Values of all params: find_ncs { input_files { ncs_in_type = None *chains sites ncs_file ncs_in = "AutoBuild_run_1_/TEMP0/refined_pdb_in.pdb" mtz_in = "AutoBuild_run_1_/TEMP0/map_coeffs.mtz" labin = "" } output_files { params_out = "AutoBuild_run_1_/TEMP0/find_ncs_params.eff" ncs_out = "find_ncs.ncs_spec" ncs_mask_file = None ncs_au_file = None } crystal_info { resolution = None } directories { temp_dir = "AutoBuild_run_1_/TEMP0" output_dir = "AutoBuild_run_1_/TEMP0" gui_output_dir = None } control { verbose = True debug = False raise_sorry = False dry_run = False require_nonzero = True } ncs_parameters { ncs_restrict = 0 force_ncs = False optimize_ncs = True try_density_after_ha = True target_ncs_operators = None ncs_copies_max = None target_ncs_cc = 0.8 minimum_ncs_cc = 0.3 fraction_ncs_min = 0.05 n_try_ncs = 3 ncs_thorough = 8 ha_ds_window = None ha_window_max = 30 dist_cut_ncs = None min_length = 15 } job_title = None } find_ncs_from_density { input_files { mtz_in = None labin = "" center_pdb_in = None density_mtz_in = None density_labin = "" } output_files { centers_pdb_out = "guess_molecular_centers.pdb" log = "find_ncs_from_density.log" ncs_spec_file = "find_ncs_from_density.ncs_spec" params_out = "find_ncs_from_density_params.eff" ncs_mask_file = None } directories { temp_dir = "temp_dir" output_dir = "" } density_search { density_radius = 10 peak_separation = 15 density_peaks = 20 delta_phi = 20 ncs_copies_max = None min_ratio_to_top_cc = 0.75 minimum_ncs_cc_from_density = 0.4 fraction_ncs_min_from_density = 0.05 dump_ncs_density = False } find_centers { smoothing_radius = None n_center_find = None n_center_use = 1 } crystal_info { resolution = 4 solvent_fraction = 0.5 } control { verbose = True debug = False raise_sorry = False dry_run = False resolve_command_list = None } } Using simple_ncs_from_pdb to find NCS from AutoBuild_run_1_/TEMP0/refined_pdb_in.pdb Optimizing NCS Reading NCS information from: AutoBuild_run_1_/TEMP0/NCS_optimize.log NCS formatted for resolve in AutoBuild_run_1_/TEMP0/find_ncs.resolve NCS formatted for phenix.refine in AutoBuild_run_1_/TEMP0/find_ncs.phenix_refine NCS formatted as ncs_spec (for autosol/autobuild etc) in AutoBuild_run_1_/TEMP0/find_ncs.ncs_spec Citations for find_ncs: 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.