Branch: rosetta:commits 「revision: №20469」
Test: linux.clang.python310.PyRosetta.unit
SubTest: T005_Bindings
SubTest files: 「file-system-view」
Daemon: hojo-3    
State: T005_Bindings

┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+5.HEAD.c9abca83f0a4dd927aceaa98f4ceeb8708e10f37 2024-09-07T17:30:08] retrieved from: git@github.com:RosettaCommons/rosetta.git ┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+5.HEAD.c9abca83f0a4dd927aceaa98f4ceeb8708e10f37 2024-09-07T17:30:08] retrieved from: git@github.com:RosettaCommons/rosetta.git Total residues: 0 Sequence: Fold tree: FOLD_TREE Total residues: 0 Sequence: Fold tree: FOLD_TREE ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: EnergyMethodOptions::show: mhc_epitope_setup_files: EnergyMethodOptions::show: netcharge_setup_files: EnergyMethodOptions::show: aspartimide_penalty_value: 25 EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid EnergyMethodOptions::show: covalent_labeling_input: EnergyMethodOptions::show: covalent_labeling_fa_input: EnergyMethodOptions::show: hrf_dynamics_input: EnergyMethodOptions::show: depc_ms_input: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false EnergyMethodOptions::show: exclude_monomer_fa_elec: false EnergyMethodOptions::show: elec_max_dis: 5.5 EnergyMethodOptions::show: elec_min_dis: 1.6 EnergyMethodOptions::show: elec_die: 10 EnergyMethodOptions::show: elec_no_dis_dep_die: false EnergyMethodOptions::show: elec_sigmoidal_die: true EnergyMethodOptions::show: elec_sigmoidal_D: 80 EnergyMethodOptions::show: elec_sigmoidal_D0: 6 EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 EnergyMethodOptions::show: smooth_fa_elec: true EnergyMethodOptions::show: grpelec_fade_type: false EnergyMethodOptions::show: grpelec_fade_param1: 1 EnergyMethodOptions::show: grpelec_fade_param2: 1 EnergyMethodOptions::show: grpelec_fade_hbond: 0 EnergyMethodOptions::show: grp_cpfxn: 1 EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat EnergyMethodOptions::show: grpelec_context_dependent: 0 EnergyMethodOptions::show: use_polarization: true EnergyMethodOptions::show: use_gen_kirkwood: true EnergyMethodOptions::show: protein_dielectric: 1 EnergyMethodOptions::show: water_dielectric: 78.3 EnergyMethodOptions::show: exclude_DNA_DNA: false EnergyMethodOptions::show: exclude_intra_res_protein: false EnergyMethodOptions::show: count_pair_hybrid: false EnergyMethodOptions::show: count_pair_full: false EnergyMethodOptions::show: put_intra_into_total: false EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true EnergyMethodOptions::show: eval_intrares_elec_ST_only: false EnergyMethodOptions::show: envsmooth_zero_negatives: false EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 EnergyMethodOptions::show: pb_bound_tag: bound EnergyMethodOptions::show: pb_unbound_tag: unbound EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 EnergyMethodOptions::show: ordered_wat_penalty: 1.221 EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 EnergyMethodOptions::show: nmer_ref_seq_length_: 9 EnergyMethodOptions::show: nmer_svm_term_length_: 3 EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 EnergyMethodOptions::show: nmer_svm_scorecut_: 0 EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_list_: EnergyMethodOptions::show: nmer_svm_defined_: 0 EnergyMethodOptions::show: nmer_svm_: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_list_: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" EnergyMethodOptions::show: hbnet_max_network_size_: 0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 EnergyMethodOptions::show: target_clash_pdb_: EnergyMethodOptions::show: dump_trajectory_prefix_: traj EnergyMethodOptions::show: dump_trajectory_gz_: FALSE EnergyMethodOptions::show: dump_trajectory_stride_: 1 EnergyMethodOptions::show: bond_angle_central_atoms_to_score: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none HBondOptions::show: hb_max_energy: 0 HBondOptions::show: exclude_DNA_DNA: false HBondOptions::show: exclude_intra_res_protein_: false HBondOptions::show: exclude_intra_res_RNA_: false HBondOptions::show: put_intra_into_total_: false HBondOptions::show: exclude_self_hbonds: true HBondOptions::show: use_hb_env_dep: false HBondOptions::show: use_hb_env_dep_DNA: true HBondOptions::show: smooth_hb_env_dep: true HBondOptions::show: bb_donor_acceptor_check: true HBondOptions::show: decompose_bb_hb_into_pair_energies: false HBondOptions::show: params_database_tag_: ref2015_params HBondOptions::show: use_sp2_chi_penalty_: true HBondOptions::show: sp2_BAH180_rise_: 0.75 HBondOptions::show: sp2_outer_width_: 0.357 HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true HBondOptions::show: fade_energy_: 1 HBondOptions::show: exclude_ether_oxygens_: 0 HBondOptions::show: Mbhbond: false HbondOptions::show: mphbond: false HBondOptions::show: hbond_energy_shift: 0 HBondOptions::show: water_hybrid_sf: false RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat FreeDOF_Options::show: free_suite_bonus: -1 FreeDOF_Options::show: free_2HOprime_bonus: -0.5 FreeDOF_Options::show: free_sugar_bonus: -1 FreeDOF_Options::show: pack_phosphate_penalty: 0.25 FreeDOF_Options::show: free_side_chain_bonus: -0.5 rosetta.protocols.toolbox.PyReturnValuePolicyTest_ScoreFunctionOP() PASSED ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: EnergyMethodOptions::show: mhc_epitope_setup_files: EnergyMethodOptions::show: netcharge_setup_files: EnergyMethodOptions::show: aspartimide_penalty_value: 25 EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid EnergyMethodOptions::show: covalent_labeling_input: EnergyMethodOptions::show: covalent_labeling_fa_input: EnergyMethodOptions::show: hrf_dynamics_input: EnergyMethodOptions::show: depc_ms_input: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false EnergyMethodOptions::show: exclude_monomer_fa_elec: false EnergyMethodOptions::show: elec_max_dis: 5.5 EnergyMethodOptions::show: elec_min_dis: 1.6 EnergyMethodOptions::show: elec_die: 10 EnergyMethodOptions::show: elec_no_dis_dep_die: false EnergyMethodOptions::show: elec_sigmoidal_die: true EnergyMethodOptions::show: elec_sigmoidal_D: 80 EnergyMethodOptions::show: elec_sigmoidal_D0: 6 EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 EnergyMethodOptions::show: smooth_fa_elec: true EnergyMethodOptions::show: grpelec_fade_type: false EnergyMethodOptions::show: grpelec_fade_param1: 1 EnergyMethodOptions::show: grpelec_fade_param2: 1 EnergyMethodOptions::show: grpelec_fade_hbond: 0 EnergyMethodOptions::show: grp_cpfxn: 1 EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat EnergyMethodOptions::show: grpelec_context_dependent: 0 EnergyMethodOptions::show: use_polarization: true EnergyMethodOptions::show: use_gen_kirkwood: true EnergyMethodOptions::show: protein_dielectric: 1 EnergyMethodOptions::show: water_dielectric: 78.3 EnergyMethodOptions::show: exclude_DNA_DNA: false EnergyMethodOptions::show: exclude_intra_res_protein: false EnergyMethodOptions::show: count_pair_hybrid: false EnergyMethodOptions::show: count_pair_full: false EnergyMethodOptions::show: put_intra_into_total: false EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true EnergyMethodOptions::show: eval_intrares_elec_ST_only: false EnergyMethodOptions::show: envsmooth_zero_negatives: false EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 EnergyMethodOptions::show: pb_bound_tag: bound EnergyMethodOptions::show: pb_unbound_tag: unbound EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 EnergyMethodOptions::show: ordered_wat_penalty: 1.221 EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 EnergyMethodOptions::show: nmer_ref_seq_length_: 9 EnergyMethodOptions::show: nmer_svm_term_length_: 3 EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 EnergyMethodOptions::show: nmer_svm_scorecut_: 0 EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_list_: EnergyMethodOptions::show: nmer_svm_defined_: 0 EnergyMethodOptions::show: nmer_svm_: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_list_: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" EnergyMethodOptions::show: hbnet_max_network_size_: 0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 EnergyMethodOptions::show: target_clash_pdb_: EnergyMethodOptions::show: dump_trajectory_prefix_: traj EnergyMethodOptions::show: dump_trajectory_gz_: FALSE EnergyMethodOptions::show: dump_trajectory_stride_: 1 EnergyMethodOptions::show: bond_angle_central_atoms_to_score: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none HBondOptions::show: hb_max_energy: 0 HBondOptions::show: exclude_DNA_DNA: false HBondOptions::show: exclude_intra_res_protein_: false HBondOptions::show: exclude_intra_res_RNA_: false HBondOptions::show: put_intra_into_total_: false HBondOptions::show: exclude_self_hbonds: true HBondOptions::show: use_hb_env_dep: false HBondOptions::show: use_hb_env_dep_DNA: true HBondOptions::show: smooth_hb_env_dep: true HBondOptions::show: bb_donor_acceptor_check: true HBondOptions::show: decompose_bb_hb_into_pair_energies: false HBondOptions::show: params_database_tag_: ref2015_params HBondOptions::show: use_sp2_chi_penalty_: true HBondOptions::show: sp2_BAH180_rise_: 0.75 HBondOptions::show: sp2_outer_width_: 0.357 HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true HBondOptions::show: fade_energy_: 1 HBondOptions::show: exclude_ether_oxygens_: 0 HBondOptions::show: Mbhbond: false HbondOptions::show: mphbond: false HBondOptions::show: hbond_energy_shift: 0 HBondOptions::show: water_hybrid_sf: false RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat FreeDOF_Options::show: free_suite_bonus: -1 FreeDOF_Options::show: free_2HOprime_bonus: -0.5 FreeDOF_Options::show: free_sugar_bonus: -1 FreeDOF_Options::show: pack_phosphate_penalty: 0.25 FreeDOF_Options::show: free_side_chain_bonus: -0.5 rosetta.protocols.toolbox.PyReturnValuePolicyTest_ScoreFunctionCOP() PASSED ScoreFunction::show(): weights: energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: EnergyMethodOptions::show: mhc_epitope_setup_files: EnergyMethodOptions::show: netcharge_setup_files: EnergyMethodOptions::show: aspartimide_penalty_value: 25 EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid EnergyMethodOptions::show: covalent_labeling_input: EnergyMethodOptions::show: covalent_labeling_fa_input: EnergyMethodOptions::show: hrf_dynamics_input: EnergyMethodOptions::show: depc_ms_input: EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false EnergyMethodOptions::show: exclude_monomer_fa_elec: false EnergyMethodOptions::show: elec_max_dis: 5.5 EnergyMethodOptions::show: elec_min_dis: 1.6 EnergyMethodOptions::show: elec_die: 10 EnergyMethodOptions::show: elec_no_dis_dep_die: false EnergyMethodOptions::show: elec_sigmoidal_die: true EnergyMethodOptions::show: elec_sigmoidal_D: 80 EnergyMethodOptions::show: elec_sigmoidal_D0: 6 EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 EnergyMethodOptions::show: smooth_fa_elec: true EnergyMethodOptions::show: grpelec_fade_type: false EnergyMethodOptions::show: grpelec_fade_param1: 1 EnergyMethodOptions::show: grpelec_fade_param2: 1 EnergyMethodOptions::show: grpelec_fade_hbond: 0 EnergyMethodOptions::show: grp_cpfxn: 1 EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat EnergyMethodOptions::show: grpelec_context_dependent: 0 EnergyMethodOptions::show: use_polarization: true EnergyMethodOptions::show: use_gen_kirkwood: true EnergyMethodOptions::show: protein_dielectric: 1 EnergyMethodOptions::show: water_dielectric: 78.3 EnergyMethodOptions::show: exclude_DNA_DNA: false EnergyMethodOptions::show: exclude_intra_res_protein: true EnergyMethodOptions::show: count_pair_hybrid: false EnergyMethodOptions::show: count_pair_full: false EnergyMethodOptions::show: put_intra_into_total: false EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true EnergyMethodOptions::show: eval_intrares_elec_ST_only: false EnergyMethodOptions::show: envsmooth_zero_negatives: false EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 EnergyMethodOptions::show: pb_bound_tag: bound EnergyMethodOptions::show: pb_unbound_tag: unbound EnergyMethodOptions::show: arg_cation_pi_his_can_be_pi: 1 EnergyMethodOptions::show: ordered_wat_penalty: 1.221 EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 EnergyMethodOptions::show: nmer_ref_seq_length_: 9 EnergyMethodOptions::show: nmer_svm_term_length_: 3 EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 EnergyMethodOptions::show: nmer_svm_scorecut_: 0 EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 EnergyMethodOptions::show: nmer_svm_aa_matrix_: EnergyMethodOptions::show: nmer_svm_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_list_: EnergyMethodOptions::show: nmer_svm_defined_: 0 EnergyMethodOptions::show: nmer_svm_: EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_list_: EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 EnergyMethodOptions::show: nmer_svm_rank_: EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" EnergyMethodOptions::show: hbnet_max_network_size_: 0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 EnergyMethodOptions::show: approximate_buried_unsat_penalty_natural_corrections1_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_cross_chain_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb_:0 EnergyMethodOptions::show: approximate_buried_unsat_penalty_lys_ok_with_1_:0 EnergyMethodOptions::show: target_clash_pdb_: EnergyMethodOptions::show: dump_trajectory_prefix_: traj EnergyMethodOptions::show: dump_trajectory_gz_: FALSE EnergyMethodOptions::show: dump_trajectory_stride_: 1 EnergyMethodOptions::show: bond_angle_central_atoms_to_score: EnergyMethodOptions::show: bond_angle_residue_type_param_set: none HBondOptions::show: hb_max_energy: 0 HBondOptions::show: exclude_DNA_DNA: false HBondOptions::show: exclude_intra_res_protein_: true HBondOptions::show: exclude_intra_res_RNA_: false HBondOptions::show: put_intra_into_total_: false HBondOptions::show: exclude_self_hbonds: true HBondOptions::show: use_hb_env_dep: true HBondOptions::show: use_hb_env_dep_DNA: true HBondOptions::show: smooth_hb_env_dep: true HBondOptions::show: bb_donor_acceptor_check: true HBondOptions::show: decompose_bb_hb_into_pair_energies: false HBondOptions::show: params_database_tag_: ref2015_params HBondOptions::show: use_sp2_chi_penalty_: true HBondOptions::show: sp2_BAH180_rise_: 0.75 HBondOptions::show: sp2_outer_width_: 0.357 HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true HBondOptions::show: fade_energy_: 1 HBondOptions::show: exclude_ether_oxygens_: 0 HBondOptions::show: Mbhbond: false HbondOptions::show: mphbond: false HBondOptions::show: hbond_energy_shift: 0 HBondOptions::show: water_hybrid_sf: false RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat FreeDOF_Options::show: free_suite_bonus: -1 FreeDOF_Options::show: free_2HOprime_bonus: -0.5 FreeDOF_Options::show: free_sugar_bonus: -1 FreeDOF_Options::show: pack_phosphate_penalty: 0.25 FreeDOF_Options::show: free_side_chain_bonus: -0.5 rosetta.protocols.toolbox.PyReturnValuePolicyTest_ScoreFunctionCOP2() PASSED <pyrosetta.rosetta.protocols.toolbox.SF_Replica object at 0x7f5e837dc130> <pyrosetta.rosetta.protocols.toolbox.SF_Replica object at 0x7f5e837dc130> <pyrosetta.rosetta.protocols.toolbox.DummyClass object at 0x7f5e837dc130> <pyrosetta.rosetta.protocols.toolbox.DummyClass object at 0x7f5e837dc130> core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+5.HEAD.c9abca8 c9abca83f0a4dd927aceaa98f4ceeb8708e10f37 git@github.com:RosettaCommons/rosetta.git 2024-09-07T17:30:08 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.17/clang-3.4.2/python-3.10/minsizerel/build/pyrosetta/database basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-394848169 seed_offset=0 real_seed=-394848169 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-394848169 RG_type=mt19937 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.18 seconds. basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.17/clang-3.4.2/python-3.10/minsizerel/build/test/T005_Bindings.py:48: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'. from rosetta.protocols.toolbox.py_inheritance_test import * Finished T005_Bindings in 0:00:07.966832