascripts": {
"log": "",
"state": "passed"
},
"trRosettaProtocolMover": {
"log": "",
"state": "passed"
},
"trRosettaProtocolMover_rosettascripts": {
"log": "",
"state": "passed"
},
"trRosettaProtocolMover_rosettascripts_diskwrite": {
"log": "",
"state": "passed"
},
"trRosettaProtocolMover_rosettascripts_diskwrite_only": {
"log": "",
"state": "passed"
},
"trRosetta_test_predict": {
"log": "",
"state": "passed"
},
"trRosetta_test_predict_ubiquitin": {
"log": "",
"state": "passed"
},
"trRosetta_test_predict_ubiquitin_cst_file_write": {
"log": "",
"state": "passed"
},
"trRosetta_test_predict_ubiquitin_cst_file_write_only": {
"log": "",
"state": "passed"
},
"trRosetta_test_predict_ubiquitin_init_by_bins": {
"log": "",
"state": "passed"
},
"unfolded_state_energy_calc": {
"log": "",
"state": "passed"
},
"validate_database": {
"log": "",
"state": "passed"
},
"vancomycin": {
"log": "",
"state": "passed"
},
"vip": {
"log": "",
"state": "passed"
},
"voids_penalty_energy_design": {
"log": "",
"state": "passed"
},
"voids_penalty_energy_design_symmetry": {
"log": "",
"state": "passed"
},
"write_mol_file": {
"log": "",
"state": "passed"
},
"zinc_heterodimer": {
"log": "",
"state": "passed"
},
"zinc_homodimer_design": {
"log": "",
"state": "passed"
},
"zinc_homodimer_setup": {
"log": "",
"state": "passed"
}
}
}