Starting phenix.dock_and_rebuild on Sat Jun 4 09:14:28 2022 by amoiseenko =============================================================================== Processing files: ------------------------------------------------------------------------------- Found phil, /home/amoiseenko/projects/D57CPhage/.phenix/project_data/dock_and_rebuild_54.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /home/amoiseenko/projects/D57CPhage/.phenix/project_data/dock_and_rebuild_54.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found real_map, /home/amoiseenko/projects/D57CPhage/protein_box_maps/gp24.ccp4 Found model, /home/amoiseenko/projects/D57CPhage/Alphafold/gp24_f0a18_unrelaxed_rank_1_model_3.pdb Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/home/amoiseenko/projects/D57CPhage/Alphafold/gp24_f0a18_unrelaxed_rank_1_model_3.pdb" } default_model = "/home/amoiseenko/projects/D57CPhage/Alphafold/gp24_f0a18_unrelaxed_rank_1_model_3.pdb" phil_files = "/home/amoiseenko/projects/D57CPhage/.phenix/project_data/dock_and_rebuild_54.eff" default_phil = "/home/amoiseenko/projects/D57CPhage/.phenix/project_data/dock_and_rebuild_54.eff" real_map_files = "/home/amoiseenko/projects/D57CPhage/protein_box_maps/gp24.ccp4" default_real_map = "/home/amoiseenko/projects/D57CPhage/protein_box_maps/gp24.ccp4" } input_files { map_model { full_map = /home/amoiseenko/projects/D57CPhage/protein_box_maps/gp24.ccp4 model = /home/amoiseenko/projects/D57CPhage/Alphafold/gp24_f0a18_unrelaxed_rank_1_model_3.pdb } } crystal_info { resolution = 5.0 asymmetric_map = True } control { nproc = 20 } job_title = """gp24""" Starting job =============================================================================== ************************************************************ PHENIX dock_and_rebuild Sat Jun 4 09:14:28 2022 ************************************************************ Working directory: /home/amoiseenko/projects/D57CPhage/DockAndRebuild_54 PHENIX VERSION: 1.20.1-4487 Output prefix for files will be: /home/amoiseenko/projects/D57CPhage/DockAndRebuild_54/gp24_f0a18_unrelaxed_rank_1_model_3_rebuilt Input parameters for dock_and_rebuild: input_files { processed_model_file = None docked_model_file = None morphed_model_file = None previous_model_file = None fragments_model_file = None symmetry_file = None pae_file = None distance_model_file = None map_model { full_map = "/home/amoiseenko/projects/D57CPhage/protein_box_maps/gp24.ccp4" half_map = None model = "/home/amoiseenko/projects/D57CPhage/Alphafold/gp24_f0a18_unrelaxed_rank_1_model_3.pdb" } search_model_copies = None search_model = None } output_files { output_model_prefix = "/home/amoiseenko/projects/D57CPhage/DockAndRebuild_54/gp24_f0a18_unrelaxed_rank_1_model_3_rebuilt" pdb_out = None temp_dir = None } crystal_info { resolution = 5 scattering_table = n_gaussian wk1995 it1992 *electron neutron wrapping = False asymmetric_map = True solvent_content = None chain_type = *PROTEIN DNA RNA } process_predicted_model { remove_low_confidence_residues = True split_model_by_compact_regions = True maximum_domains = 3 domain_size = 15 minimum_domain_length = 10 maximum_fraction_close = 0.3 minimum_sequential_residues = 5 minimum_remainder_sequence_length = 15 b_value_field_is = *lddt rmsd b_value input_lddt_is_fractional = None minimum_lddt = None maximum_rmsd = 1.5 default_maximum_rmsd = 1.5 subtract_minimum_b = False pae_power = 1 pae_cutoff = 5 pae_graph_resolution = 1 weight_by_ca_ca_distance = False distance_power = 1 } search { dock_chains_individually = False create_unique_chain_at_end = None minimum_cc_to_keep_domain = 0.2 weight_sequential_fragments_by_distance = None choose_better_of_individual_and_group_docking = None low_res_search = True ssm_search = None refine_cycles = 3 ssm_search_min_cc = 0.3 backup_resolution_cutoff_searches = 2 backup_resolution_ratio = 1.67 resolution_radius_scale = 0.5 align_moments = False max_radius_ratio = 2 radius_scale = 1.5 use_symmetry = True skip_if_low_cc = True rigid_body_refinement = True rigid_body_refinement_single_unit = True rigid_body_refinement_split_method = *chain_id segid rigid_body_refinement_resolution = None append_to_fixed_model = True min_cc = 0.4 run_in_boxes = True target_box_size = 60 target_boxes = None box_to_run = None box_overlap_scale = 1 edge_ratio = 10 density_radius = None model_radius = 3 zero_value = 0 density_peaks = 20 delta_phi = 20 max_rot = None rotz_only = None single_positions_to_try = 10 max_position_shift_frac = 0.05 min_relative_cc = 0.67 sieve_fit = None ncs_copies_max = None start_rot = None search_center = None search_center_selection = None target_search_center = None model_search_position = None target_search_position = None search_position_radius = None rot_id_n = None rot_id_group = None map_box = True fix_search_position = False search_box_size = None lower_bounds = None upper_bounds = None keep_search_order = None remove_water = False } build { run_fit_loops = True run_iterative_morph = True run_trace_loops_through_density = True run_refine = True run_iterative_resolution_refine = True run_extend = True extract_unique = True use_symmetry_in_extract_unique = True acceptable_docking_cc = 0.5 minimum_docking_cc = 0.15 cc_sd_ratio = 3 cc_sd_ratio_end = 2 maximum_connectivity_deviation = 15 keep_fraction_of_best = 0.5 keep_maximum_entries = 10 rmsd_for_similar_placement = None rigid_body_refine_cycles = 1 overlap_ca_ca_distance = 3 ca_ca_distance = 3.8 allowed_fraction_overlapping = 0.1 maximum_combinations = 100000 proceed_with_any_symmetry = False box_cushion = 20 refine_cycles = 3 loop_refine_cycles = 5 residues_to_trim = 5 } control { stop_after_dock = None read_files = False write_files = True nproc = 20 ignore_symmetry_conflicts = True random_seed = 171731 max_dirs = 1000 verbose = False quick = True } gui { output_dir = None } job_title = "gp24" Set rmsd_for_similar_placement to 5.00 A Created new temp dir: dock_and_rebuild_0 ... temp-dir will be deleted at end =============================================================================== Processing input model =============================================================================== B-value field interpreted as LDDT (0 - 100) Maximum rmsd of 1.50 A used Maximum B-value to be included: 59.22 A**2 Total of 261 of 300 residues kept after B-factor filtering Selecting domains as compact chains Generating map at resolution of 15.0 A to identify domains Clusters: 9 Threshold: 3.81 Merging groups with 66 sets of close residues Selection list based on domains: (resseq 9:23) or (resseq 29:39) or (resseq 49:202) or (resseq 205:229) or (resseq 240:295) (261 residues) Total of 1 regions identified Obtained processed model with 261 residues (of 300) Wrote processed model to /home/amoiseenko/projects/D57CPhage/DockAndRebuild_54/gp24_f0a18_unrelaxed_rank_1_model_3_processed.pdb =============================================================================== Extracting unique part of map =============================================================================== Setting map-model-manager and model shift to zero during run Split model into chains: A1 Chain number: 1 id: A1 Residues: 261 ============================================================================== Searching with each chain as a seed ============================================================================== Getting helices-strands model to use in docking Working in 2 boxes Combining the following models: Residues: 55 CC_mask: 0.465 Residues: 101 CC_mask: 0.519 Running combine models on 156 residues in 2 models After combine models: 153 residues in 13 models Returning new model Obtained ss model with 153 residues Wrote helices_strands model to /home/amoiseenko/projects/D57CPhage/DockAndRebuild_54/gp24_f0a18_unrelaxed_rank_1_model_3_hs.pdb Helices-strands model has map CC of 0.52 ============================================================================== Running dock-in map on domain A1 with 261 residues ============================================================================== Running dock-in-map at overall resolution of 5.0 A Density radius set to: 30.0 A Placing model in map Map has been not been offset New cell after running map_box: (64.40, 91.00, 61.60, 90.00, 90.00, 90.00) Target boxes set to 1 Choosing local part of search model to use in search... Shifting search model coordinates (268.1, 240.5, 302.3) to origin and creating search map coefficients Map-model CC for target model in ssm_match: 0.41 Read model from supplied model Total in clusters: 147 Read model from supplied model Total in clusters: 204 Running forward match Total of 1 DB entries Indexing target structure... Done indexing target structure... Getting match info with brute force method Running 16 jobs to evaluate superpositions No superpositions to check... Getting match info with brute force method offsetting first Running 17 jobs to evaluate superpositions No superpositions to check... Getting match info with brute force method offsetting second Running 16 jobs to evaluate superpositions No superpositions to check... Getting match info with brute force method offsetting first offsetting second Running 17 jobs to evaluate superpositions No superpositions to check... Getting match info with brute force method including reverse offsetting first offsetting second Running 17 jobs to evaluate superpositions No superpositions to check... Unable to SSM match Unable to SSM match Running low-resolution search Radius of molecule: 21.4 A. Resolution for low-res search will be 10.7 A ================================================================================ Running quick search without rotations ================================================================================ ================================================================================ Running dock model at resolution of 10.7 A ================================================================================ Placing model in map Map has been not been offset New cell after running map_box: (64.40, 91.00, 61.60, 90.00, 90.00, 90.00) Target boxes set to 1 Choosing local part of search model to use in search... Shifting search model coordinates (0.0, -0.0, -0.0) to origin and creating search map coefficients ================================================================================ -------- Running in boxes ---------- Resolution = 10.7 A ================================================================================ Setting up about 1 boxes Cell grid: (46, 65, 44) Box dimensions: (45, 64, 43) Overlaps : (0, 0, 0) Boxes: (1, 1, 1) Running with Rotations = True Running 1 search Best local CC so far: 0.62 Best fit in density search with CC = 0.62 Transformation of original search model to match original map: ROTA 1: 0.9962 -0.0298 0.0819 ROTA 2: -0.0298 0.7665 0.6416 ROTA 3: -0.0819 -0.6416 0.7626 TRANS: 31.0109 60.0820 34.0918 Overall final transformation applied to input search model: ROTA 1: 0.9962 -0.0298 0.0819 ROTA 2: -0.0298 0.7665 0.6416 ROTA 3: -0.0819 -0.6416 0.7626 TRANS: 31.0109 60.0820 34.0918 ================================================================================ Running rigid-body refinement at resolution of 5.0 A ================================================================================ Starting map-model cc (CC_mask): 0.083 Skipping as CC_mask is < 1/2 min_cc ================================================================================ Done running dock model at resolution of 10.7 A Local CC value: -1.00 ================================================================================ Overall transformation: ROTA 1: 0.9962 -0.0298 0.0819 ROTA 2: -0.0298 0.7665 0.6416 ROTA 3: -0.0819 -0.6416 0.7626 TRANS: 31.0109 60.0820 34.0918 Results for this local search: CC = -1.00 Map shift: -0.0000 -0.0000 -0.0000 Search_model shift: 268.1251 240.4959 302.2906 Transformation of local model to match local map: ROTA 1: 0.9962 -0.0298 0.0819 ROTA 2: -0.0298 0.7665 0.6416 ROTA 3: -0.0819 -0.6416 0.7626 TRANS: 31.0109 60.0820 34.0918 ================================================================================ Running rigid-body refinement at resolution of 5.0 A ================================================================================ Starting map-model cc (CC_mask): 0.012 Final map-model cc (CC_mask): 0.049 Transformation for final_model -> final_model_refined: ROTA 1: 1.0000 -0.0000 -0.0000 ROTA 2: 0.0000 1.0000 -0.0000 ROTA 3: 0.0000 0.0000 1.0000 TRANS: 2.4000 -2.4000 -2.4000 Transformation for input model -> final_model_refined: ROTA 1: 0.9962 -0.0298 0.0819 ROTA 2: -0.0298 0.7665 0.6416 ROTA 3: -0.0819 -0.6416 0.7627 TRANS: 318.1002 427.9701 85.9865 Map correlation low ...continuing search: CC = 0.05 (min_cc = 0.40) Setting starting rotation based on this search Running low-resolution search Radius of molecule: 21.4 A. Resolution for low-res search will be 10.7 A ================================================================================ Running full low-res search with rotations ================================================================================ ================================================================================ Running dock model at resolution of 10.7 A ================================================================================ Placing model in map Map has been not been offset New cell after running map_box: (64.40, 91.00, 61.60, 90.00, 90.00, 90.00) Target boxes set to 1 Choosing local part of search model to use in search... Shifting search model coordinates (0.0, -0.0, -0.0) to origin and creating search map coefficients ================================================================================ -------- Running in boxes ---------- Resolution = 10.7 A ================================================================================ Setting up about 1 boxes Cell grid: (46, 65, 44) Box dimensions: (45, 64, 43) Overlaps : (0, 0, 0) Boxes: (1, 1, 1) Running with Rotations = True Running 1 search Best local CC so far: 0.86 Best fit in density search with CC = 0.86 Transformation of original search model to match original map: ROTA 1: 0.4555 0.3802 0.8049 ROTA 2: 0.7891 -0.5910 -0.1674 ROTA 3: 0.4122 0.7115 -0.5692 TRANS: 37.1980 52.1320 32.1336 Overall final transformation applied to input search model: ROTA 1: 0.4555 0.3802 0.8049 ROTA 2: 0.7891 -0.5910 -0.1674 ROTA 3: 0.4122 0.7115 -0.5692 TRANS: 37.1980 52.1320 32.1336 ================================================================================ Running rigid-body refinement at resolution of 5.0 A ================================================================================ Starting map-model cc (CC_mask): 0.316 Final map-model cc (CC_mask): 0.541 Transformation for final_model -> final_model_refined: ROTA 1: 0.9990 -0.0148 -0.0427 ROTA 2: 0.0133 0.9992 -0.0366 ROTA 3: 0.0432 0.0360 0.9984 TRANS: 1.7599 1.0502 -3.3273 Transformation for input model -> final_model_refined: ROTA 1: 0.4258 0.3582 0.8309 ROTA 2: 0.7794 -0.6116 -0.1357 ROTA 3: 0.4596 0.7054 -0.5396 TRANS: 36.7743 52.4593 32.2410 Updated final transformation: ROTA 1: 0.4258 0.3582 0.8309 ROTA 2: 0.7794 -0.6116 -0.1357 ROTA 3: 0.4596 0.7054 -0.5396 TRANS: 36.7743 52.4593 32.2410 ================================================================================ Done running dock model at resolution of 10.7 A Local CC value: 0.54 ================================================================================ Overall transformation: ROTA 1: 0.4258 0.3582 0.8309 ROTA 2: 0.7794 -0.6116 -0.1357 ROTA 3: 0.4596 0.7054 -0.5396 TRANS: 36.7743 52.4593 32.2410 Results for this local search: CC = 0.54 Map shift: -0.0000 -0.0000 -0.0000 Search_model shift: 268.1251 240.4959 302.2906 Transformation of local model to match local map: ROTA 1: 0.4258 0.3582 0.8309 ROTA 2: 0.7794 -0.6116 -0.1357 ROTA 3: 0.4596 0.7054 -0.5396 TRANS: 36.7743 52.4593 32.2410 ================================================================================ Running rigid-body refinement at resolution of 5.0 A ================================================================================ Starting map-model cc (CC_mask): 0.501 Final map-model cc (CC_mask): 0.536 Transformation for final_model -> final_model_refined: ROTA 1: 1.0000 -0.0000 -0.0000 ROTA 2: 0.0000 1.0000 0.0000 ROTA 3: 0.0000 -0.0000 1.0000 TRANS: -0.2000 -0.0000 0.0000 Transformation for input model -> final_model_refined: ROTA 1: 0.4258 0.3582 0.8309 ROTA 2: 0.7794 -0.6116 -0.1357 ROTA 3: 0.4596 0.7054 -0.5396 TRANS: 488.0500 73.3195 162.0245 Quick run and CC (0.54) > min_cc (0.40) ...ending search Best fit in density search with CC = 0.54 Transformation of original search model to match original map: ROTA 1: 0.4258 0.3582 0.8309 ROTA 2: 0.7794 -0.6116 -0.1357 ROTA 3: 0.4596 0.7054 -0.5396 TRANS: 488.0500 73.3195 162.0245 Overall final transformation applied to input search model: ROTA 1: 0.4258 0.3582 0.8309 ROTA 2: 0.7794 -0.6116 -0.1357 ROTA 3: 0.4596 0.7054 -0.5396 TRANS: 488.0500 73.3195 162.0245 Placements for chain A1 Placement 1 of chain A1 with CC= 0.60 Removing unlikely placements =============================================================================== Summary of current placements =============================================================================== Chain A1: Chain id: A1 placement: 1 CC: 0.60 ============================================================================== Applying RT 1 for chain A1 to all chains ============================================================================== ================================================================================ Applying RT 1 for chain A1 to chain A1 ================================================================================ Chain A1 Starting CC: 0.60 ================================================================================ Running rigid-body refinement at resolution of 5.0 A ================================================================================ Refinement successful with CC_mask = 0.53 Refined model has worse CC (0.60 vs 0.60)...skipping Chain A1 Placement 2 CC= 0.60 =============================================================================== Building full placement =============================================================================== Removing unlikely placements =============================================================================== Summary of current placements =============================================================================== Chain A1: Chain id: A1 placement: 1 CC: 0.60 Combinations to try: Group 1: (A1 #1 CC=0.60) Scoring combination Group 1: (A1 #1 CC=0.60) Fraction covered: 1.00 Mean CC: 0.60 Min: 0.60: Analyzing NCS combination 1 of this combination... Group 1: (A1 #1 CC=0.60) Groups of similar transformations: 1 Overlapping CA-CA pairs: 0 (0.0 %) Connectivity deviation: 0.0 A Acceptable cc 300 Single group 500 Domains covered 700 OK overlap 900 Connectivity ok 1100 Min CC: 0.60: 1100.60 Avg CC: 0.60: 1101.21 Groups 0.00: 1101.21 Overlaps: 0.10: 1101.31 Connectivity: -0.00: 1101.31 Summary of top combinations # 1 Score: 1101.3 Coverage: 100.0 % Min CC: 0.60 Avg CC: 0.60 Overlapping fraction: 0.00 Connectivity dev: 0.0 Group 1: (A1 #1 CC=0.60) OK solution found ...ending search Docking information written to /home/amoiseenko/projects/D57CPhage/DockAndRebuild_54/gp24_f0a18_unrelaxed_rank_1_model_3_dock_info.pkl Final model has 261 residues Docked model before getting unique part written to /home/amoiseenko/projects/D57CPhage/DockAndRebuild_54/gp24_f0a18_unrelaxed_rank_1_model_3_full_docked.pdb Final model with unique chain has 261 residues Map-model CC for docked model with 261 residues: 0.60 Wrote docked model to /home/amoiseenko/projects/D57CPhage/DockAndRebuild_54/gp24_f0a18_unrelaxed_rank_1_model_3_docked.pdb OK solution found ================================================================================ Morphing full model to match docked model ================================================================================ Unable to morph model...may not match exactly in chain ID or residue numbers No morphed model obtained... No docked model to work with Wrote rebuilt model with 261 residues to: /home/amoiseenko/projects/D57CPhage/DockAndRebuild_54/gp24_f0a18_unrelaxed_rank_1_model_3_rebuilt.pdb Processed model with 1 domains and 261 residues Residues by domain (as chains): CHAIN: A1 Residues: 261 Top docked model # 1 Score: 1101.3 Percentage of domains docked: 100.0 % Lowest docking CC: 0.60 Average docking CC: 0.60 Highest fraction of docked domains overlapping: 0.00 Highest deviation of docking connectivity from expected distance: 0.0 Group 1: (A1 #1 CC=0.60) Finished with dock_and_rebuild =============================================================================== Job complete usr+sys time: 118.16 seconds wall clock time: 3 minutes 16.82 seconds (196.82 seconds total)