Test: linux.clang.integration.release_debug_no_symbols 「view this page in B3 βῆτα server」
Branch: master 「revision: №62041」
Test files: 「file-system-view」 「file-list-view」
Daemon: hojo-4     Started at: 2023-08-30 16:44:27     Run time: 1:04:12      State: failed

Failed sub-tests (click for more details):
ddG_of_mutation dgdp_script energy_based_clustering_alpha_aa_scorefile glycan_tree_relax ligand_dock_ensemble simple_cycpep_predict_square_pyramidal_metal

AddConstraintsToCurrentConformationMover AlignPDBInfoToSequences AlterSpecDisruption AnchorFinder AnchoredDesign AnchoredPDBCreator BFactorSelector BuildPeptide CCD_loop_closure CCS_PARCS ConsensusLoopDesign ContactMolecularSurface DARC_electrostatics DARC_make_ray_files DARC_sampling_on_the_fly DARC_shapeonly DNA_methylation DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FavorSequenceProfileMover FilterReportAsPoseExtraScoresMover FlipChirality FloppyTail HDXEnergy HOW_TO_MAKE_TESTS HelixBendFilter InterfaceAnalyzer InterfaceAnalyzer_allscores InterfaceAnalyzer_bothpack InterfaceAnalyzer_ligand InterfaceAnalyzer_prepack InterfaceAnalyzer_resfile InterfaceAnalyzer_tracer InterfaceDdG KIC_refine KIC_vicinity KIC_with_fragments LayerDesign LayerDesign_symm LayerSelector LoopAnalyzer LoopLengthChange ModifyVariantTypeMover MutateResidue_selector N-terminal_acetylation OversaturatedHbondAcceptorFilter PDB_diagnostic PTMPrediction PeptideCyclizeMover PeptideStubMover_prependRepeat PolarDesign2019 ProQ RBOut ReadResfile_with_selector RescorePDDF RescoreSAXS ResidueDisorder RunSimpleMetric_b_factor_test SID_ERMS_prediction SID_rescore SSElementSelector SecondaryStructureFilter SnugDock StrandCurvatureByLevels StrandHelixGeometryFilter ThreadingInputter TryDisulfPermutations UBQ_E2_thioester UBQ_E2_thioester_extra_bodies UBQ_E2_thioester_two_ubiquitins UBQ_Gp_CYD-CYD UBQ_Gp_LYX-Cterm UnsatSelector Werror_check abinitio abinitio_with_trRosetta add_constraints_to_current_conformation add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data angle_recovery_stats antibody_H3 antibody_H3_camelid antibody_cc antibody_designer antibody_designer_camelid antibody_designer_xml antibody_graft antibody_numbering_converter app_exception_handling assemble_domains_jd2 auto-drrafter_final_results auto-drrafter_setup_run_R1 auto-drrafter_setup_run_R2 auto-drrafter_setup_run_R3 autoNOE_rosetta autosetup_metals_centroid backbonegridsampler backbonegridsampler_multiresidue backbonegridsampler_nstruct_mode backrub backrub_interface_ddG backrub_pilot balancedKIC basic_gcn_tensorflow_test batch_relax beta_strand_homodimer bin_initialization bin_perturbation binselector binselector_probins broker broker_membrane bundlegridsampler bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_multirepeat bundlegridsampler_z0_offset bundlegridsampler_z1_offset bundlereporter_filter burial_measure_centroid buried_area_filter buried_unsat_kinemage buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm c-term_conjugation calculate_sasa carbohydrates cart_min_glycans cartesianddg case_sensitive_filenames ccd_ends_graft_mover_rs central_class_modification centroid_disulfide_scores centroid_from_fullatom cl_complex_rescore classic_relax_1a19 cleanAlignment cluster cluster_alns cluster_calibur cluster_filter cmaes_minimizer coarse_rna_scoring code_template_tests_app code_template_tests_citations code_template_tests_src code_template_tests_unit coenzymes combine_silent composition_energy_layers constel constraints_metric contactMap control_flow_rs copy_rotamer_mover count_cycpep_sequences coupled_moves crankshaft_flip create_clash-based_repack_shell create_sequence_motif crossaln crosslinkermover_1_4_bbmb_asymm crosslinkermover_1_4_bbmb_c2_symmetry crosslinkermover_1_4_bbmb_s2_symm crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_thioether crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cs_rosetta_rna cst_info cstfile_to_theozyme_pdb custom_basetype_packer_palette cyclization cycpep_design_pipeline cycpep_rdkit_metric cycpep_rigid_body_permutation_mover cycpep_symmetry_filter d_workflow database_jd2_compact_io database_jd2_io database_md5 database_session_resource ddG_ensemble ddG_of_mutation ddG_scan ddG_sym density_denovo density_refine density_refine_symm density_tools design_glycans design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA dgdp_aio dgdp_script distances disulfidize_beta_cys dna_interface_design dock_glycans dock_with_hotspot_place_simultaneously docking_distance_constraints docking_ensemble docking_ensemble_prepack docking_full_protocol docking_local_refine docking_local_refine_min docking_low_res docking_prepack docking_site_constraints doug_dock_design_min_mod2_cal_cal drrafter_error_estimation drrafter_run drrafter_setup drrafter_setup_build_missing drrafter_setup_protein_dock drrafter_setup_real_test_H drrafter_setup_real_test_H_no_init drrafter_setup_ribosome_test drrafter_setup_simple duplicate_header_guards energy_based_clustering_alpha_aa energy_based_clustering_alpha_aa_bin_analysis energy_based_clustering_alpha_aa_dihedral energy_based_clustering_alpha_aa_scorefile entropy_correction enumerative_sampling enzdes enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym erraser_minimize esm_model_perplexity evolution exclusively_shared_jumps explicit_membrane extract_atomtree_diffs extract_pdbs farfar_mrna farnesyl fast_relax fast_relax_scripts favor_coupling_tensor favor_native_residue features features_database_schema features_parallel features_pdb features_pdb_mpi features_postgres features_scientific_benchmark fiber_diffraction fiber_diffraction_fad fit_helixparams fit_helixparams_a3b fit_helixparams_rms fix_alignment_to_match_pdb fixbb flexpepdock flexpepdock_abinitio fold_and_dock fold_cst_new fold_from_loops fragment_picker fragmentpicker_integration_demo fuzzy ga_ligand_dock ga_ligand_dock_amino_acid ga_ligand_dock_macrocycle gen_apo_grids gen_lig_grids generate_6Dloopclose genkic_bin_perturbing genkic_bin_sampling genkic_bin_setting genkic_dihedral_copying genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars geometric_solvation glycan_anomers glycan_clash_check glycan_refinment glycan_relax glycan_sequon_scanner glycan_tree_relax glycomutagenesis glycopeptidedocking glycopeptidedocking_diglyco_long glycosylation grid_scores_features hbnet hbnet_asymm hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm hbnet_use_input_rot hbonds hbonds_sp2 hbondstoresidue_selector hbs_design header_using_check helical_bundle helical_bundle_nonideal helical_bundle_predict helical_bundle_predict_psipred helical_bundle_predict_psipred_with_helix_globals helical_bundle_predict_sequence helical_bundle_predict_skipping_residues helix_from_sequence hierarchical_clustering homodimer_fnd_ref2015_memb hotspot_graft hotspot_hashing hotspot_stub_constraints hshash_utils hts_io hybridization hydrate hydrate_relax identify_cdr_clusters ig_dump include_cc_check interaction_graph_summary_metric interface_energy inv_kin_lig_loop_design iphold jd2test_PDBIO jd2test_PDBin_mmCIFout jd2test_PDBin_mmCIFout_extra_data_separate jd2test_mmCIFIO jd2test_mmCIFin_PDBout job_definition_script_vars jrelax jscore kinemage_grid_output kinematic_looprelax ld_converter ligand_database_io ligand_dock_7cpa ligand_dock_cholesterol ligand_dock_ensemble ligand_dock_grid ligand_dock_script ligand_motif_design ligand_motif_discovery ligand_motif_identification ligand_water_docking longest_continuous_polar_segment_filter loop_creation loop_grower_N_term_symm loop_hash loop_modeling make_and_perturb_bundle_multirepeat make_exemplar make_mainchain_potential make_mainchain_potential_symm make_mainchain_potential_symm_preproline make_rot_lib make_symmdef_file match_1c2t match_1n9l match_6cpa match_xml measure_lcaa_radii membrane_abinitio metal_setup metalloprotein_abrelax metalloprotein_broker metropolis_hastings mf_fixbb_des mf_fixbb_sc mf_flexbb_sc mg_modeler mg_modeler_lores mhc_epitope mhc_epitope_nmer_preload min_pack_min minimize_6Dloopclose minimize_with_elec_dens mirror_symm mixed_monte_carlo mm_params mmtfIO_score_test molfile_to_params molfile_to_params_polymer motif_dna_packer_design motif_extraction motif_score_filter mp_dock mp_dock_ensemble mp_dock_prepack mp_dock_setup mp_domain_assembly mp_domain_assembly_FtsQ mp_find_interface mp_interface_statistics mp_ligand_interface mp_loadtime mp_mutate_relax mp_mutate_repack mp_quick_relax mp_quick_relax_ref2015_memb mp_range_relax mp_relax mp_score_jd2 mp_span_ang_ref2015_memb mp_span_from_pdb mp_symdock mp_symmetry_load mp_transform mp_transform_optimize mp_vis_emb mpi_multistate_design mpi_simple_cycpep_predict mpi_simple_cycpep_predict_4level mpi_simple_cycpep_predict_computing_pnear_to_all mpil_find_pore_ahelical mpil_find_pore_bbarrel mpil_load_implicit_lipids mr_protocols multistage_rosetta_scripts multistage_rosetta_scripts_clustering multithreaded_fastdesign multithreaded_fixbb multithreaded_interaction_graph_accuracy multithreaded_interaction_graph_accuracy_symm multithreaded_packrotamersmover mutate ncaa_fixbb ncbb_packer_palette netcharge_design netcharge_design_symm next_generation_KIC noe_assignment non-canonical_connectivities nonideal_rtmin nucleobase_sample_around number_of_residuetypes oligourea_design oligourea_predict oop_create oop_design oop_dock_design orbitals output_schema pH_mode pepspec_anchor_dock peptiderive per_residue_energies per_residue_sc_sasa per_residue_solvent_exposure pertmin perturb_helical_bundle perturb_helical_bundle_copying_pitch perturb_helical_bundle_epsilon perturb_helical_bundle_setting perturb_helical_bundle_z_offset phiselector phosphonate phosphorylation place_simultaneously pmut_scan pna pna_base_pairs pocket_measure pocket_relax pocket_suggest_targets polyaramid_test_trivial pose_sewing posttranslationalmod_io ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric pwsho pymol_cif r_pdb2top r_rmsf ralford_dump_rotamers rama_mutation_selector range_relax_w_cst rb_recces rdkit_metrics read_polymeric_components readin_dna_rna_protein real_virt_mover recces_turner recon_design recon_design_mpi referencepose_mutateresidue relax_w_allatom_cst remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens repeat_propagate repeat_propagate_v2 repeat_propagate_v3 repeat_relax replica_docking report_hbonds_for_plugin res_lipo_ref2015_memb residue_energy_breakdown resource_database_locator restype_converter rings rna_add_WC_stats rna_assemble rna_cluster rna_denovo rna_denovo_RNP_low_res rna_denovo_RNP_refine_native rna_denovo_base_pair_constraints rna_denovo_base_pair_setup rna_denovo_bps rna_denovo_bps_fixed_ends rna_denovo_bps_helix_ends rna_denovo_dna_bridge rna_denovo_fragment_homology_exclusion rna_denovo_grid_vdw rna_denovo_lariat rna_denovo_new_FT_2in_dens rna_denovo_new_FT_5P_j12_leadzyme rna_denovo_new_FT_RNP_2prot_dens rna_denovo_new_FT_rna_two_chains rna_denovo_new_libs rna_denovo_symm_hack rna_design rna_farfar_block_stack rna_farfar_noncanonical_hairpin rna_farfar_syn_chi_res rna_helix rna_minimize rna_minimize_6D_loop_close rna_motif rna_predict_chem_map rna_puzzle11_H2H3H4_run3_connectU40 rna_puzzle12_P5P6P7_DMS rna_puzzle5_P15P3P8_noP4P6_4RB_G208phosphate_ligation rna_puzzle5_p2_GAAA_mini rna_puzzle6_U75G76A77_on_thread1 rna_puzzle6_j67_into_p6p7rigidbody_thread1 rna_ribosome_tether rna_score rna_screen_phosphates rna_suitename rnp_ddg_calc_mut rnp_ddg_calc_setup rnp_ddg_calc_wt rnp_ddg_finalize rnp_ddg_relax_command_1 rnp_ddg_relax_command_2 rnp_ddg_relax_finalize rnp_ddg_relax_setup rollmover rosetta_scripts_hbond_options rosetta_scripts_include rosetta_scripts_info rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rotamer_recovery rotamer_recovery_compare_two_structures rs_flexbbmoves rs_loophash sasa_metric_options score12_docking score_aln score_jd2 score_only_silence sdf_reader secondary_structure_output seed_ensemble_JD2_JI select_best_unique_ligand_poses selected_residue_count_metric sequence_profile_constraints sequence_recovery sequence_tolerance set_torsion shobuns silent2frag simple_cycpep_predict simple_cycpep_predict_1_4_bbmb simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_beta_thioether_lariat simple_cycpep_predict_bondangle_bondlength simple_cycpep_predict_cartesian simple_cycpep_predict_cispro simple_cycpep_predict_cterm_isopeptide_lariat simple_cycpep_predict_cterm_isopeptide_lariat_tailless simple_cycpep_predict_design simple_cycpep_predict_nmethyl simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_octahedral_metal simple_cycpep_predict_peptoid simple_cycpep_predict_setting simple_cycpep_predict_sidechain_isopeptide simple_cycpep_predict_sidechain_isopeptide_reverse simple_cycpep_predict_square_planar_metal simple_cycpep_predict_square_pyramidal_metal simple_cycpep_predict_symm_gly simple_cycpep_predict_symmetric_sampling simple_cycpep_predict_tbmb simple_cycpep_predict_terminal_disulfide simple_cycpep_predict_terminal_disulfide_internal_permutations simple_cycpep_predict_terminal_disulfide_tails simple_cycpep_predict_terminal_disulfide_tails_2 simple_cycpep_predict_tetrahedral_metal simple_cycpep_predict_tetrahedral_metal_asp simple_cycpep_predict_thioether_cis_sampling simple_cycpep_predict_thioether_lariat simple_cycpep_predict_tma simple_cycpep_predict_trigonal_planar_metal simple_cycpep_predict_trigonal_pyramidal_metal simple_dna_test simple_glycosylation simple_glycosylation_alternate_AAs simple_grafting_movers simple_hbondstoatom simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_in_protocols simple_metrics_per_residue site_constraint small_molecule_lattice_dock smallmover_resselector smart_annealer splice_in_4loops_longer splice_in_4loops_shorter splice_out_H1_H2_longer splice_out_H1_H2_same splice_out_H1_H2_shorter splice_out_H3_longer splice_out_H3_same splice_out_H3_shorter splice_out_L1_L2_longer splice_out_L1_L2_same splice_out_L1_L2_shorter splice_out_L3_longer splice_out_L3_same splice_out_L3_shorter startfrom_file stepwise_lores stored_residue_subset struc_set_fragment_picker super_aln supercharge surface_docking swa_protein_CCDclose swa_protein_build_at_Cterminus swa_protein_build_at_Nterminus swa_protein_cluster swa_protein_combine_loops swa_protein_loop_sampler swa_protein_prepack swa_rna_erraser swa_rna_gagu_01_append swa_rna_gagu_02_prepend swa_rna_gagu_03_append_to_silent swa_rna_gagu_04_clustering swa_rna_gagu_05_prepend_to_5primeterminus swa_rna_gagu_06_append_to_3primeterminus swa_rna_gagu_07_prepend_dinucleotide swa_rna_gagu_08_append_dinucleotide swa_rna_gagu_09_sample_virtual_ribose swa_rna_gagu_10_prepend_and_ccd_close swa_rna_gagu_11_append_and_ccd_close swa_rna_gagu_12_helix_addition swa_rna_gagu_13_chunk_combination_and_closure swa_rna_gagu_14_combine_long_loop_filtering swa_rna_gagu_15_combine_long_loop_sampling swa_rna_gagu_16_prepend_dinucleotide_on_dinucleotide swa_rna_gagu_17_append_floating_base swa_rna_gagu_18_rebuild_bulge swa_rna_gagu_19_prepend_floating_base_by_jump swa_rna_gagu_20_append_floating_base_by_jump swa_rna_gagu_21_prepend_dinucleotide_on_dinucleotide_by_jump swa_rna_gagu_22_prepend_and_kic_close swa_rna_gagu_23_append_and_kic_close swa_rna_loop_clusterer swa_rna_loop_sampler sweep_respair_energies swm_add_rosettascripts swm_beta_peptide_loop swm_build_full_model swm_dna_bridge swm_dna_loop swm_general_polymer_sampler swm_l_rna swm_protein_CCDmove swm_protein_from_scratch swm_protein_loop_sampler swm_protein_move_inside_coiledcoil_by_bond swm_protein_move_inside_helix_by_bond swm_protein_preminimize swm_rna_base_pair_constraints swm_rna_checkpoint_partition swm_rna_fourwayjunction swm_rna_loop_design swm_rna_move_align_dock swm_rna_move_inside_helix_by_bond swm_rna_move_inside_helix_by_jump swm_rna_move_two_strands swm_rna_nickedhelix swm_rna_protonated_adenosine swm_rna_singleloop swm_rna_srl_triplet symm_disulfidize symm_rotamer_boltzmann symmetric_cycpep_align_and_symmetrize symmetric_docking symmetrical_residue_selector symmetry_data_resource symmetry_multicomponent target_clash task_selector tcrmodel template_features tensorflow_connection_test tensorflow_manager tensorflow_simple_model_load_and_evaluate test1_benchmark test_computed_saxs_spectrum test_d_l_readin test_degreaser test_energy_method_options test_idealize test_rosetta_thread_manager_advanced_API test_rosetta_thread_manager_basic_API thermal_sampler thread_local_tracers_check threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs torsion_restricted_sampling trRosetta trRosettaConstraintGenerator trRosettaConstraintGenerator_rosettascripts trRosettaProtocolMover trRosettaProtocolMover_rosettascripts trRosettaProtocolMover_rosettascripts_diskwrite trRosettaProtocolMover_rosettascripts_diskwrite_only trRosetta_test_predict trRosetta_test_predict_ubiquitin trRosetta_test_predict_ubiquitin_cst_file_write trRosetta_test_predict_ubiquitin_cst_file_write_only trRosetta_test_predict_ubiquitin_init_by_bins unfolded_state_energy_calc validate_database vancomycin vip voids_penalty_energy_design voids_penalty_energy_design_symmetry write_mol_file zinc_heterodimer zinc_homodimer_design zinc_homodimer_setup
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"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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"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 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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" }, "entropy_correction": { "log": "", "state": "passed" }, "enumerative_sampling": { "log": "", "state": "passed" }, "enzdes": { "log": "", "state": "passed" }, "enzscore_filter_dimetal": { "log": "", "state": "passed" }, "enzscore_filter_dimetal_sym": { "log": "", "state": "passed" }, "enzscore_filter_ligand": { "log": "", "state": "passed" }, "enzscore_filter_metal": { "log": "", "state": "passed" }, "enzscore_filter_metal_sym": { "log": "", "state": "passed" }, "erraser_minimize": { "log": "", "state": "passed" }, "esm_model_perplexity": { "log": "", "state": "passed" }, "evolution": { "log": "", "state": "passed" }, "exclusively_shared_jumps": { "log": "", "state": "passed" }, "explicit_membrane": { "log": "", "state": "passed" }, "extract_atomtree_diffs": { "log": "", "state": "passed" }, 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"state": "passed" }, "helical_bundle_predict_psipred_with_helix_globals": { "log": "", "state": "passed" }, "helical_bundle_predict_sequence": { "log": "", "state": "passed" }, "helical_bundle_predict_skipping_residues": { "log": "", "state": "passed" }, "helix_from_sequence": { "log": "", "state": "passed" }, "hierarchical_clustering": { "log": "", "state": "passed" }, "homodimer_fnd_ref2015_memb": { "log": "", "state": "passed" }, "hotspot_graft": { "log": "", "state": "passed" }, "hotspot_hashing": { "log": "", "state": "passed" }, "hotspot_stub_constraints": { "log": "", "state": "passed" }, "hshash_utils": { "log": "", "state": "passed" }, "hts_io": { "log": "", "state": "passed" }, "hybridization": { "log": "", "state": "passed" }, "hydrate": { "log": "", "state": "passed" }, "hydrate_relax": { "log": "", "state": "passed" }, "identify_cdr_clusters": { "log": "", "state": "passed" }, "ig_dump": { "log": "", "state": "passed" }, "include_cc_check": { "log": "", "state": "passed" }, "interaction_graph_summary_metric": { "log": "", "state": "passed" }, "interface_energy": { "log": "", "state": "passed" }, "inv_kin_lig_loop_design": { "log": "", "state": "passed" }, "iphold": { "log": "", "state": "passed" }, "jd2test_PDBIO": { "log": "", "state": "passed" }, "jd2test_PDBin_mmCIFout": { "log": "", "state": "passed" }, "jd2test_PDBin_mmCIFout_extra_data_separate": { "log": "", "state": "passed" }, "jd2test_mmCIFIO": { "log": "", "state": "passed" }, "jd2test_mmCIFin_PDBout": { "log": "", "state": "passed" }, "job_definition_script_vars": { "log": "", "state": "passed" }, "jrelax": { "log": "", "state": "passed" }, "jscore": { "log": "", "state": "passed" }, "kinemage_grid_output": { "log": "", "state": "passed" }, "kinematic_looprelax": { "log": "", "state": "passed" }, "ld_converter": { "log": "", "state": "passed" }, "ligand_database_io": { "log": "", "state": "passed" }, "ligand_dock_7cpa": { "log": "", "state": "passed" }, "ligand_dock_cholesterol": { "log": "", "state": "passed" }, "ligand_dock_ensemble": { "log": "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", "state": "failed" }, "ligand_dock_grid": { "log": "", "state": "passed" }, "ligand_dock_script": { "log": "", "state": "passed" }, "ligand_motif_design": { "log": "", "state": "passed" }, "ligand_motif_discovery": { "log": "", "state": "passed" }, "ligand_motif_identification": { "log": "", "state": "passed" }, "ligand_water_docking": { "log": "", "state": "passed" }, "longest_continuous_polar_segment_filter": { "log": "", "state": "passed" }, "loop_creation": { "log": "", "state": "passed" }, "loop_grower_N_term_symm": { "log": "", "state": "passed" }, "loop_hash": { "log": "", "state": "passed" }, "loop_modeling": { "log": "", "state": "passed" }, "make_and_perturb_bundle_multirepeat": { "log": "", "state": "passed" }, 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/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", "state": "failed" }, "simple_cycpep_predict_symm_gly": { "log": "", "state": "passed" }, "simple_cycpep_predict_symmetric_sampling": { "log": "", "state": "passed" }, "simple_cycpep_predict_tbmb": { "log": "", "state": "passed" }, "simple_cycpep_predict_terminal_disulfide": { "log": "", "state": "passed" }, "simple_cycpep_predict_terminal_disulfide_internal_permutations": { "log": "", "state": "passed" }, "simple_cycpep_predict_terminal_disulfide_tails": { "log": "", "state": "passed" }, "simple_cycpep_predict_terminal_disulfide_tails_2": { "log": "", "state": "passed" }, "simple_cycpep_predict_tetrahedral_metal": { "log": "", "state": "passed" }, "simple_cycpep_predict_tetrahedral_metal_asp": { "log": "", "state": "passed" }, "simple_cycpep_predict_thioether_cis_sampling": { "log": "", "state": "passed" }, "simple_cycpep_predict_thioether_lariat": { "log": "", "state": "passed" }, "simple_cycpep_predict_tma": { "log": "", "state": "passed" }, "simple_cycpep_predict_trigonal_planar_metal": { "log": "", "state": "passed" }, "simple_cycpep_predict_trigonal_pyramidal_metal": { "log": "", "state": "passed" }, "simple_dna_test": { "log": "", "state": "passed" }, "simple_glycosylation": { "log": "", "state": "passed" }, "simple_glycosylation_alternate_AAs": { "log": "", "state": "passed" }, "simple_grafting_movers": { "log": "", "state": "passed" }, "simple_hbondstoatom": { "log": "", "state": "passed" }, "simple_metric_cache": { "log": "", "state": "passed" }, "simple_metric_features": { "log": "", "state": "passed" }, "simple_metric_filter": { "log": "", "state": "passed" }, "simple_metrics": { "log": "", "state": "passed" }, "simple_metrics_in_protocols": { "log": "", "state": "passed" }, "simple_metrics_per_residue": { "log": "", "state": "passed" }, "site_constraint": { "log": "", "state": "passed" }, "small_molecule_lattice_dock": { "log": "", "state": "passed" }, "smallmover_resselector": { "log": "", "state": "passed" }, "smart_annealer": { "log": "", "state": "passed" }, "splice_in_4loops_longer": { "log": "", "state": "passed" }, "splice_in_4loops_shorter": { "log": "", "state": "passed" }, "splice_out_H1_H2_longer": { "log": "", "state": "passed" }, "splice_out_H1_H2_same": { "log": "", "state": "passed" }, "splice_out_H1_H2_shorter": { "log": "", "state": "passed" }, "splice_out_H3_longer": { "log": "", "state": "passed" }, "splice_out_H3_same": { "log": "", "state": "passed" }, "splice_out_H3_shorter": { "log": "", "state": "passed" }, "splice_out_L1_L2_longer": { "log": "", "state": "passed" }, "splice_out_L1_L2_same": { "log": "", "state": "passed" }, "splice_out_L1_L2_shorter": { "log": "", "state": "passed" }, "splice_out_L3_longer": { "log": "", "state": 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