Test: ubuntu.gcc.integration.addsan 「view this page in B3 βῆτα server」
Branch: master 「revision: №61954」
Test files: 「file-system-view」 「file-list-view」
Daemon: nobu-4     Started at: 2022-10-16 15:46:29     Run time: 0:56:18      State: failed

Failed sub-tests (click for more details):
simple_cycpep_predict_square_pyramidal_metal

Test Log

Sub-Tests Results

All sub-tests

AddConstraintsToCurrentConformationMover AlignPDBInfoToSequences AlterSpecDisruption AnchorFinder AnchoredDesign AnchoredPDBCreator 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 FilterReportAsPoseExtraScoresMover FlipChirality FloppyTail 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 PeptideCyclizeMover PeptideStubMover_prependRepeat PolarDesign2019 ProQ RBOut ReadResfile_with_selector RescorePDDF RescoreSAXS ResidueDisorder 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 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 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 entropy_correction enumerative_sampling enzdes enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym erraser_minimize 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_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 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_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_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

JSON output

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"sdf_reader": { "log": "", "state": "passed" }, "secondary_structure_output": { "log": "", "state": "passed" }, "seed_ensemble_JD2_JI": { "log": "", "state": "passed" }, "select_best_unique_ligand_poses": { "log": "", "state": "passed" }, "selected_residue_count_metric": { "log": "", "state": "passed" }, "sequence_profile_constraints": { "log": "", "state": "passed" }, "sequence_recovery": { "log": "", "state": "passed" }, "sequence_tolerance": { "log": "", "state": "passed" }, "set_torsion": { "log": "", "state": "passed" }, "shobuns": { "log": "", "state": "passed" }, "silent2frag": { "log": "", "state": "passed" }, "simple_cycpep_predict": { "log": "", "state": "passed" }, "simple_cycpep_predict_1_4_bbmb": { "log": "", "state": "passed" }, "simple_cycpep_predict_angle": { "log": "", "state": "passed" }, "simple_cycpep_predict_anglelength": { "log": "", "state": "passed" }, "simple_cycpep_predict_beta_thioether_lariat": { "log": "", "state": "passed" }, "simple_cycpep_predict_bondangle_bondlength": { "log": "", "state": "passed" }, "simple_cycpep_predict_cartesian": { "log": "", "state": "passed" }, "simple_cycpep_predict_cispro": { "log": "", "state": "passed" }, "simple_cycpep_predict_cterm_isopeptide_lariat": { "log": "", "state": "passed" }, "simple_cycpep_predict_cterm_isopeptide_lariat_tailless": { "log": "", "state": "passed" }, "simple_cycpep_predict_design": { "log": "", "state": "passed" }, "simple_cycpep_predict_nmethyl": { "log": "", "state": "passed" }, "simple_cycpep_predict_nterm_isopeptide_lariat": { "log": "", "state": "passed" }, "simple_cycpep_predict_nterm_isopeptide_lariat_tailless": { "log": "", "state": "passed" }, "simple_cycpep_predict_octahedral_metal": { "log": "", "state": "passed" }, "simple_cycpep_predict_peptoid": { "log": "", "state": "passed" }, "simple_cycpep_predict_setting": { "log": "", "state": "passed" }, "simple_cycpep_predict_sidechain_isopeptide": { "log": "", "state": "passed" }, "simple_cycpep_predict_sidechain_isopeptide_reverse": { "log": "", "state": "passed" }, "simple_cycpep_predict_square_planar_metal": { "log": "", "state": "passed" }, "simple_cycpep_predict_square_pyramidal_metal": { "log": "\n\nLogFile log\ncore.init: command: ROSETTA/source/bin/simple_cycpep_predict.default.linuxgccaddsan -in:path:database_cache_dir ROSETTA/.database-binaries/ubuntugccaddsan @flags -database ROSETTA/database -run:constant_seed -nodelay -testing:INTEGRATION_TEST\nbasic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111\nbasic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937\napps.public.cyclic_peptide.simple_cycpep_predict: Starting simple_cycpep_predict.cc\napps.public.cyclic_peptide.simple_cycpep_predict: Application created 16 September 2015 by Vikram K. Mulligan, Ph.D., Baker laboratory.\napps.public.cyclic_peptide.simple_cycpep_predict: For questions, contact vmullig@uw.edu.\napps.public.cyclic_peptide.simple_cycpep_predict: \ncore.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015\ncore.scoring.etable: Starting energy table calculation\ncore.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well\ncore.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)\ncore.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)\ncore.scoring.etable: Finished calculating energy tables.\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\nbasic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\ncore.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Parsed square pyramidal metal setup where res1=5, res2=10, res3=15, res4=20, res5=25, metal=Ni2\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Opened inputs/seq.txt for read.\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Parsing \"GLY GLY GLY GLY ASP GLY GLY GLY GLY DHIS GLY GLY GLY GLY HIS GLY GLY GLY GLY DASP GLY GLY GLY GLY HIS GLY GLY GLY GLY GLY\".\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Parsed the following sequence:\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: GLY, GLY, GLY, GLY, ASP, GLY, GLY, GLY, GLY, DHIS, GLY, GLY, GLY, GLY, HIS, GLY, GLY, GLY, GLY, DASP, GLY, GLY, GLY, GLY, HIS, GLY, GLY, GLY, GLY, GLY.\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Importing native structure from inputs/native.pdb.\ncore.import_pose.import_pose: File 'inputs/native.pdb' automatically determined to be of type PDB\ncore.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue DHIS:CtermProteinFull 30\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Improrting native structure from inputs/native.pdb.\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Stripping termini from native structure.\ncore.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue GLY 1. Returning BOGUS ID instead.\ncore.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! \ncore.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates.\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Removed lower terminus type from first residue.\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Removed upper terminus type from last residue.\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Setting up terminal bond for the native pose between residue 1, atom N and residue 30, atom C .\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Circularly shifted residue list by 0. New list is: GLY, GLY, GLY, GLY, ASP, GLY, GLY, GLY, GLY, DHIS, GLY, GLY, GLY, GLY, HIS, GLY, GLY, GLY, GLY, DASP, GLY, GLY, GLY, GLY, HIS, GLY, GLY, GLY, GLY, GLY\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Building sequence GLY GLY GLY GLY ASP GLY GLY GLY GLY DHIS GLY GLY GLY GLY HIS GLY GLY GLY GLY DASP GLY GLY GLY GLY HIS GLY GLY GLY GLY GLY.\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Build successful.\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Setting up terminal bond between residue 1, atom N and residue 30, atom C .\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Setting up cutpoint variants.\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Setting up cyclic constraints.\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: The following four atoms define the terminal bond:\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: 1.\tRes=30\tAtom= CA \nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: 2.\tRes=30\tAtom= C \nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: 3.\tRes=1\tAtom= N \nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: 4.\tRes=1\tAtom= CA \nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Finished setting up constraints.\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Randomizing mainchain torsions.\ncore.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\nbasic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Performing GeneralizedKIC closure of loop.\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Setting up terminal bond between residue 1, atom N and residue 30, atom C .\nprotocols.relax.RelaxScriptManager: Reading relax scripts list from database.\nprotocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt\nprotocols.relax.RelaxScriptManager: ================== Reading script file: ROSETTA/database/sampling/relax_scripts/MonomerRelax2019.txt ==================\nprotocols.relax.RelaxScriptManager: repeat %%nrepeats%%\nprotocols.relax.RelaxScriptManager: coord_cst_weight 1.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.040\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.051\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.5\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.265\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.280\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.559\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: scale:fa_rep 0.581\nprotocols.relax.RelaxScriptManager: min 0.01\nprotocols.relax.RelaxScriptManager: coord_cst_weight 0.0\nprotocols.relax.RelaxScriptManager: scale:fa_rep 1\nprotocols.relax.RelaxScriptManager: repack\nprotocols.relax.RelaxScriptManager: min 0.00001\nprotocols.relax.RelaxScriptManager: accept_to_best\nprotocols.relax.RelaxScriptManager: endrepeat\nprotocols.generalized_kinematic_closure.GeneralizedKIC: Applying pre-selection mover to solution 1 from attempt 4.\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_1=======================\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 1\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is s6 symmetric.\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\nprotocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER CrosslinkerMover - square_pyramidal_metal_link_1=======================\nprotocols.cyclic_peptide.CrosslinkerMover: Sidechain distance filter PASSED.\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\nbasic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat\ncore.scoring.elec.util: Read 40 countpair representative atoms\ncore.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.\nprotocols.relax.FastRelax: CMD: repeat 3.50967e+06 0 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 3.50967e+06 0 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 3.50684e+06 0 0 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 97 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 76878.8\nprotocols.relax.FastRelax: CMD: repack 76895.5 0 0 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 76896.8 0 0 0.02805\nprotocols.relax.FastRelax: CMD: min 7879.21 0 0 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 7879.21 0 0 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7934.88 0 0 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 71 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7916.64\nprotocols.relax.FastRelax: CMD: repack 7934.88 0 0 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7938.78 0 0 0.154\nprotocols.relax.FastRelax: CMD: min 7938.5 0 0 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 7938.5 0 0 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 8010.41 0 0 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 63 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7990.01\nprotocols.relax.FastRelax: CMD: repack 8010.41 0 0 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 8016.08 0 0 0.31955\nprotocols.relax.FastRelax: CMD: min 8015.56 0 0 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 8015.56 0 0 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 8122.22 0 0 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 54 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 8097.74\nprotocols.relax.FastRelax: CMD: repack 8122.22 0 0 0.55\nprotocols.relax.FastRelax: CMD: min 8121.12 0 0 0.55\nprotocols.relax.FastRelax: MRP: 0 8121.12 8121.12 0 0 \nprotocols.relax.FastRelax: CMD: accept_to_best 8121.12 0 0 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 8121.12 0 0 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\nprotocols.relax.FastRelax: CMD: repeat 8121.12 0 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 8121.12 0 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7881.15 0 0 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 97 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7864.58\nprotocols.relax.FastRelax: CMD: repack 7881.15 0 0 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7883.9 0 0 0.02805\nprotocols.relax.FastRelax: CMD: min 7879.26 0 0 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 7879.26 0 0 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7934.86 0 0 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 71 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7916.64\nprotocols.relax.FastRelax: CMD: repack 7934.86 0 0 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7938.76 0 0 0.154\nprotocols.relax.FastRelax: CMD: min 7938.51 0 0 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 7938.51 0 0 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 8010.33 0 0 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 63 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7989.93\nprotocols.relax.FastRelax: CMD: repack 8010.33 0 0 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 8015.99 0 0 0.31955\nprotocols.relax.FastRelax: CMD: min 8015.6 0 0 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 8015.6 0 0 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 8122.3 0 0 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 54 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 8098.59\nprotocols.relax.FastRelax: CMD: repack 8122.3 0 0 0.55\nprotocols.relax.FastRelax: CMD: min 8121.11 0 0 0.55\nprotocols.relax.FastRelax: MRP: 0 8121.11 8121.11 0 0 \nprotocols.relax.FastRelax: CMD: accept_to_best 8121.11 0 0 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 8121.11 0 0 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\nprotocols.relax.FastRelax: CMD: repeat 8121.11 0 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 8121.11 0 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7881.3 0 0 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 97 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7864.7\nprotocols.relax.FastRelax: CMD: repack 7881.3 0 0 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7884.05 0 0 0.02805\nprotocols.relax.FastRelax: CMD: min 7879.21 0 0 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 7879.21 0 0 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7934.87 0 0 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 71 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7916.46\nprotocols.relax.FastRelax: CMD: repack 7934.87 0 0 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7938.77 0 0 0.154\nprotocols.relax.FastRelax: CMD: min 7938.52 0 0 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 7938.52 0 0 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 8010.42 0 0 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 63 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7990.03\nprotocols.relax.FastRelax: CMD: repack 8010.42 0 0 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 8016.09 0 0 0.31955\nprotocols.relax.FastRelax: CMD: min 8015.53 0 0 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 8015.53 0 0 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 8122.13 0 0 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 54 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 8098.52\nprotocols.relax.FastRelax: CMD: repack 8122.13 0 0 0.55\nprotocols.relax.FastRelax: CMD: min 8121.12 0 0 0.55\nprotocols.relax.FastRelax: MRP: 0 8121.12 8121.12 0 0 \nprotocols.relax.FastRelax: CMD: accept_to_best 8121.12 0 0 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 8121.12 0 0 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\nprotocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper: Constraint energy for crosslinked pose is 7813.97. Filter passes.\nprotocols.cyclic_peptide.CrosslinkerMover: Linker constraints filter PASSED.\nprotocols.cyclic_peptide.CrosslinkerMover: CrosslinkerMover reports SUCCESS. Updating pose.\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - High_Hbond_FastRelax=======================\nprotocols.relax.FastRelax: CMD: repeat 8121.12 0 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 8121.12 0 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7881.24 0 0 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 122 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 7881.2\nprotocols.relax.FastRelax: CMD: repack 7881.24 0 0 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7883.99 0 0 0.02805\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.96046e-08 Deriv= -4580.54 Finite Diff= 6104.27\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.86443e-09 Deriv= -74306.2 Finite Diff= 11196.9\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.53221e-09 Deriv= -19808.9 Finite Diff= 4997.58\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.85551e-09 Deriv= -31471.8 Finite Diff= 1378.28\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.54224e-09 Deriv= -104495 Finite Diff= 9406.44\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.59074e-09 Deriv= -8534.05 Finite Diff= 1672.83\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.66377e-09 Deriv= -57071.9 Finite Diff= 12757.3\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.04161e-09 Deriv= -4334.81 Finite Diff= 315.19\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.26215e-07 Deriv= -3653.94 Finite Diff= -295.819\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#100\nprotocols.relax.FastRelax: CMD: min 1232.68 1.83901 1.83901 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1232.68 1.83901 1.83901 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1327.82 1.83901 1.83901 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 125 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1327.18\nprotocols.relax.FastRelax: CMD: repack 1327.82 1.83901 1.83901 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1334.49 1.83901 1.83901 0.154\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.76837e-09 Deriv= -89164.4 Finite Diff= 4738.86\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.6742e-09 Deriv= -15383.6 Finite Diff= 3305.04\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.30907e-09 Deriv= -11588.4 Finite Diff= 2685.09\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.29335e-09 Deriv= -9890.33 Finite Diff= 1921.3\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.25803e-09 Deriv= -41435.8 Finite Diff= 10562.3\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.45585e-09 Deriv= -2750.77 Finite Diff= 1417.75\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.98966e-09 Deriv= -7939.14 Finite Diff= 1527.32\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.87567e-09 Deriv= -7155.18 Finite Diff= 1258.42\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.07587e-09 Deriv= -18742.9 Finite Diff= 3311.76\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.10673e-09 Deriv= -1951.97 Finite Diff= 725.811\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.67166e-07 Deriv= -2082.97 Finite Diff= -195.334\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#68\nprotocols.relax.FastRelax: CMD: min 1324.97 1.84475 1.84475 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1324.97 1.84475 1.84475 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1437.84 1.84475 1.84475 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 108 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1436.86\nprotocols.relax.FastRelax: CMD: repack 1437.84 1.84475 1.84475 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1446.73 1.84475 1.84475 0.31955\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -44748.6 Finite Diff= 3915.44\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.27168e-10 Deriv= -12332.9 Finite Diff= -736.727\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.55436e-09 Deriv= -15284.8 Finite Diff= 2347.86\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.11495e-09 Deriv= -5167.02 Finite Diff= 1838.22\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.05163e-09 Deriv= -8517.99 Finite Diff= 915.956\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.40262e-09 Deriv= -26160.8 Finite Diff= 5918.9\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.98715e-09 Deriv= -729666 Finite Diff= 70034.3\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.78331e-07 Deriv= -1830.31 Finite Diff= 14.673\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#55\nprotocols.relax.FastRelax: CMD: min 1432.04 1.86232 1.86232 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1432.04 1.86232 1.86232 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1579.96 1.86232 1.86232 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 106 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1578.9\nprotocols.relax.FastRelax: CMD: repack 1579.96 1.86232 1.86232 0.55\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.76837e-09 Deriv= -156178 Finite Diff= 20681\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.62741e-09 Deriv= -4013.31 Finite Diff= 563.657\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.78541e-09 Deriv= -4265.87 Finite Diff= -255.729\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.53267e-09 Deriv= -10099.1 Finite Diff= -948.225\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.52939e-09 Deriv= -35435.9 Finite Diff= 2120.46\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.61607e-09 Deriv= -253865 Finite Diff= 36873.2\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.97056e-10 Deriv= -5464.85 Finite Diff= -169.113\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.13913e-09 Deriv= -7350.54 Finite Diff= 688.188\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.62054e-14 Deriv= -161289 Finite Diff= 6790.86\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.7447e-07 Deriv= -1912.23 Finite Diff= -64.5826\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#73\nprotocols.relax.FastRelax: CMD: min 1556.96 1.89476 1.89476 0.55\nprotocols.relax.FastRelax: MRP: 0 1556.96 1556.96 1.89476 1.89476 \nprotocols.relax.FastRelax: CMD: accept_to_best 1556.96 1.89476 1.89476 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 1556.96 1.89476 1.89476 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1556.96 1.89476 1.89476 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1276.1 1.89476 1.89476 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 135 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1273.04\nprotocols.relax.FastRelax: CMD: repack 1276.1 1.89476 1.89476 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1279.32 1.89476 1.89476 0.02805\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.72529e-09 Deriv= -3361.79 Finite Diff= 351.972\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.29949e-08 Deriv= -137.333 Finite Diff= 2.9933\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.40312e-09 Deriv= -12831.9 Finite Diff= 2002.58\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.18288e-12 Deriv= -46338.5 Finite Diff= -2948.91\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.89684e-08 Deriv= -9334.12 Finite Diff= 866.664\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#114\nprotocols.relax.FastRelax: CMD: min 1130.08 1.92594 1.92594 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1130.08 1.92594 1.92594 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1261.23 1.92594 1.92594 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 129 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1259.41\nprotocols.relax.FastRelax: CMD: repack 1261.23 1.92594 1.92594 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1270.42 1.92594 1.92594 0.154\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -60452.1 Finite Diff= 10926.6\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.96173e-09 Deriv= -334396 Finite Diff= 15840.2\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.93191e-09 Deriv= -17097.3 Finite Diff= 727.494\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.21331e-08 Deriv= -8628.67 Finite Diff= -689.73\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#20\nprotocols.relax.FastRelax: CMD: min 1266.92 1.9291 1.9291 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1266.92 1.9291 1.9291 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1433.93 1.9291 1.9291 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 124 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1432.1\nprotocols.relax.FastRelax: CMD: repack 1433.93 1.9291 1.9291 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1447.09 1.9291 1.9291 0.31955\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.31323e-10 Deriv= -1176.08 Finite Diff= -48.6687\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.22688e-07 Deriv= -3867 Finite Diff= -112.076\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#72\nprotocols.relax.FastRelax: CMD: min 1306.75 1.99441 1.99441 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1306.75 1.99441 1.99441 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1399.03 1.99441 1.99441 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 111 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1397.45\nprotocols.relax.FastRelax: CMD: repack 1399.03 1.99441 1.99441 0.55\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -285596 Finite Diff= 6257.75\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.00526e-09 Deriv= -319891 Finite Diff= 29715.9\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.09521e-07 Deriv= -4852.71 Finite Diff= -476.145\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#12\nprotocols.relax.FastRelax: CMD: min 1397.73 1.99431 1.99431 0.55\nprotocols.relax.FastRelax: MRP: 1 1397.73 1397.73 1.99431 1.99431 \nprotocols.relax.FastRelax: CMD: accept_to_best 1397.73 1.99431 1.99431 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 1397.73 1.99431 1.99431 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1397.73 1.99431 1.99431 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1192.96 1.99431 1.99431 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 132 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1191.28\nprotocols.relax.FastRelax: CMD: repack 1192.96 1.99431 1.99431 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1195.31 1.99431 1.99431 0.02805\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.76837e-09 Deriv= -152002 Finite Diff= 16220.9\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.48288e-09 Deriv= -515471 Finite Diff= 36392.1\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.09378e-09 Deriv= -221947 Finite Diff= 10256.2\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.01806e-07 Deriv= -5616.12 Finite Diff= 1586.83\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#16\nprotocols.relax.FastRelax: CMD: min 1188.8 1.98741 1.98741 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1188.8 1.98741 1.98741 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1238.69 1.98741 1.98741 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 121 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1237.08\nprotocols.relax.FastRelax: CMD: repack 1238.69 1.98741 1.98741 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1242.18 1.98741 1.98741 0.154\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -5282.1 Finite Diff= 441.154\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.04975e-07 Deriv= -5282.1 Finite Diff= 441.567\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\nprotocols.relax.FastRelax: CMD: min 1242.18 1.98741 1.98741 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1242.18 1.98741 1.98741 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1307.22 1.98741 1.98741 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 118 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1305.24\nprotocols.relax.FastRelax: CMD: repack 1307.22 1.98741 1.98741 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1312.35 1.98741 1.98741 0.31955\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -46324.4 Finite Diff= 8918.45\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.78313e-09 Deriv= -236937 Finite Diff= 41439\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.85321e-08 Deriv= -5995.49 Finite Diff= 362.646\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#10\nprotocols.relax.FastRelax: CMD: min 1311.69 1.98632 1.98632 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1311.69 1.98632 1.98632 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1406.19 1.98632 1.98632 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 109 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1403.32\nprotocols.relax.FastRelax: CMD: repack 1406.19 1.98632 1.98632 0.55\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -511876 Finite Diff= 45440.4\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.75335e-09 Deriv= -81496.4 Finite Diff= 7105.49\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.21494e-07 Deriv= -3943.41 Finite Diff= 308.589\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#11\nprotocols.relax.FastRelax: CMD: min 1405.68 1.9865 1.9865 0.55\nprotocols.relax.FastRelax: MRP: 2 1405.68 1397.73 1.99431 1.99431 \nprotocols.relax.FastRelax: CMD: accept_to_best 1405.68 1.9865 1.9865 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 1405.68 1.9865 1.9865 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_2=======================\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 0\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is not s6 symmetric.\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\nprotocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: Filter reports failure!\nprotocols.generalized_kinematic_closure.GeneralizedKIC: Preselection mover failed! Continuing to next solution.\nprotocols.generalized_kinematic_closure.GeneralizedKIC: Applying pre-selection mover to solution 1 from attempt 10.\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_1=======================\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 0\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is not s6 symmetric.\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\nprotocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: Filter reports failure!\nprotocols.generalized_kinematic_closure.GeneralizedKIC: Preselection mover failed! Continuing to next solution.\nprotocols.generalized_kinematic_closure.GeneralizedKIC: Applying pre-selection mover to solution 2 from attempt 10.\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_1=======================\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 0\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is not s6 symmetric.\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\nprotocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: Filter reports failure!\nprotocols.generalized_kinematic_closure.GeneralizedKIC: Preselection mover failed! Continuing to next solution.\nprotocols.generalized_kinematic_closure.GeneralizedKIC: Applying pre-selection mover to solution 1 from attempt 18.\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_1=======================\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 1\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is s6 symmetric.\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\nprotocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER CrosslinkerMover - square_pyramidal_metal_link_1=======================\nprotocols.cyclic_peptide.CrosslinkerMover: Sidechain distance filter PASSED.\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\nprotocols.relax.FastRelax: CMD: repeat 2.77015e+06 0 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 2.77015e+06 0 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 2.76636e+06 0 0 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 110 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 215005\nprotocols.relax.FastRelax: CMD: repack 214988 0 0 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 215008 0 0 0.02805\nprotocols.relax.FastRelax: CMD: min 7270.09 0 0 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 7270.09 0 0 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7462.71 0 0 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 99 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7477.06\nprotocols.relax.FastRelax: CMD: repack 7462.71 0 0 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7476.21 0 0 0.154\nprotocols.relax.FastRelax: CMD: min 7475.15 0 0 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 7475.15 0 0 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7723.72 0 0 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 93 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7735.14\nprotocols.relax.FastRelax: CMD: repack 7723.72 0 0 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7743.32 0 0 0.31955\nprotocols.relax.FastRelax: CMD: min 7741.44 0 0 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 7741.44 0 0 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 8109.55 0 0 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 71 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 8116.33\nprotocols.relax.FastRelax: CMD: repack 8109.55 0 0 0.55\nprotocols.relax.FastRelax: CMD: min 8097.1 0 0 0.55\nprotocols.relax.FastRelax: MRP: 0 8097.1 8097.1 0 0 \nprotocols.relax.FastRelax: CMD: accept_to_best 8097.1 0 0 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 8097.1 0 0 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\nprotocols.relax.FastRelax: CMD: repeat 8097.1 0 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 8097.1 0 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7278.85 0 0 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 110 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7294.54\nprotocols.relax.FastRelax: CMD: repack 7278.85 0 0 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7288.22 0 0 0.02805\nprotocols.relax.FastRelax: CMD: min 7270.3 0 0 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 7270.3 0 0 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7460.52 0 0 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 99 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7475.24\nprotocols.relax.FastRelax: CMD: repack 7460.52 0 0 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7473.85 0 0 0.154\nprotocols.relax.FastRelax: CMD: min 7472.91 0 0 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 7472.91 0 0 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7718.62 0 0 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 93 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7730.09\nprotocols.relax.FastRelax: CMD: repack 7718.62 0 0 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7737.99 0 0 0.31955\nprotocols.relax.FastRelax: CMD: min 7736.31 0 0 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 7736.31 0 0 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 8100.62 0 0 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 71 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 8107.43\nprotocols.relax.FastRelax: CMD: repack 8100.62 0 0 0.55\nprotocols.relax.FastRelax: CMD: min 8097.1 0 0 0.55\nprotocols.relax.FastRelax: MRP: 0 8097.1 8097.1 0 0 \nprotocols.relax.FastRelax: CMD: accept_to_best 8097.1 0 0 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 8097.1 0 0 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\nprotocols.relax.FastRelax: CMD: repeat 8097.1 0 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 8097.1 0 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7278.75 0 0 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 110 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7295.67\nprotocols.relax.FastRelax: CMD: repack 7278.75 0 0 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7288.13 0 0 0.02805\nprotocols.relax.FastRelax: CMD: min 7270.3 0 0 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 7270.3 0 0 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7460.52 0 0 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 99 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7475.06\nprotocols.relax.FastRelax: CMD: repack 7460.52 0 0 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7473.85 0 0 0.154\nprotocols.relax.FastRelax: CMD: min 7472.91 0 0 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 7472.91 0 0 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7718.62 0 0 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 93 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 7729.36\nprotocols.relax.FastRelax: CMD: repack 7718.62 0 0 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7737.99 0 0 0.31955\nprotocols.relax.FastRelax: CMD: min 7736.31 0 0 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 7736.31 0 0 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 8100.62 0 0 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 71 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 8108.03\nprotocols.relax.FastRelax: CMD: repack 8100.62 0 0 0.55\nprotocols.relax.FastRelax: CMD: min 8097.1 0 0 0.55\nprotocols.relax.FastRelax: MRP: 0 8097.1 8097.1 0 0 \nprotocols.relax.FastRelax: CMD: accept_to_best 8097.1 0 0 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 8097.1 0 0 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\nprotocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper: Constraint energy for crosslinked pose is 7283.91. Filter passes.\nprotocols.cyclic_peptide.CrosslinkerMover: Linker constraints filter PASSED.\nprotocols.cyclic_peptide.CrosslinkerMover: CrosslinkerMover reports SUCCESS. Updating pose.\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - High_Hbond_FastRelax=======================\nprotocols.relax.FastRelax: CMD: repeat 8097.1 1.57973 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 8097.1 1.57973 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7278.75 1.57973 0 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 135 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 7279.88\nprotocols.relax.FastRelax: CMD: repack 7278.75 1.57973 0 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 7288.13 1.57973 0 0.02805\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.96046e-10 Deriv= -1025.88 Finite Diff= -31.8481\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.56806e-08 Deriv= -313.759 Finite Diff= -21.2618\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.81028e-09 Deriv= -8732.81 Finite Diff= 1244.8\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.77645e-09 Deriv= -2198.83 Finite Diff= 317.231\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.57507e-11 Deriv= -67012.2 Finite Diff= -2589.63\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.65336e-09 Deriv= -63499.4 Finite Diff= 2591.29\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.56227e-09 Deriv= -167826 Finite Diff= 9283.74\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.79048e-07 Deriv= -1815.68 Finite Diff= -106.872\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#174\nprotocols.relax.FastRelax: CMD: min 1813.99 3.36873 3.06183 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1813.99 3.36873 3.06183 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 3014.28 3.36873 3.06183 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 83 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 3013.88\nprotocols.relax.FastRelax: CMD: repack 3014.28 3.36873 3.06183 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 3098.41 3.36873 3.06183 0.154\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -6.01384e+08 Finite Diff= 1.24848e+08\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.65663e-09 Deriv= -864.359 Finite Diff= 299.176\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.82353e-09 Deriv= -3985.61 Finite Diff= 665.762\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.69534e-09 Deriv= -12327.2 Finite Diff= 1191.31\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.17456e-09 Deriv= -37777 Finite Diff= 6410.98\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.34563e-09 Deriv= -4756.24 Finite Diff= 768.036\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.85996e-07 Deriv= -1682.57 Finite Diff= -59.7016\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#79\nprotocols.relax.FastRelax: CMD: min 1937.96 2.96623 2.48931 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1937.96 2.96623 2.48931 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 2254.25 2.96623 2.48931 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 87 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 2254.59\nprotocols.relax.FastRelax: CMD: repack 2254.25 2.96623 2.48931 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 2279.19 2.96623 2.48931 0.31955\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.45058e-09 Deriv= -37027.9 Finite Diff= 1242.58\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.25242e-09 Deriv= -23085.9 Finite Diff= 2328.59\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.88988e-09 Deriv= -28616.1 Finite Diff= 1962.1\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.0814e-09 Deriv= -16143.8 Finite Diff= 1205.04\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.50956e-07 Deriv= -2554.34 Finite Diff= -190.705\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#168\nprotocols.relax.FastRelax: CMD: min 2095.17 2.97952 2.41616 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 2095.17 2.97952 2.41616 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 2379.78 2.97952 2.41616 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 88 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 2379.02\nprotocols.relax.FastRelax: CMD: repack 2379.78 2.97952 2.41616 0.55\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -1447.22 Finite Diff= 154.708\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.54478e-09 Deriv= -54995.9 Finite Diff= 358.197\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.12479e-09 Deriv= -6312 Finite Diff= 388.218\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.72414e-09 Deriv= -42777.1 Finite Diff= 1495.78\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.97527e-07 Deriv= -657.548 Finite Diff= -50.2457\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#39\nprotocols.relax.FastRelax: CMD: min 2347.3 2.92547 2.36394 0.55\nprotocols.relax.FastRelax: MRP: 0 2347.3 2347.3 2.92547 2.36394 \nprotocols.relax.FastRelax: CMD: accept_to_best 2347.3 2.92547 2.36394 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 2347.3 2.92547 2.36394 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 2347.3 2.92547 2.36394 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1833.87 2.92547 2.36394 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 129 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1833.69\nprotocols.relax.FastRelax: CMD: repack 1833.87 2.92547 2.36394 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1839.75 2.92547 2.36394 0.02805\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.38419e-07 Deriv= -23.0916 Finite Diff= 0.462414\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.21452e-09 Deriv= -3680.38 Finite Diff= 223.174\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.0293e-07 Deriv= -5494.09 Finite Diff= -305.736\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#83\nprotocols.relax.FastRelax: CMD: min 1556.93 3.08095 2.59699 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1556.93 3.08095 2.59699 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1965.58 3.08095 2.59699 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 83 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1965.42\nprotocols.relax.FastRelax: CMD: repack 1965.58 3.08095 2.59699 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1994.22 3.08095 2.59699 0.154\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.05176e-07 Deriv= -139.923 Finite Diff= -1.18151\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.50041e-09 Deriv= -14864.6 Finite Diff= 1770.87\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.02972e-07 Deriv= -1412.89 Finite Diff= 484.614\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#43\nprotocols.relax.FastRelax: CMD: min 1818.51 3.00803 2.49234 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1818.51 3.00803 2.49234 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 2057.65 3.00803 2.49234 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 88 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 2058.03\nprotocols.relax.FastRelax: CMD: repack 2057.65 3.00803 2.49234 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 2076.51 3.00803 2.49234 0.31955\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -3139.11 Finite Diff= 381.614\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.40913e-09 Deriv= -5069.28 Finite Diff= 386.316\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.26429e-09 Deriv= -17024.3 Finite Diff= 1862.34\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.29017e-09 Deriv= -19780.2 Finite Diff= 702.572\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.75797e-09 Deriv= -36486.8 Finite Diff= 3363.18\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.13235e-07 Deriv= -593.252 Finite Diff= 169.109\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#33\nprotocols.relax.FastRelax: CMD: min 2059 2.96963 2.45095 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 2059 2.96963 2.45095 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 2352.55 2.96963 2.45095 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 86 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 2352.92\nprotocols.relax.FastRelax: CMD: repack 2352.55 2.96963 2.45095 0.55\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.19209e-09 Deriv= -394.331 Finite Diff= -1.33286\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.17952e-10 Deriv= -2107.5 Finite Diff= -160.921\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.75249e-11 Deriv= -1609.97 Finite Diff= -125.417\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.05845e-09 Deriv= -1852.78 Finite Diff= 202.86\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.90773e-09 Deriv= -3920.95 Finite Diff= 274.053\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.22713e-09 Deriv= -17480 Finite Diff= 1008.99\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.03538e-07 Deriv= -357.446 Finite Diff= -29.1656\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#78\nprotocols.relax.FastRelax: CMD: min 2292.41 3.02309 2.50937 0.55\nprotocols.relax.FastRelax: MRP: 1 2292.41 2292.41 3.02309 2.50937 \nprotocols.relax.FastRelax: CMD: accept_to_best 2292.41 3.02309 2.50937 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 2292.41 3.02309 2.50937 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 2292.41 3.02309 2.50937 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1817.29 3.02309 2.50937 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 127 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1817.25\nprotocols.relax.FastRelax: CMD: repack 1817.29 3.02309 2.50937 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1822.73 3.02309 2.50937 0.02805\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.38419e-07 Deriv= -192.95 Finite Diff= 103.566\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.38053e-09 Deriv= -1.73808e+06 Finite Diff= 165051\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.88647e-09 Deriv= -1589.51 Finite Diff= 616.165\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.10434e-09 Deriv= -8093.96 Finite Diff= 405.321\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.92309e-07 Deriv= -681.232 Finite Diff= 10.5201\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#52\nprotocols.relax.FastRelax: CMD: min 1586.39 3.20794 2.80892 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1586.39 3.20794 2.80892 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1947.43 3.20794 2.80892 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 89 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1947.21\nprotocols.relax.FastRelax: CMD: repack 1947.43 3.20794 2.80892 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1972.74 3.20794 2.80892 0.154\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -1300.56 Finite Diff= 283.997\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.70026e-09 Deriv= -17721.7 Finite Diff= 64.8908\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.15767e-09 Deriv= -14064.3 Finite Diff= -396.418\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.99551e-09 Deriv= -4536.67 Finite Diff= 322.342\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.19217e-09 Deriv= -4663.02 Finite Diff= 340.651\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.54775e-09 Deriv= -17417.6 Finite Diff= 866.112\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.73512e-07 Deriv= -1933.4 Finite Diff= -179.268\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#66\nprotocols.relax.FastRelax: CMD: min 1834.13 3.07319 2.59309 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1834.13 3.07319 2.59309 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 2071.36 3.07319 2.59309 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 89 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 2071.56\nprotocols.relax.FastRelax: CMD: repack 2071.36 3.07319 2.59309 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 2090.07 3.07319 2.59309 0.31955\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -4.25825 Finite Diff= 0.155973\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.08651e-09 Deriv= -32762.8 Finite Diff= 4028.35\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.91908e-09 Deriv= -11708.6 Finite Diff= 1974.47\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.28982e-09 Deriv= -11860.1 Finite Diff= 1995.81\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.50013e-07 Deriv= -2586.57 Finite Diff= -254.534\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#95\nprotocols.relax.FastRelax: CMD: min 2066.01 3.04339 2.55887 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 2066.01 3.04339 2.55887 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 2365.72 3.04339 2.55887 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 85 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 2366.01\nprotocols.relax.FastRelax: CMD: repack 2365.72 3.04339 2.55887 0.55\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.72529e-09 Deriv= -1169 Finite Diff= 223.962\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.72529e-09 Deriv= -7.71333 Finite Diff= 1.78784\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.83193e-09 Deriv= -72.7475 Finite Diff= 15.9514\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.23031e-09 Deriv= -144.765 Finite Diff= 44.516\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.88974e-09 Deriv= -47.5057 Finite Diff= 13.0158\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.16761e-09 Deriv= -215.711 Finite Diff= 8.6366\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.85117e-06 Deriv= -16.9858 Finite Diff= 4.54884\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1274\nprotocols.relax.FastRelax: CMD: min 1925.35 4.65209 4.45928 0.55\nprotocols.relax.FastRelax: MRP: 2 1925.35 1925.35 4.65209 4.45928 \nprotocols.relax.FastRelax: CMD: accept_to_best 1925.35 4.65209 4.45928 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 1925.35 4.65209 4.45928 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_2=======================\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 0\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is not s6 symmetric.\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\nprotocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: Filter reports failure!\nprotocols.generalized_kinematic_closure.GeneralizedKIC: Preselection mover failed! Continuing to next solution.\nprotocols.generalized_kinematic_closure.GeneralizedKIC: Applying pre-selection mover to solution 2 from attempt 18.\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_1=======================\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 0\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is not s6 symmetric.\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\nprotocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: Filter reports failure!\nprotocols.generalized_kinematic_closure.GeneralizedKIC: Preselection mover failed! Continuing to next solution.\nprotocols.generalized_kinematic_closure.GeneralizedKIC: Applying pre-selection mover to solution 1 from attempt 19.\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_1=======================\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 1\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is s6 symmetric.\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\nprotocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER CrosslinkerMover - square_pyramidal_metal_link_1=======================\nprotocols.cyclic_peptide.CrosslinkerMover: Sidechain distance filter PASSED.\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\nprotocols.relax.FastRelax: CMD: repeat 2.27604e+06 0 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 2.27604e+06 0 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 2.27462e+06 0 0 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 94 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 316331\nprotocols.relax.FastRelax: CMD: repack 316349 0 0 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 316394 0 0 0.02805\nprotocols.relax.FastRelax: CMD: min 11835.5 0 0 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 11835.5 0 0 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 12981.4 0 0 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 64 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 12958.3\nprotocols.relax.FastRelax: CMD: repack 12981.4 0 0 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 13061.7 0 0 0.154\nprotocols.relax.FastRelax: CMD: min 13060.7 0 0 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 13060.7 0 0 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 14552.1 0 0 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 56 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 14523.3\nprotocols.relax.FastRelax: CMD: repack 14552.1 0 0 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 14669.7 0 0 0.31955\nprotocols.relax.FastRelax: CMD: min 14667.9 0 0 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 14667.9 0 0 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 16902.5 0 0 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 53 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 16862.9\nprotocols.relax.FastRelax: CMD: repack 16902.5 0 0 0.55\nprotocols.relax.FastRelax: CMD: min 16898.9 0 0 0.55\nprotocols.relax.FastRelax: MRP: 0 16898.9 16898.9 0 0 \nprotocols.relax.FastRelax: CMD: accept_to_best 16898.9 0 0 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 16898.9 0 0 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\nprotocols.relax.FastRelax: CMD: repeat 16898.9 0 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 16898.9 0 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 11795.5 0 0 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 94 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 11777.3\nprotocols.relax.FastRelax: CMD: repack 11795.5 0 0 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 11853.9 0 0 0.02805\nprotocols.relax.FastRelax: CMD: min 11835.5 0 0 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 11835.5 0 0 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 12981.4 0 0 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 64 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 12958.3\nprotocols.relax.FastRelax: CMD: repack 12981.4 0 0 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 13061.7 0 0 0.154\nprotocols.relax.FastRelax: CMD: min 13060.7 0 0 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 13060.7 0 0 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 14552.1 0 0 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 56 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 14522.6\nprotocols.relax.FastRelax: CMD: repack 14552.1 0 0 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 14669.7 0 0 0.31955\nprotocols.relax.FastRelax: CMD: min 14667.8 0 0 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 14667.8 0 0 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 16902.4 0 0 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 53 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 16862.4\nprotocols.relax.FastRelax: CMD: repack 16902.4 0 0 0.55\nprotocols.relax.FastRelax: CMD: min 16898.9 0 0 0.55\nprotocols.relax.FastRelax: MRP: 0 16898.9 16898.9 0 0 \nprotocols.relax.FastRelax: CMD: accept_to_best 16898.9 0 0 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 16898.9 0 0 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\nprotocols.relax.FastRelax: CMD: repeat 16898.9 0 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 16898.9 0 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 11795.5 0 0 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 94 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 11777.3\nprotocols.relax.FastRelax: CMD: repack 11795.5 0 0 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 11854 0 0 0.02805\nprotocols.relax.FastRelax: CMD: min 11835.5 0 0 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 11835.5 0 0 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 12981.4 0 0 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 64 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 12957.7\nprotocols.relax.FastRelax: CMD: repack 12981.4 0 0 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 13061.7 0 0 0.154\nprotocols.relax.FastRelax: CMD: min 13060.7 0 0 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 13060.7 0 0 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 14552.1 0 0 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 56 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 14523.1\nprotocols.relax.FastRelax: CMD: repack 14552.1 0 0 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 14669.7 0 0 0.31955\nprotocols.relax.FastRelax: CMD: min 14667.8 0 0 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 14667.8 0 0 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 16902.4 0 0 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 53 rotamers at 5 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: DHHDH, best_energy: 16863.3\nprotocols.relax.FastRelax: CMD: repack 16902.4 0 0 0.55\nprotocols.relax.FastRelax: CMD: min 16898.9 0 0 0.55\nprotocols.relax.FastRelax: MRP: 0 16898.9 16898.9 0 0 \nprotocols.relax.FastRelax: CMD: accept_to_best 16898.9 0 0 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 16898.9 0 0 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\ncore.scoring.constraints.ConstraintsIO: Read in 1 constraints\nprotocols.cyclic_peptide.crosslinker.CrosslinkerMoverHelper: Constraint energy for crosslinked pose is 11572.6. Filter passes.\nprotocols.cyclic_peptide.CrosslinkerMover: Linker constraints filter PASSED.\nprotocols.cyclic_peptide.CrosslinkerMover: CrosslinkerMover reports SUCCESS. Updating pose.\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - High_Hbond_FastRelax=======================\nprotocols.relax.FastRelax: CMD: repeat 16898.9 2.00488 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 16898.9 2.00488 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 11795.5 2.00488 0 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 119 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 11795.5\nprotocols.relax.FastRelax: CMD: repack 11795.5 2.00488 0 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 11854 2.00488 0 0.02805\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.19209e-07 Deriv= -191.675 Finite Diff= -9.31294\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.59013e-07 Deriv= -305.807 Finite Diff= -28.7572\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.13495e-09 Deriv= -10854.9 Finite Diff= 2037.12\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.38419e-07 Deriv= -286.734 Finite Diff= 29.1336\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.51474e-09 Deriv= -10367.2 Finite Diff= 534.814\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.74815e-09 Deriv= -68026.2 Finite Diff= 17066.2\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.28127e-09 Deriv= -14885.8 Finite Diff= 1738.01\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.87374e-09 Deriv= -55319.5 Finite Diff= 9810.51\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.88058e-07 Deriv= -1645.87 Finite Diff= 549.151\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#132\nprotocols.relax.FastRelax: CMD: min 1173.07 2.57139 2.19549 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1173.07 2.57139 2.19549 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1291.03 2.57139 2.19549 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 109 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1288.96\nprotocols.relax.FastRelax: CMD: repack 1291.03 2.57139 2.19549 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1299.3 2.57139 2.19549 0.154\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.76837e-09 Deriv= -25734.1 Finite Diff= 2381.06\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.97792e-09 Deriv= -24293 Finite Diff= 4569.25\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.11994e-09 Deriv= -46462.8 Finite Diff= 7056.33\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.25996e-09 Deriv= -8684.12 Finite Diff= 321.654\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.0035e-07 Deriv= -5780.19 Finite Diff= -569.947\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#19\nprotocols.relax.FastRelax: CMD: min 1299.1 2.56946 2.19539 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1299.1 2.56946 2.19539 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1451.61 2.56946 2.19539 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 104 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1450.27\nprotocols.relax.FastRelax: CMD: repack 1451.61 2.56946 2.19539 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1463.63 2.56946 2.19539 0.31955\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.65661e-10 Deriv= -193.157 Finite Diff= -2.89746\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.74762e-09 Deriv= -15469.2 Finite Diff= 973.583\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.17213e-09 Deriv= -85799.2 Finite Diff= 2211.62\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.07562e-08 Deriv= -11626.6 Finite Diff= 1777.07\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#49\nprotocols.relax.FastRelax: CMD: min 1345.24 2.60714 2.21991 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1345.24 2.60714 2.21991 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1480.99 2.60714 2.21991 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 106 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1480.02\nprotocols.relax.FastRelax: CMD: repack 1480.99 2.60714 2.21991 0.55\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -16619.6 Finite Diff= -1570.15\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.91807e-08 Deriv= -16619.6 Finite Diff= -1569.06\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\nprotocols.relax.FastRelax: CMD: min 1480.99 2.60714 2.21991 0.55\nprotocols.relax.FastRelax: MRP: 0 1480.99 1480.99 2.60714 2.21991 \nprotocols.relax.FastRelax: CMD: accept_to_best 1480.99 2.60714 2.21991 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 1480.99 2.60714 2.21991 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1480.99 2.60714 2.21991 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1169.95 2.60714 2.21991 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 126 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1168.21\nprotocols.relax.FastRelax: CMD: repack 1169.95 2.60714 2.21991 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1173.52 2.60714 2.21991 0.02805\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.05176e-07 Deriv= -172.842 Finite Diff= 7.43715\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.1924e-09 Deriv= -8017.77 Finite Diff= 1781.39\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.89979e-08 Deriv= -12226.7 Finite Diff= -967.826\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#39\nprotocols.relax.FastRelax: CMD: min 1134.28 2.6401 2.21915 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1134.28 2.6401 2.21915 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1229.29 2.6401 2.21915 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 109 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1228.29\nprotocols.relax.FastRelax: CMD: repack 1229.29 2.6401 2.21915 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1235.95 2.6401 2.21915 0.154\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.76837e-09 Deriv= -40533.5 Finite Diff= 8218.89\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.52324e-08 Deriv= -8012.55 Finite Diff= 1193.46\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#6\nprotocols.relax.FastRelax: CMD: min 1234.82 2.63818 2.22017 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1234.82 2.63818 2.22017 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1356.85 2.63818 2.22017 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 103 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1355.87\nprotocols.relax.FastRelax: CMD: repack 1356.85 2.63818 2.22017 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1366.47 2.63818 2.22017 0.31955\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.76837e-09 Deriv= -62968.2 Finite Diff= 1908.32\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.2628e-08 Deriv= -11035 Finite Diff= -298.709\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#8\nprotocols.relax.FastRelax: CMD: min 1365.95 2.64072 2.22312 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1365.95 2.64072 2.22312 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1546.58 2.64072 2.22312 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 95 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1545.34\nprotocols.relax.FastRelax: CMD: repack 1546.58 2.64072 2.22312 0.55\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.90735e-06 Deriv= -347.63 Finite Diff= 121.273\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.61206e-09 Deriv= -12084.8 Finite Diff= 798.047\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.6693e-09 Deriv= -7510.53 Finite Diff= 2182.57\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.60471e-09 Deriv= -7176.46 Finite Diff= 337.069\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.47173e-09 Deriv= -5983.24 Finite Diff= 745.971\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.19969e-07 Deriv= -4044.27 Finite Diff= 295.008\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#59\nprotocols.relax.FastRelax: CMD: min 1382.32 2.92034 2.57542 0.55\nprotocols.relax.FastRelax: MRP: 1 1382.32 1382.32 2.92034 2.57542 \nprotocols.relax.FastRelax: CMD: accept_to_best 1382.32 2.92034 2.57542 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 1382.32 2.92034 2.57542 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1382.32 2.92034 2.57542 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1215.29 2.92034 2.57542 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 125 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1213.23\nprotocols.relax.FastRelax: CMD: repack 1215.29 2.92034 2.57542 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1217.2 2.92034 2.57542 0.02805\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.76837e-09 Deriv= -31333.3 Finite Diff= 8438.16\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.98102e-09 Deriv= -18112 Finite Diff= -1659.67\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.43075e-09 Deriv= -45137.8 Finite Diff= 4608.19\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.23358e-09 Deriv= -951589 Finite Diff= 56644.8\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.68167e-09 Deriv= -80488.2 Finite Diff= -1285.97\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.17503e-11 Deriv= -437835 Finite Diff= -14682\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.95003e-09 Deriv= -76639.7 Finite Diff= 627.048\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.80542e-08 Deriv= -6054.08 Finite Diff= -380.572\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#40\nprotocols.relax.FastRelax: CMD: min 1192.16 2.88467 2.54286 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1192.16 2.88467 2.54286 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1240.81 2.88467 2.54286 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 110 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1238.92\nprotocols.relax.FastRelax: CMD: repack 1240.81 2.88467 2.54286 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1244.22 2.88467 2.54286 0.154\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -5668.11 Finite Diff= -317.136\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.01338e-07 Deriv= -5668.11 Finite Diff= -316.31\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\nprotocols.relax.FastRelax: CMD: min 1244.22 2.88467 2.54286 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1244.22 2.88467 2.54286 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1307.65 2.88467 2.54286 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 108 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1304.43\nprotocols.relax.FastRelax: CMD: repack 1307.65 2.88467 2.54286 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1312.65 2.88467 2.54286 0.31955\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.76837e-09 Deriv= -41516.6 Finite Diff= 2692.69\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.9197e-09 Deriv= -109333 Finite Diff= 12206.7\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.31731e-08 Deriv= -8414.23 Finite Diff= -764.142\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#11\nprotocols.relax.FastRelax: CMD: min 1311.76 2.88425 2.54411 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1311.76 2.88425 2.54411 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1404.68 2.88425 2.54411 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 106 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1402.82\nprotocols.relax.FastRelax: CMD: repack 1404.68 2.88425 2.54411 0.55\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -5423.41 Finite Diff= 720.933\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.2295e-13 Deriv= -2799.48 Finite Diff= 876.577\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.77737e-09 Deriv= -4033.68 Finite Diff= 297.738\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.74889e-09 Deriv= -3007.34 Finite Diff= 130.775\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.84995e-07 Deriv= -1700.82 Finite Diff= -120.398\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#38\nprotocols.relax.FastRelax: CMD: min 1400.45 2.89585 2.56116 0.55\nprotocols.relax.FastRelax: MRP: 2 1400.45 1382.32 2.92034 2.57542 \nprotocols.relax.FastRelax: CMD: accept_to_best 1400.45 2.89585 2.56116 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 1400.45 2.89585 2.56116 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER DeclareBond - Update_cyclization_point_polymer_dependent_atoms_2=======================\nprotocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: Set filter value for in pose: 1\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: This peptide is s6 symmetric.\nprotocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================\nprotocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================\nprotocols.rosetta_scripts.ParsedProtocol: setting status to success\nprotocols.generalized_kinematic_closure.GeneralizedKIC: Storing solution 1 from attempt 19.\nprotocols.generalized_kinematic_closure.selector.GeneralizedKICselector: Choosing GeneralizedKIC solution.\nprotocols.generalized_kinematic_closure.GeneralizedKIC: Closure successful.\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Closure successful.\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Setting up terminal bond between residue 1, atom N and residue 30, atom C .\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Applying final FastRelax, round 1.\nprotocols.relax.FastRelax: CMD: repeat 1469.33 0 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1469.33 0 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1302.32 0 0 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 125 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1301.11\nprotocols.relax.FastRelax: CMD: repack 1302.32 0 0 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1304.23 0 0 0.02805\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.45058e-09 Deriv= -95.2445 Finite Diff= 8.25647\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.33587e-09 Deriv= -350249 Finite Diff= 66962.9\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.26239e-10 Deriv= -315984 Finite Diff= -8167.47\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.27153e-09 Deriv= -295195 Finite Diff= 13359.6\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.98865e-09 Deriv= -143184 Finite Diff= 7845.65\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.35148e-07 Deriv= -3186.85 Finite Diff= -148.283\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#58\nprotocols.relax.FastRelax: CMD: min 1196.09 0.462972 0.462972 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1196.09 0.462972 0.462972 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1302.02 0.462972 0.462972 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 108 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1300.71\nprotocols.relax.FastRelax: CMD: repack 1302.02 0.462972 0.462972 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1309.44 0.462972 0.462972 0.154\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -5663.02 Finite Diff= -179.938\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.01383e-07 Deriv= -5663.02 Finite Diff= -179.411\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1\nprotocols.relax.FastRelax: CMD: min 1309.44 0.462972 0.462972 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1309.44 0.462972 0.462972 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1447.55 0.462972 0.462972 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 102 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1446.56\nprotocols.relax.FastRelax: CMD: repack 1447.55 0.462972 0.462972 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1458.44 0.462972 0.462972 0.31955\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.49012e-08 Deriv= -485.247 Finite Diff= 127.986\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.2035e-09 Deriv= -26416.7 Finite Diff= 4816.26\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.82318e-09 Deriv= -34861.9 Finite Diff= 6359.85\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.2788e-09 Deriv= -26789 Finite Diff= 8039.87\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.39839e-07 Deriv= -2976.64 Finite Diff= -280.293\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#51\nprotocols.relax.FastRelax: CMD: min 1366.17 0.245638 0.245638 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1366.17 0.245638 0.245638 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1459.85 0.245638 0.245638 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 104 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1460.6\nprotocols.relax.FastRelax: CMD: repack 1459.85 0.245638 0.245638 0.55\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.76837e-09 Deriv= -4838.76 Finite Diff= 724.382\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.18727e-09 Deriv= -40655 Finite Diff= 4803.01\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.12395e-10 Deriv= -17074.6 Finite Diff= -376.632\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.9975e-09 Deriv= -96068.3 Finite Diff= 1784.37\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.54845e-08 Deriv= -6384.32 Finite Diff= -583.777\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#25\nprotocols.relax.FastRelax: CMD: min 1458.25 0.250845 0.250845 0.55\nprotocols.relax.FastRelax: MRP: 0 1458.25 1458.25 0.250845 0.250845 \nprotocols.relax.FastRelax: CMD: accept_to_best 1458.25 0.250845 0.250845 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 1458.25 0.250845 0.250845 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Applying final FastRelax, round 2.\nprotocols.relax.FastRelax: CMD: repeat 1458.54 0.250845 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1458.54 0.250845 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1252.22 0.250845 0 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 110 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1252.18\nprotocols.relax.FastRelax: CMD: repack 1252.22 0.250845 0 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1254.58 0.250845 0 0.02805\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.76837e-09 Deriv= -2.997e+06 Finite Diff= 239239\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.06579e-11 Deriv= -67756.3 Finite Diff= -1232.92\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.78986e-09 Deriv= -23299.1 Finite Diff= 33.6277\ncore.optimization.LineMinimizer: Inaccurate G in step= 7.95986e-09 Deriv= -276526 Finite Diff= 22489.7\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.26727e-07 Deriv= -3624.45 Finite Diff= 132.059\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#26\nprotocols.relax.FastRelax: CMD: min 1243.87 0.253463 0.0414033 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1243.87 0.253463 0.0414033 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1298.12 0.253463 0.0414033 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 105 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1298.46\nprotocols.relax.FastRelax: CMD: repack 1298.12 0.253463 0.0414033 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1301.92 0.253463 0.0414033 0.154\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.76837e-09 Deriv= -33262 Finite Diff= 6656.11\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.11173e-07 Deriv= -4709.61 Finite Diff= -338.873\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#6\nprotocols.relax.FastRelax: CMD: min 1301.91 0.25345 0.0414407 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1301.91 0.25345 0.0414407 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1372.62 0.25345 0.0414407 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 105 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1372.42\nprotocols.relax.FastRelax: CMD: repack 1372.62 0.25345 0.0414407 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1378.19 0.25345 0.0414407 0.31955\ncore.optimization.LineMinimizer: Inaccurate G in step= 4.76837e-09 Deriv= -13483.5 Finite Diff= 800.002\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.45719e-09 Deriv= -28983.8 Finite Diff= 2674.17\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.86356e-09 Deriv= -28250.8 Finite Diff= 2906.32\ncore.optimization.LineMinimizer: Inaccurate G in step= 2.57097e-09 Deriv= -27696.2 Finite Diff= 3007.79\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.56407e-08 Deriv= -7936.32 Finite Diff= -702.591\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#15\nprotocols.relax.FastRelax: CMD: min 1377.52 0.254536 0.0444211 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1377.52 0.254536 0.0444211 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1481.36 0.254536 0.0444211 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 104 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1481.32\nprotocols.relax.FastRelax: CMD: repack 1481.36 0.254536 0.0444211 0.55\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.8147e-08 Deriv= -461.039 Finite Diff= -36.7345\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.26662e-09 Deriv= -10772.1 Finite Diff= 1621.76\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.31202e-09 Deriv= -107130 Finite Diff= 16475.1\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.23838e-09 Deriv= -445255 Finite Diff= 80448.2\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.00688e-07 Deriv= -5741.5 Finite Diff= 1637.52\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#31\nprotocols.relax.FastRelax: CMD: min 1455.17 0.289373 0.11156 0.55\nprotocols.relax.FastRelax: MRP: 0 1455.17 1455.17 0.289373 0.11156 \nprotocols.relax.FastRelax: CMD: accept_to_best 1455.17 0.289373 0.11156 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 1455.17 0.289373 0.11156 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Applying final FastRelax, round 3.\nprotocols.relax.FastRelax: CMD: repeat 1455.61 0.289373 0 0.55\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1455.61 0.289373 0 0.55\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1279.06 0.289373 0 0.022\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 111 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1279.02\nprotocols.relax.FastRelax: CMD: repack 1279.06 0.289373 0 0.022\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1281.08 0.289373 0 0.02805\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.49012e-08 Deriv= -2656.09 Finite Diff= 69.3866\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.82358e-09 Deriv= -156493 Finite Diff= 4289.54\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.71461e-10 Deriv= -47200.5 Finite Diff= -3092.83\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.36984e-07 Deriv= -3101.99 Finite Diff= 298.019\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#48\nprotocols.relax.FastRelax: CMD: min 1194.07 0.505442 0.413936 0.02805\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1194.07 0.505442 0.413936 0.02805\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1305.3 0.505442 0.413936 0.14575\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 100 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1304.8\nprotocols.relax.FastRelax: CMD: repack 1305.3 0.505442 0.413936 0.14575\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1313.1 0.505442 0.413936 0.154\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -45277.9 Finite Diff= 934.555\ncore.optimization.LineMinimizer: Inaccurate G in step= 8.92259e-09 Deriv= -45855.9 Finite Diff= 5844.32\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.40968e-07 Deriv= -2929.13 Finite Diff= 1045.61\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#14\nprotocols.relax.FastRelax: CMD: min 1310.35 0.509989 0.419643 0.154\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1310.35 0.509989 0.419643 0.154\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1449.5 0.509989 0.419643 0.30745\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 97 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1448.93\nprotocols.relax.FastRelax: CMD: repack 1449.5 0.509989 0.419643 0.30745\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1460.48 0.509989 0.419643 0.31955\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -105338 Finite Diff= 3490.19\ncore.optimization.LineMinimizer: Inaccurate G in step= 5.13346e-09 Deriv= -49832 Finite Diff= 955.168\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.78437e-07 Deriv= -1828.14 Finite Diff= -132.408\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#66\nprotocols.relax.FastRelax: CMD: min 1358.42 0.358905 0.236546 0.31955\nprotocols.relax.FastRelax: CMD: coord_cst_weight 1358.42 0.358905 0.236546 0.31955\nprotocols.relax.FastRelax: CMD: scale:fa_rep 1443.82 0.358905 0.236546 0.55\ncore.pack.task: Packer task: initialize from command line() \ncore.pack.pack_rotamers: built 103 rotamers at 30 positions.\ncore.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph\ncore.pack.annealer.FixbbSimAnnealer: pack_rotamers run final: GGGGDGGGGHGGGGHGGGGDGGGGHGGGGG, best_energy: 1442.31\nprotocols.relax.FastRelax: CMD: repack 1443.82 0.358905 0.236546 0.55\ncore.optimization.LineMinimizer: Inaccurate G in step= 9.53674e-09 Deriv= -7256.59 Finite Diff= 813.799\ncore.optimization.LineMinimizer: Inaccurate G in step= 6.84785e-09 Deriv= -3913.87 Finite Diff= 1418.91\ncore.optimization.LineMinimizer: Inaccurate G in step= 3.57508e-09 Deriv= -2362.57 Finite Diff= 966.002\ncore.optimization.LineMinimizer: Inaccurate G in step= 1.36995e-07 Deriv= -3101.48 Finite Diff= -147.667\ncore.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#18\nprotocols.relax.FastRelax: CMD: min 1441.93 0.36303 0.233076 0.55\nprotocols.relax.FastRelax: MRP: 0 1441.93 1441.93 0.36303 0.233076 \nprotocols.relax.FastRelax: CMD: accept_to_best 1441.93 0.36303 0.233076 0.55\nprotocols.relax.FastRelax: CMD: endrepeat 1441.93 0.36303 0.233076 0.55\nprotocols::checkpoint: Deleting checkpoints of FastRelax\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: Final symmetry filter failed. This peptide lost s6symmetry during the final relaxation.\nprotocols.cyclic_peptide_predict.SimpleCycpepPredictApplication: 1 jobs attempted. 0 jobs returned solutions.\nbasic.citation_manager.CitationManager: \nThe following Rosetta modules were used during this run of Rosetta, and should be cited:\n\nsimple_cycpep_predict Application's citation(s):\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.)\n\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.)\n\nMulligan 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.\n\n\napps.public.cyclic_peptide.simple_cycpep_predict: Finished simple_cycpep_predict.cc. 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