PHENIX autobuild Tue Oct 7 12:41:57 2014 Phenix developers include: Paul Adams, Pavel Afonine, Vincent Chen, Ian Davis, Nathaniel Echols, Kreshna Gopal, Ralf Grosse-Kunstleve, Jeff Headd, Li-Wei Hung, Robert Immormino, Tom Ioerger, Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read, Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini, Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger, Peter Zwart Phenix home page: http://www.phenix-online.org/ ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Phenix components are copyrighted by: - Lawrence Berkeley National Laboratory - Los Alamos National Laboratory - University of Cambridge - Duke University - Texas Agricultural Experiment Station & Texas Engineering Experiment Station ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Major third-party components of Phenix include: Python, wxwidgets, wxPython, Boost, SCons, Clipper, PULCHRA, CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS Enter phenix.acknowledgments for details. If you use PHENIX please cite: Adams, P.D., Afonine, P.V., Chen, V., Echols, N., Headd, J. J., Hung, L.-W., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C. and Zwart, P. H. (2010) PHENIX - A Comprehensive Python-based System for Macromolecular Structure Solution. Acta Cryst. D66, 213-221. For help type: phenix.doc For access to full documentation please type: phenix.doc ------------------------------------------------------------ Starting AutoBuild with the command: phenix.autobuild data=../original_001.mtz model=../original_001.pdb \ maps_only=True seq_file=2G38.fa refine=False autobuild { data = "../original_001.mtz" model = "../original_001.pdb" seq_file = "2G38.fa" map_file = Auto refinement_file = Auto hires_file = Auto crystal_info { unit_cell = None space_group = None solvent_fraction = None chain_type = *Auto PROTEIN DNA RNA resolution = 0 dmax = 500 overall_resolution = 0 sequence = None } input_files { input_labels = None input_hires_labels = None input_map_labels = None input_refinement_labels = None input_ha_file = None include_ha_in_model = True cif_def_file_list = None input_lig_file_list = None keep_input_ligands = True keep_input_waters = False keep_pdb_atoms = True remove_residues_on_special_positions = False refine_eff_file_list = None map_file_is_density_modified = True map_file_fom = None use_map_file_as_hklstart = False use_map_in_resolve_with_model = False identity_from_remark = True } aniso { remove_aniso = True b_iso = None max_b_iso = 40 target_b_ratio = 10 } decision_making { acceptable_r = 0.25 r_switch = 0.4 semi_acceptable_r = 0.3 reject_weak = False min_weak_z = 0.2 min_cc_res_rebuild = 0.4 min_seq_identity_percent = 50 dist_close = None dist_close_overlap = 1.5 loop_cc_min = 0.4 group_ca_length = 4 group_length = 2 include_molprobity = False ok_molp_score = None scale_molp_score = None } density_modification { add_classic_denmod = None skip_classic_if_worse_fom = True skip_ncs_in_add_classic = True thorough_denmod = *Auto True False hl = False mask_type = *histograms probability wang classic mask_from_pdb = None mask_type_extreme_dm = histograms probability *wang classic mask_cycles_extreme_dm = 1 minor_cycles_extreme_dm = 4 wang_radius_extreme_dm = 20 precondition = False minimum_ncs_cc = 0.3 extreme_dm = False fom_for_extreme_dm_rebuild = 0.1 fom_for_extreme_dm = 0.35 rad_mask_from_pdb = 2 modify_outside_delta_solvent = 0.05 modify_outside_model = False truncate_ha_sites_in_resolve = *Auto True False rad_mask = None s_step = None res_start = None use_resolve_fragments = True use_resolve_pattern = True use_hl_anom_in_denmod = False use_hl_anom_in_denmod_with_model = False mask_as_mtz = False protein_output_mask_file = None ncs_output_mask_file = None omit_output_mask_file = None } maps { maps_only = True n_xyz_list = None } model_building { build_type = *RESOLVE RESOLVE_AND_BUCCANEER allow_negative_residues = False highest_resno = None semet = False use_met_in_align = *Auto True False base_model = None consider_main_chain_list = None dist_connect_max_helices = None edit_pdb = True helices_strands_only = False resolution_helices_strands = 3 helices_strands_start = False cc_helix_min = None cc_strand_min = None loop_lib = False standard_loops = True trace_loops = False refine_trace_loops = True density_of_points = None max_density_of_points = None cutout_model_radius = None max_cutout_model_radius = 20 padding = 1 max_span = 30 max_overlap = None min_overlap = None include_input_model = True input_compare_file = None merge_models = False morph = False morph_main = False dist_cut_base = 3 morph_cycles = 2 morph_rad = 7 n_ca_enough_helices = None delta_phi = 20 offsets_list = 53 7 23 all_maps_in_rebuild = False ps_in_rebuild = False use_ncs_in_ps = False remove_outlier_segments_z_cut = 3 refine = False refine_final_model_vs_orig_data = True reference_model = None resolution_build = 0 restart_cycle_after_morph = 5 retrace_before_build = False reuse_chain_prev_cycle = True richardson_rotamers = *Auto True False rms_random_frag = None rms_random_loop = None start_chains_list = None trace_as_lig = False track_libs = False two_fofc_denmod_in_rebuild = False rebuild_from_fragments = False two_fofc_in_rebuild = False refine_map_coeff_labels = "2FOFCWT PH2FOFCWT" filled_2fofc_maps = True map_phasing = False use_any_side = True use_cc_in_combine_extend = False sort_hetatms = False map_to_object = None } multiple_models { combine_only = False multiple_models = False multiple_models_first = 1 multiple_models_group_number = 5 multiple_models_last = 20 multiple_models_number = 20 multiple_models_starting = True multiple_models_starting_resolution = 4 place_waters_in_combine = None } ncs { find_ncs = *Auto True False input_ncs_file = None ncs_copies = None ncs_refine_coord_sigma_from_rmsd = False ncs_refine_coord_sigma_from_rmsd_ratio = 1 no_merge_ncs_copies = False optimize_ncs = True use_ncs_in_build = True ncs_in_refinement = *torsion cartesian None } omit { composite_omit_type = *None simple_omit refine_omit sa_omit \ iterative_build_omit n_box_target = None n_cycle_image_min = 3 n_cycle_rebuild_omit = 10 offset_boundary = 2 omit_boundary = 2 omit_box_start = 0 omit_box_end = 0 omit_box_pdb_list = None omit_chain_list = None omit_offset_list = 0 0 0 0 0 0 omit_on_rebuild = False omit_selection = None omit_region_specification = *composite_omit omit_around_pdb \ omit_selection omit_res_start_list = None omit_res_end_list = None } rebuild_in_place { min_seq_identity_percent_rebuild_in_place = 95 n_cycle_rebuild_in_place = None n_rebuild_in_place = 1 rebuild_chain_list = None rebuild_in_place = *Auto True False rebuild_near_chain = None rebuild_near_dist = 7.5 rebuild_near_res = None rebuild_res_end_list = None rebuild_res_start_list = None rebuild_side_chains = False redo_side_chains = True replace_existing = True delete_bad_residues_only = False touch_up = False touch_up_extra_residues = None worst_percent_res_rebuild = 2 smooth_range = None smooth_minimum_length = None } refinement { refine_b = True refine_se_occ = True skip_clash_guard = True correct_special_position_tolerance = None use_mlhl = True generate_hl_if_missing = False place_waters = True refinement_resolution = 0 ordered_solvent_low_resolution = None link_distance_cutoff = 3 r_free_flags_fraction = 0.1 r_free_flags_max_free = 2000 r_free_flags_use_lattice_symmetry = True r_free_flags_lattice_symmetry_max_delta = 5 allow_overlapping = None fix_ligand_occupancy = None remove_outlier_segments = True twin_law = None max_occ = None refine_before_rebuild = True refine_with_ncs = True refine_xyz = True s_annealing = False skip_hexdigest = False use_hl_anom_in_refinement = False } thoroughness { build_outside = True connect = True extensive_build = False fit_loops = True insert_helices = True n_cycle_build = None n_cycle_build_max = 6 n_cycle_build_min = 1 n_cycle_rebuild_max = 15 n_cycle_rebuild_min = 1 n_mini = 10 n_random_frag = 0 n_random_loop = 3 n_try_rebuild = 2 ncycle_refine = 3 number_of_models = None number_of_parallel_models = 0 skip_combine_extend = False fully_skip_combine_extend = False thorough_loop_fit = True } general { coot_name = "coot" i_ran_seed = 72432 raise_sorry = False background = True check_wait_time = 1 max_wait_time = 1 wait_between_submit_time = 1 cache_resolve_libs = True resolve_size = "12" check_run_command = False run_command = "sh " queue_commands = None condor_universe = "vanilla" add_double_quotes_in_condor = True condor = None last_process_is_local = True skip_r_factor = False test_flag_value = Auto skip_xtriage = False base_path = None temp_dir = None clean_up = None print_citations = True solution_output_pickle_file = None title = None top_output_dir = None wizard_directory_number = None verbose = False extra_verbose = False debug = False require_nonzero = True remove_path_word_list = None fill = False res_fill = None check_only = False keep_files = "overall_best*" "AutoBuild_run_*.log" after_autosol = False nbatch = 3 nproc = 1 quick = False resolve_command_list = None resolve_pattern_command_list = None ignore_errors_in_subprocess = False send_notification = False notify_email = None } special_keywords { write_run_directory_to_file = None } run_control { coot = None ignore_blanks = None stop = None display_facts = None display_summary = None carry_on = None run = None copy_run = None display_runs = None delete_runs = None display_labels = None dry_run = False params_only = False display_all = False } non_user_parameters { gui_output_dir = None background_map = None boundary_background_map = None extend_try_list = True force_combine_extend = False model_list = None oasis_cnos = None offset_boundary_background_map = None skip_refine = False sg = None input_data_file = None input_map_file = Auto input_refinement_file = Auto input_pdb_file = None input_seq_file = Auto super_quick = None require_test_set = False } } Working directory: /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_ HOST = chevy.lbl.gov HOSTTYPE = x86_64-linux USER = afonine PID = 30809 ************************************************************ PHENIX AutoBuild Tue Oct 7 12:41:57 2014 ************************************************************ Working directory: /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild AutoBuild_start AutoBuild Run 1 Tue Oct 7 12:41:57 2014 Setting default value of True for thorough_denmod Setting default value of True for find_ncs Setting default value of False for use_met_in_align Setting default value of True for truncate_ha_sites_in_resolve Guessing chain type from /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.pdb Setting chain type to PROTEIN Using /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.mtz for refinement SG: P 2 2 21 Cell: [40.862, 46.758, 283.125, 90.0, 90.0, 90.0] Getting column labels from /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.mtz for input data file Resolution from datafile: 2.17998074616 SG: P 2 2 21 Cell: [40.862, 46.758, 283.125, 90.0, 90.0, 90.0] Input labels: ['F-obs', 'SIGF-obs', 'None', 'None', 'None', 'None', 'None', 'None'] Getting column labels from /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.mtz for refinement data file SG: P 2 2 21 Cell: [40.862, 46.758, 283.125, 90.0, 90.0, 90.0] Refinement file program labels: ['FP', 'SIGFP', 'FreeR_flag'] Refinement file input labels: ['F-obs', 'SIGF-obs', 'R-free-flags'] Refinement file all input labels: ['F-obs', 'SIGF-obs', 'R-free-flags', 'F-obs-filtered', 'SIGF-obs-filtered', 'F-model', 'PHIF-model', '2FOFCWT', 'PH2FOFCWT', '2FOFCWT_no_fill', 'PH2FOFCWT_no_fill', 'FOFCWT', 'PHFOFCWT', 'None'] Input sequence file is /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/seq_from_file.dat Copied /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/seq_from_file.dat to /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/sequence_autobuild.dat AutoBuild_set_overall_params AutoBuild Run 1 Tue Oct 7 12:42:02 2014 Setting rebuild_in_place=False as maps_only=True Saving all but water and ligands in AutoBuild_run_1_/TEMP0/NO_LIG_NO_WAT_original_001.pdb model id="" #chains=10 chain id="A" #conformers=1 chain id="B" #conformers=1 chain id="C" #conformers=1 chain id="D" #conformers=1 chain id="B" #conformers=1 Saving input ligand: MN 199 chain id="D" #conformers=1 Saving input ligand: MN 199 chain id="A" #conformers=1 chain id="B" #conformers=1 chain id="C" #conformers=1 chain id="D" #conformers=1 Getting NCS copies from chains used... Copies of chain 1 : 2 : ['A', 'C'] Copies of chain 2 : 2 : ['B', 'D'] Ligands from /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.pdb are in: AutoBuild_run_1_/TEMP0/LIGANDS.pdb Generating any necessary cif files for AutoBuild_run_1_/TEMP0/LIGANDS.pdb ------------------------------------------------------------------------------ electronic Ligand Builder & Optimisation Workbench (eLBOW) None None - Nigel W. Moriarty (NWMoriarty@LBL.Gov) ------------------------------------------------------------------------------ Random number seed: 3628800 Initial processing time : 0.02 seconds 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing P No unknown residues NOTE: The following residues (and similar residues) from /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.pdb are not PROTEIN or do not match the sequence and will not be part of the building process : HOH A100, HOH B200, HOH C100, HOH D200, NOTE: The following residues from /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.pdb are saved as ligands and will be added to any models just prior to refinement MN B199, MN D199, Using model without ligands or waters as work_pdb_file. Ligands will be added back just before refinement Setting initial guess of ncs_copies to 2 based on copies of each chain in input PDB file Looking for NCS ... using /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.pdb NCS found from /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.pdb Number of ncs_copies from this file ignored. AutoBuild_datafile_info_inputs AutoBuild Run 1 Tue Oct 7 12:42:06 2014 Number of residues in unique chains in seq file: 297 Cell volume: 540945.82 Equivalent positions:4 Testing NCS copies value of 2 Best guess of number of NCS copies: 2 Estimate of solvent fraction: 0.41 Merging refinement file /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.mtz with data file /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.mtz to create /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/refinement_PHX.mtz Selecting arrays from /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.mtz : ['F-obs', 'SIGF-obs'] ['R-free-flags'] Selecting arrays from /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.mtz : The label ['F-obs'] is already used...skipping ['F-obs', 'SIGF-obs'] Output space group: P 2 2 21 (No. 17) Columns of data in /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/refinement_PHX.mtz: H K L F-obs SIGF-obs R-free-flags Unit cell: (40.862, 46.758, 283.125, 90, 90, 90) Space group: P 2 2 21 (No. 17) Using /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/refinement_PHX.mtz for refinement Correcting data file /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.mtz for anisotropy and sharpening and writing to /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/aniso_data_PHX.mtz Getting overall aniso B from datafile... Aniso-corrected data to be written to /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/aniso_data_PHX.mtz Max b_iso target allowed is 40.00 A**2 Min B aniso from datafiles is 16.70 A**2 Target aniso B set to 16.70 A**2 Removing anisotropy from data file now # remove_aniso # # Correct columns in MTZ file for anisotropy # Type phenix.doc for help Values of all params: remove_aniso { input_files { mtz_in = "/net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.mtz" obs_labels = None } output_files { mtz_out = "/net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/aniso_data_PHX.mtz" log = "remove_aniso.log" extension = None params_out = "remove_aniso_params.eff" } directories { temp_dir = "AutoBuild_run_1_/TEMP0" output_dir = "AutoBuild_run_1_" } aniso { b_iso = 16.70235984 } control { verbose = False raise_sorry = False debug = False dry_run = False resolve_command_list = None } } Correction for anisotropy Arrays in input file /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.mtz: ['F-obs', 'SIGF-obs'] ['R-free-flags'] ['F-obs-filtered', 'SIGF-obs-filtered'] ['F-model', 'PHIF-model'] ['2FOFCWT', 'PH2FOFCWT'] ['2FOFCWT_no_fill', 'PH2FOFCWT_no_fill'] ['FOFCWT', 'PHFOFCWT'] Columns for anisotropy correction: F-obs,SIGF-obs Trace of aniso B: 38.49 65.55 16.70 A**2. Minimum: 16.70 Mean: 40.25 Applying aniso correction now with target B set with b_iso= 16.70 Offset in B will be: -23.54 (negative is sharpening) Aniso-corrected data to be written to /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/aniso_data_PHX.mtz Intermediate data file (for everything but refinement): /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/aniso_data_PHX.mtz Intermediate data file (for refinement): /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/refinement_PHX.mtz AutoBuild_general_params AutoBuild Run 1 Tue Oct 7 12:42:15 2014 Resolution for model-building: 2.18 A Setting n_cycle_build=1 as nbatch >1 (nbatch =3) Setting number_of_models=1 as nbatch >1 (nbatch =3) AutoBuild_uncommon_inputs AutoBuild Run 1 Tue Oct 7 12:42:15 2014 AutoBuild_check_params AutoBuild Run 1 Tue Oct 7 12:42:15 2014 AutoBuild_set_up_build AutoBuild Run 1 Tue Oct 7 12:42:15 2014 Using data from /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/aniso_data_PHX.mtz for density modification as: exptl_phases_and_amplitudes_for_density_modification_aniso.mtz Columns used: FP=F-obs SIGFP=SIGF-obs Running xtriage on /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/refinement_PHX.mtz . Output: /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/refinement_PHX.mtz_xtriage.log Copying refinement_PHX.mtz to exptl_fobs_phases_freeR_flags.mtz Columns used: FP=F-obs SIGFP=SIGF-obs FreeR_flag=R-free-flags Refinement file with freeR flags is in AutoBuild_run_1_/TEMP0/exptl_fobs_phases_freeR_flags.mtz Test flag value from the PDB file /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.pdb is: 1 Using test_flag_value of 1 from /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.pdb Removing anisotropy and sharpening refinement file (AutoBuild_run_1_/TEMP0/exptl_fobs_phases_freeR_flags.mtz) to b_iso= 16.70... yielding AutoBuild_run_1_/TEMP0/aniso_refinement_data_PHX.mtz Aniso-corrected data to be written to AutoBuild_run_1_/TEMP0/aniso_refinement_data_PHX.mtz Aniso B offset for refinement file: -23.55 NOTE: Not using phase information from input files in refinement and density modification Refinement file with free R flags (not aniso corrected): /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz AutoBuild_build_cycle AutoBuild Run 1 Tue Oct 7 12:42:25 2014 Build cycle 1 of 2 method:rebuild Initial rebuild cycle: just combining previous models or copying over initial PDB file Using NO_LIG_NO_WAT_original_001.pdb for rebuild, copied to unrefined.pdb_1 Getting R for model: unrefined.pdb_1 Using test_flag_value of 1 in refinement Model: refine.pdb_1 R/Rfree=0.31/0.37 Made copy of refined model: /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/TEMP0/refine.pdb_1 to /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/TEMP0/refined_pdb_in.pdb Moving refinement file AutoBuild_run_1_/TEMP0/refine_001_f_model.mtz to AutoBuild_run_1_/TEMP0/refine_pdb_in_fmodel.mtz Moving refinement file AutoBuild_run_1_/TEMP0/refine_001.mtz to AutoBuild_run_1_/TEMP0/refine_pdb_in.mtz Moving refinement file AutoBuild_run_1_/TEMP0/refine_001.eff to AutoBuild_run_1_/TEMP0/refine_pdb_in.eff Copying refine map file AutoBuild_run_1_/TEMP0/refine_pdb_in.mtz to map_coeffs.mtz Maps from refinement will be filled (2FOFCWT PH2FOFCWT) AutoBuild_build_cycle AutoBuild Run 1 Tue Oct 7 12:44:22 2014 Build cycle 2 of 2 method:rebuild New best NCS from AutoBuild_run_1_/TEMP0/refined_pdb_in.pdb AutoBuild_run_1_/TEMP0/map_coeffs.mtz : GROUP 1 Summary of NCS group with 2 operators: ID of chain/residue where these apply: [['B', 'D'], [[[2, 121], [128, 173]], [[2, 121], [128, 173]]]] RMSD (A) from chain B: 0.0 0.64 Number of residues matching chain B:[166, 166] Source of NCS info: AutoBuild_run_1_/TEMP0/refined_pdb_in.pdb Correlation of NCS: 0.67 OPERATOR 1 CENTER: 0.5247 19.5577 88.8252 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: -0.0000 -0.0000 -0.0000 OPERATOR 2 CENTER: 15.3292 1.7930 123.4250 ROTA 1: -0.0131 0.9980 0.0630 ROTA 2: 0.9995 0.0150 -0.0291 ROTA 3: -0.0300 0.0626 -0.9976 TRANS: -8.8332 7.8010 212.3064 GROUP 2 Summary of NCS group with 2 operators: ID of chain/residue where these apply: [['A', 'C'], [[[8, 83]], [[8, 83]]]] RMSD (A) from chain A: 0.0 0.3 Number of residues matching chain A:[76, 76] Source of NCS info: AutoBuild_run_1_/TEMP0/refined_pdb_in.pdb Correlation of NCS: 0.6 OPERATOR 1 CENTER: 0.4016 19.8559 109.8749 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: -0.0000 -0.0000 -0.0000 OPERATOR 2 CENTER: 14.8294 2.9104 102.3073 ROTA 1: -0.0248 0.9981 0.0561 ROTA 2: 0.9985 0.0275 -0.0469 ROTA 3: -0.0484 0.0549 -0.9973 TRANS: -7.8780 9.7659 212.4616 new_ncs_group rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth -0.0000 -0.0000 -0.0000 center_orth 0.5247 19.5577 88.8252 rota_matrix -0.0131 0.9980 0.0630 rota_matrix 0.9995 0.0150 -0.0291 rota_matrix -0.0300 0.0626 -0.9976 tran_orth -8.8332 7.8010 212.3064 center_orth 15.3292 1.7930 123.4250 new_ncs_group rota_matrix 1.0000 0.0000 0.0000 rota_matrix 0.0000 1.0000 0.0000 rota_matrix 0.0000 0.0000 1.0000 tran_orth -0.0000 -0.0000 -0.0000 center_orth 0.4016 19.8559 109.8749 rota_matrix -0.0248 0.9981 0.0561 rota_matrix 0.9985 0.0275 -0.0469 rota_matrix -0.0484 0.0549 -0.9973 tran_orth -7.8780 9.7659 212.4616 center_orth 14.8294 2.9104 102.3073 Re-using input PDB coordinates in build this cycle Density modifying image of refine.pdb_1 - refine.pdb_1 ->resolve_denmod_2.log Unit cell: (40.862, 46.758, 283.125, 90, 90, 90) Space group: P 2 2 21 (No. 17) Unit cell: (40.862, 46.758, 283.125, 90, 90, 90) Space group: P 2 2 21 (No. 17) Skipping model-building as 'maps_only' is set Recovering fact n_cycle_build of 1 Recovering fact number_of_models of 1 NOTE: Nothing to score... Cycle 2 R/Rfree=999.90/999.90 Built=0 Placed=0 Copying files: cycle_best.pdb -> working_best.pdb (etc.) Copied cycle_best_denmod_map_coeffs.mtz to working_best_denmod_map_coeffs.mtz Copied cycle_best.log_denmod to working_best.log_denmod New best overall: AutoBuild_run_1_/working_best.pdb Model obtained on cycle 2 R (work): 999.9 R (free): 999.9 Residues built: 0 Residues placed: 0 Model-map CC: 0.0 Chains: 0 Creating overall_best files ... Copying files to overall_best Copying /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/AutoBuild_2.ncs_spec to /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/overall_best_ncs_file.ncs_spec Copying /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz to /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/overall_best_refine_data.mtz Copying /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/cycle_best_2.log_denmod to /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/overall_best.log_denmod Copying /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/cycle_best_2.mtz to /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/overall_best_denmod_map_coeffs.mtz AutoBuild_build_cycle AutoBuild Run 1 Tue Oct 7 12:56:09 2014 Ending these rebuild cycles as the limit is reached All done with build cycles in this region AutoBuild_set_up_build AutoBuild Run 1 Tue Oct 7 12:56:09 2014 All omit/non-omit regions completed finished AutoBuild Run 1 Tue Oct 7 12:56:09 2014 Finishing AutoBuild Run 1 Facts written to AutoBuild_run_1_/AutoBuild_Facts.dat Warnings: NOTE: The following residues (and similar residues) from /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.pdb are not PROTEIN or do not match the sequence and will not be part of the building process : HOH A100, HOH B200, HOH C100, HOH D200, NOTE: The following residues from /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.pdb are saved as ligands and will be added to any models just prior to refinement MN B199, MN D199, AutoBuild Run 1 Summary of model-building for run 1 Tue Oct 7 12:56:09 2014 Files are in the directory: /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/ Starting mtz file: /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/original_001.mtz Sequence file: /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/seq_from_file.dat Summary of output files for Solution 1 from rebuild cycle 2 --- NCS information file --- ncs_file: /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/overall_best_ncs_file.ncs_spec --- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- refine_data: /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/overall_best_refine_data.mtz --- Density-modification log file --- log_denmod: /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/overall_best.log_denmod --- Density-modified map coefficients FWT PHWT --- denmod_map_coeffs: /net/chevy/raid1/afonine/work/crom/final/fig_21_results_2G38/autobuild/AutoBuild_run_1_/overall_best_denmod_map_coeffs.mtz Citations for AutoBuild: Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. D66:213-221. Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD. (2012) Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D Biol Crystallogr 68:352-67. Moriarty NW, Grosse-Kunstleve RW, Adams PD. (2009) electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation. Acta Crystallogr D Biol Crystallogr 65:1074-80. Terwilliger T. (2003) SOLVE and RESOLVE: automated structure solution, density modification and model building. J Synchrotron Radiat 11:49-52. Terwilliger TC. (2002) Rapid automatic NCS identification using heavy-atom substructures. Acta Crystallogr D Biol Crystallogr 58:2213-5. Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Moriarty NW, Zwart PH, Hung L-W, Read RJ, Adams PD. (2008) Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard. Acta Cryst. D64:61-69. Zwart PH, Grosse-Kunstleve RW, Adams PD. (2005) Xtriage and Fest: automatic assessment of X-ray data and substructure structure factor estimation. CCP4 Newsletter Winter:Contribution 7.