# Default parameters for subsequent refinement # Date 2024-04-04 Time 09:07:13 PDT -0700 (1712246833.77 s) # Command to extract only non-defaults: # phenix.refine --diff_params "1OTH_ref.pdb_fitted_modified_refine_002.def" data_manager { phil_files = None default_phil = None miller_array { file = "1fb5.mtz" labels { name = None type = *x_ray neutron electron array_type = *unknown amplitude bool complex hendrickson_lattman \ integer intensity nonsense } user_selected_labels = None } fmodel { xray_data { high_resolution = None low_resolution = None twin_law = None outliers_rejection = True french_wilson_scale = True french_wilson { max_bins = 60 min_bin_size = 40 } sigma_fobs_rejection_criterion = None sigma_iobs_rejection_criterion = None ignore_all_zeros = True force_anomalous_flag_to_be_equal_to = None convert_to_non_anomalous_if_ratio_pairs_lone_less_than_threshold = 0.5 r_free_flags { required = True test_flag_value = 0 ignore_r_free_flags = False disable_suitability_test = False ignore_pdb_hexdigest = False generate = False fraction = 0.1 max_free = 2000 lattice_symmetry_max_delta = 5 use_lattice_symmetry = True use_dataman_shells = False n_shells = 20 } } neutron_data { ignore_xn_free_r_mismatch = False high_resolution = None low_resolution = None twin_law = None outliers_rejection = True french_wilson_scale = True french_wilson { max_bins = 60 min_bin_size = 40 } sigma_fobs_rejection_criterion = None sigma_iobs_rejection_criterion = None ignore_all_zeros = True force_anomalous_flag_to_be_equal_to = None convert_to_non_anomalous_if_ratio_pairs_lone_less_than_threshold = 0.5 r_free_flags { required = True test_flag_value = None ignore_r_free_flags = False disable_suitability_test = False ignore_pdb_hexdigest = False generate = False fraction = 0.1 max_free = 2000 lattice_symmetry_max_delta = 5 use_lattice_symmetry = True use_dataman_shells = False n_shells = 20 } } } default_miller_array = "1fb5.mtz" restraint_files = None default_restraint = None model { file = "1OTH_ref.pdb_fitted_modified.pdb" type = *x_ray neutron electron reference } default_model = "1OTH_ref.pdb_fitted_modified.pdb" } refinement { dry_run = False crystal_symmetry { unit_cell = None space_group = None } input { symmetry_safety_check = *error warning } output { job_title = None write_eff_file = True write_geo_file = True write_final_geo_file = False write_def_file = True write_model_cif_file = True write_final_pdb_file = True write_mtz_file = True write_files = True write_reflection_cif_file = False export_final_f_model = False write_maps = False write_map_coefficients = True write_map_coefficients_only = False pickle_fmodel = False n_resolution_bins = None } electron_density_maps { apply_default_maps = None map_coefficients { map_type = "2mFo-DFc" format = *mtz phs mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True acentrics_scale = 2 centrics_pre_scale = 1 sharpening = False sharpening_b_factor = None exclude_free_r_reflections = False isotropize = True dev { complete_set_up_to_d_min = False aply_same_incompleteness_to_complete_set_at = randomly low high } } map_coefficients { map_type = "2mFo-DFc" format = *mtz phs mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" fill_missing_f_obs = False acentrics_scale = 2 centrics_pre_scale = 1 sharpening = False sharpening_b_factor = None exclude_free_r_reflections = False isotropize = True dev { complete_set_up_to_d_min = False aply_same_incompleteness_to_complete_set_at = randomly low high } } map_coefficients { map_type = "mFo-DFc" format = *mtz phs mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" fill_missing_f_obs = False acentrics_scale = 2 centrics_pre_scale = 1 sharpening = False sharpening_b_factor = None exclude_free_r_reflections = False isotropize = True dev { complete_set_up_to_d_min = False aply_same_incompleteness_to_complete_set_at = randomly low high } } map_coefficients { map_type = "anomalous" format = *mtz phs mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" fill_missing_f_obs = False acentrics_scale = 2 centrics_pre_scale = 1 sharpening = False sharpening_b_factor = None exclude_free_r_reflections = False isotropize = True dev { complete_set_up_to_d_min = False aply_same_incompleteness_to_complete_set_at = randomly low high } } map { map_type = "2mFo-DFc" format = xplor *ccp4 file_name = None fill_missing_f_obs = True grid_resolution_factor = 0.25 scale = *sigma volume region = *selection cell atom_selection = None atom_selection_buffer = 3 acentrics_scale = 2 centrics_pre_scale = 1 sharpening = False sharpening_b_factor = None exclude_free_r_reflections = False isotropize = True } map { map_type = "2mFo-DFc" format = xplor *ccp4 file_name = None fill_missing_f_obs = False grid_resolution_factor = 0.25 scale = *sigma volume region = *selection cell atom_selection = None atom_selection_buffer = 3 acentrics_scale = 2 centrics_pre_scale = 1 sharpening = False sharpening_b_factor = None exclude_free_r_reflections = False isotropize = True } map { map_type = "mFo-DFc" format = xplor *ccp4 file_name = None fill_missing_f_obs = False grid_resolution_factor = 0.25 scale = *sigma volume region = *selection cell atom_selection = None atom_selection_buffer = 3 acentrics_scale = 2 centrics_pre_scale = 1 sharpening = False sharpening_b_factor = None exclude_free_r_reflections = False isotropize = True } } refine { strategy = *individual_sites *individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den sites { individual = None torsion_angles = None rigid_body = None } adp { individual { isotropic = None anisotropic = None } group_adp_refinement_mode = *one_adp_group_per_residue \ two_adp_groups_per_residue group_selection group = None tls = None } occupancies { individual = None remove_selection = None constrained_group { selection = None } } anomalous_scatterers { group { selection = None f_prime = 0 f_double_prime = 0 refine = *f_prime *f_double_prime } } } custom_scattering_factors = None main { show_process_info = False stop_for_unknowns = True bulk_solvent_and_scale = True apply_overall_isotropic_scale_to_adp = True flip_peptides = False nqh_flips = True simulated_annealing = False simulated_annealing_torsion = False ordered_solvent = False real_space_refinement = *local global rotamer_restraints = False place_ions = None backbone_sample = False ias = False number_of_macro_cycles = 5 max_number_of_iterations = 100 use_form_factor_weights = False tan_u_iso = False use_geometry_restraints = True use_convergence_test = False target = *auto ml mlhl ml_sad ls mli min_number_of_test_set_reflections_for_max_likelihood_target = 50 max_number_of_resolution_bins = 30 use_experimental_phases = None random_seed = 2772306 scattering_table = wk1995 it1992 *n_gaussian electron neutron wavelength = None use_normalized_geometry_target = True target_weights_only = False use_f_model_scaled = False max_d_min = 0.25 fake_f_obs = False optimize_mask = False occupancy_max = 1 occupancy_min = 0 stir = None show_residual_map_peaks_and_holes = False fft_vs_direct = False switch_to_isotropic_high_res_limit = 1.5 find_and_add_hydrogens = False correct_special_position_tolerance = 1 nproc = 50 update_f_part1 = True tncs_correction = False ddr { enable = False bond_weighting = True angle_weighting = True trans_peptide = True } } statistical_model_for_missing_atoms { solvent_content = 0.5 map_type = *2mFo-DFc resolution_factor = 0.25 probability_mask = True diff_map_cutoff = 1.5 output_all_masks = False use_dm_map = False } modify_start_model { modify { remove = None keep = None put_into_box_with_buffer = None selection = None flip_symmetric_amino_acids = False adp { atom_selection = None randomize = False set_b_iso = None convert_to_isotropic = False convert_to_anisotropic = False shift_b_iso = None scale_adp = None } sites { atom_selection = None shake = None switch_rotamers = max_distant min_distant exact_match fix_outliers translate = 0 0 0 rotate = 0 0 0 euler_angle_convention = *xyz zyz } occupancies { atom_selection = None randomize = False set = None } rotate_about_axis { axis = None angle = None atom_selection = None } change_of_basis = None renumber_residues = False increment_resseq = None truncate_to_polyala = False truncate_to_polygly = False remove_alt_confs = False always_keep_one_conformer = False altloc_to_keep = None set_chemical_element_simple_if_necessary = None set_seg_id_to_chain_id = False clear_seg_id = False convert_semet_to_met = False convert_met_to_semet = False rename_chain_id { old_id = None new_id = None } set_charge { charge_selection = None charge = None } neutralize_scatterers = False remove_fraction = None random_seed = None move_waters_last = False } output { file_name = None format = *pdb mmcif } } fake_f_obs { fmodel { k_sol = 0 b_sol = 0 b_cart = 0 0 0 0 0 0 scale = 1 } structure_factors_accuracy { algorithm = *fft direct cos_sin_table = False grid_resolution_factor = 0.3333333333 quality_factor = None u_base = None b_base = None wing_cutoff = None exp_table_one_over_step_size = None } mask { use_asu_masks = True solvent_radius = 1.1 shrink_truncation_radius = 0.9 use_resolution_based_gridding = False step = 0.6 n_real = None grid_step_factor = 4 verbose = 1 mean_shift_for_mask_update = 0.1 ignore_zero_occupancy_atoms = True ignore_hydrogens = True n_radial_shells = 1 radial_shell_width = 1.3 Fmask_res_high = 3 } r_free_flags_fraction = None scattering_table = wk1995 it1992 *n_gaussian neutron } hydrogens { refine = individual *riding Auto force_riding_adp = None optimize_scattering_contribution = True contribute_to_f_calc = True high_resolution_limit_to_include_scattering_from_h = 1.6 real_space_optimize_x_h_orientation = True xh_bond_distance_deviation_limit = 0 build { map_type = "mFobs-DFmodel" map_cutoff = 2 secondary_map_type = "2mFobs-DFmodel" secondary_map_cutoff = 1.4 angular_step = 3 dod_and_od = False filter_dod = False min_od_dist = 0.6 max_od_dist = 1.35 min_dod_angle = 85 max_dod_angle = 170 h_bond_min_mac = 1.8 h_bond_max = 3.9 use_sigma_scaled_maps = True grid_step = 0.6 map_next_to_model { min_model_peak_dist = 0.7 max_model_peak_dist = 1.05 min_peak_peak_dist = 0.7 use_hydrogens = False } max_number_of_peaks = None peak_search { peak_search_level = 1 max_peaks = 0 interpolate = True min_distance_sym_equiv = None general_positions_only = True min_cross_distance = 1 min_cubicle_edge = 5 } } local_real_space_fit_angular_step = 0.5 } group_b_iso { number_of_macro_cycles = 3 max_number_of_iterations = 25 convergence_test = False run_finite_differences_test = False use_restraints = True restraints_weight = None } adp { iso { max_number_of_iterations = 25 scaling { scale_max = 3 scale_min = 10 } } } tls { find_automatically = None one_residue_one_group = None refine_T = True refine_L = True refine_S = True number_of_macro_cycles = 2 max_number_of_iterations = 25 start_tls_value = None run_finite_differences_test = False eps = 1e-06 min_tls_group_size = 5 verbose = True } adp_restraints { iso { use_u_local_only = False sphere_radius = 5 distance_power = 1.69 average_power = 1.03 wilson_b_weight_auto = False wilson_b_weight = None plain_pairs_radius = 5 refine_ap_and_dp = False } } group_occupancy { number_of_macro_cycles = 3 max_number_of_iterations = 25 convergence_test = False run_finite_differences_test = False constrain_correlated_3d_groups = False } group_anomalous { number_of_minimizer_cycles = 3 lbfgs_max_iterations = 20 number_of_finite_difference_tests = 0 find_automatically = False } rigid_body { mode = *first_macro_cycle_only every_macro_cycle target = ls_wunit_k1 ml *auto target_auto_switch_resolution = 6 disable_final_r_factor_check = False refine_rotation = True refine_translation = True max_iterations = 25 bulk_solvent_and_scale = True euler_angle_convention = *xyz zyz lbfgs_line_search_max_function_evaluations = 10 min_number_of_reflections = 200 multi_body_factor = 1 zone_exponent = 3 high_resolution = 3 max_low_high_res_limit = None number_of_zones = 5 } ncs { type = *torsion cartesian constraints constraints { refine_operators = True apply_to_coordinates = True apply_to_adp = True } coordinate_sigma = 0.05 restrain_b_factors = False b_factor_weight = 10 excessive_distance_limit = 1.5 special_position_warnings_only = False torsion { sigma = 2.5 limit = 15 fix_outliers = False check_rotamer_consistency = Auto target_damping = False damping_limit = 10 filter_phi_psi_outliers = True restrain_to_master_chain = False silence_warnings = False } } modify_f_obs { remove = random strong weak strong_and_weak low other remove_fraction = 0.1 fill_mode = fobs_mean_mixed_with_dfmodel random fobs_mean *dfmodel } pdb_interpretation { restraints_library { cdl = True mcl = True cis_pro_eh99 = True omega_cdl = False cdl_nucleotides { enable = False esd = *phenix csd factor = 2 } cdl_svl = False rdl = False rdl_selection = *all TRP hpdl = False } sort_atoms = True flip_symmetric_amino_acids = True superpose_ideal_ligand = *None all SF4 F3S DVT disable_uc_volume_vs_n_atoms_check = False allow_polymer_cross_special_position = False correct_hydrogens = True secondary_structure { protein { enabled = True search_method = *ksdssp from_ca cablam distance_ideal_n_o = 2.9 distance_cut_n_o = 3.5 remove_outliers = True restrain_hbond_angles = True helix { serial_number = "1" helix_identifier = "1" enabled = True selection = chain 'A' and resid 45 through 47 helix_type = alpha pi *3_10 unknown sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 angle_sigma_set = None hbond { donor = None acceptor = None } } helix { serial_number = "2" helix_identifier = "2" enabled = True selection = chain 'A' and resid 50 through 68 helix_type = *alpha pi 3_10 unknown sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 angle_sigma_set = None hbond { donor = None acceptor = None } } helix { serial_number = "3" helix_identifier = "3" enabled = True selection = chain 'A' and resid 92 through 103 helix_type = *alpha pi 3_10 unknown sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 angle_sigma_set = None hbond { donor = None acceptor = None } } helix { serial_number = "4" helix_identifier = "4" enabled = True selection = chain 'A' and resid 124 through 134 helix_type = *alpha pi 3_10 unknown sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 angle_sigma_set = None hbond { donor = None acceptor = None } } helix { serial_number = "5" helix_identifier = "5" enabled = True selection = chain 'A' and resid 145 through 154 helix_type = *alpha pi 3_10 unknown sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 angle_sigma_set = None hbond { donor = None acceptor = None } } helix { serial_number = "6" helix_identifier = "6" enabled = True selection = chain 'A' and resid 169 through 183 helix_type = *alpha pi 3_10 unknown sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 angle_sigma_set = None hbond { donor = None acceptor = None } } helix { serial_number = "7" helix_identifier = "7" enabled = True selection = chain 'A' and resid 199 through 205 helix_type = *alpha pi 3_10 unknown sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 angle_sigma_set = None hbond { donor = None acceptor = None } } helix { serial_number = "8" helix_identifier = "8" enabled = True selection = chain 'A' and resid 209 through 211 helix_type = alpha pi *3_10 unknown sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 angle_sigma_set = None hbond { donor = None acceptor = None } } helix { serial_number = "9" helix_identifier = "9" enabled = True selection = chain 'A' and resid 227 through 240 helix_type = *alpha pi 3_10 unknown sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 angle_sigma_set = None hbond { donor = None acceptor = None } } helix { serial_number = "10" helix_identifier = "10" enabled = True selection = chain 'A' and resid 250 through 254 helix_type = *alpha pi 3_10 unknown sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 angle_sigma_set = None hbond { donor = None acceptor = None } } helix { serial_number = "11" helix_identifier = "11" enabled = True selection = chain 'A' and resid 271 through 280 helix_type = alpha pi *3_10 unknown sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 angle_sigma_set = None hbond { donor = None acceptor = None } } helix { serial_number = "12" helix_identifier = "12" enabled = True selection = chain 'A' and resid 288 through 293 helix_type = *alpha pi 3_10 unknown sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 angle_sigma_set = None hbond { donor = None acceptor = None } } helix { serial_number = "13" helix_identifier = "13" enabled = True selection = chain 'A' and resid 313 through 316 helix_type = *alpha pi 3_10 unknown sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 angle_sigma_set = None hbond { donor = None acceptor = None } } helix { serial_number = "14" helix_identifier = "14" enabled = True selection = chain 'A' and resid 323 through 342 helix_type = *alpha pi 3_10 unknown sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 angle_sigma_set = None hbond { donor = None acceptor = None } } sheet { enabled = True first_strand = chain 'A' and resid 107 through 112 sheet_id = " A" strand { selection = chain 'A' and resid 81 through 86 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 82 and name N bond_start_previous = chain 'A' and resid 107 and name O } strand { selection = chain 'A' and resid 137 through 141 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 137 and name N bond_start_previous = chain 'A' and resid 83 and name O } strand { selection = chain 'A' and resid 158 through 161 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 158 and name N bond_start_previous = chain 'A' and resid 138 and name O } sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 angle_sigma_set = None hbond { donor = None acceptor = None } } sheet { enabled = True first_strand = chain 'A' and resid 299 through 302 sheet_id = " B" strand { selection = chain 'A' and resid 259 through 262 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 260 and name N bond_start_previous = chain 'A' and resid 299 and name O } strand { selection = chain 'A' and resid 190 through 194 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 192 and name N bond_start_previous = chain 'A' and resid 259 and name O } strand { selection = chain 'A' and resid 214 through 218 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 214 and name N bond_start_previous = chain 'A' and resid 191 and name O } strand { selection = chain 'A' and resid 244 through 247 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 245 and name N bond_start_previous = chain 'A' and resid 215 and name O } sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 angle_sigma_set = None hbond { donor = None acceptor = None } } } nucleic_acid { enabled = True hbond_distance_cutoff = 3.4 angle_between_bond_and_nucleobase_cutoff = 35 scale_bonds_sigma = 1 base_pair { enabled = True base1 = None base2 = None saenger_class = 0 restrain_planarity = False planarity_sigma = 0.176 restrain_hbonds = True restrain_hb_angles = True restrain_parallelity = True parallelity_target = 0 parallelity_sigma = 0.0335 } stacking_pair { enabled = True base1 = None base2 = None angle = 0 sigma = 0.027 } } ss_by_chain = True from_ca_conservative = False max_rmsd = 1 use_representative_chains = True max_representative_chains = 100 enabled = True } c_beta_restraints = True reference_coordinate_restraints { enabled = False exclude_outliers = True selection = all sigma = 0.2 limit = 1 top_out = False } automatic_linking { link_all = False link_none = False link_metals = Auto link_residues = False link_amino_acid_rna_dna = False link_carbohydrates = True link_ligands = True link_small_molecules = False metal_coordination_cutoff = 3.5 amino_acid_bond_cutoff = 1.9 inter_residue_bond_cutoff = 2.2 buffer_for_second_row_elements = 0.5 carbohydrate_bond_cutoff = 1.99 ligand_bond_cutoff = 1.99 small_molecule_bond_cutoff = 1.98 exclude_hydrogens_from_bonding_decisions = False } include_in_automatic_linking { selection_1 = None selection_2 = None bond_cutoff = 4.5 } exclude_from_automatic_linking { selection_1 = None selection_2 = None } use_neutron_distances = False apply_cis_trans_specification { cis_trans_mod = cis *trans residue_selection = None } apply_cif_restraints { restraints_file_name = None residue_selection = None } apply_cif_modification { data_mod = None residue_selection = None } apply_cif_link { data_link = None residue_selection_1 = None residue_selection_2 = None } disulfide_bond_exclusions_selection_string = None exclusion_distance_cutoff = 3 link_distance_cutoff = 3 disulfide_distance_cutoff = 3 add_angle_and_dihedral_restraints_for_disulfides = True dihedral_function_type = *determined_by_sign_of_periodicity \ all_sinusoidal all_harmonic chir_volume_esd = 0.2 peptide_link { ramachandran_restraints = False cis_threshold = 45 apply_all_trans = False discard_omega = False discard_psi_phi = True apply_peptide_plane = False omega_esd_override_value = None rama_weight = 1 scale_allowed = 1 rama_potential = *oldfield emsley oldfield { esd = 10 weight_scale = 1 dist_weight_max = 10 weight = None plot_cutoff = 0.027 } rama_selection = None restrain_rama_outliers = True restrain_rama_allowed = True restrain_allowed_outliers_with_emsley = False } ramachandran_plot_restraints { enabled = True favored = *oldfield emsley emsley8k phi_psi_2 allowed = *oldfield emsley emsley8k phi_psi_2 outlier = *oldfield emsley emsley8k phi_psi_2 selection = None inject_emsley8k_into_oldfield_favored = True oldfield { weight = 0 weight_scale = 0.01 distance_weight_min = 2 distance_weight_max = 10 plot_cutoff = 0.027 } emsley { weight = 1 scale_allowed = 1 } emsley8k { weight_favored = 5 weight_allowed = 10 weight_outlier = 10 } phi_psi_2 { favored_strategy = *closest highest_probability random \ weighted_random allowed_strategy = *closest highest_probability random \ weighted_random outlier_strategy = *closest highest_probability random \ weighted_random } } max_reasonable_bond_distance = 50 nonbonded_distance_cutoff = None default_vdw_distance = 1 min_vdw_distance = 1 nonbonded_buffer = 1 nonbonded_weight = 100 const_shrink_donor_acceptor = 0.6 vdw_1_4_factor = 0.8 min_distance_sym_equiv = 0.5 custom_nonbonded_symmetry_exclusions = None translate_cns_dna_rna_residue_names = None proceed_with_excessive_length_bonds = False rna_sugar_pucker_analysis { bond_min_distance = 1.2 bond_max_distance = 1.8 epsilon_range_min = 155 epsilon_range_max = 310 delta_range_2p_min = 129 delta_range_2p_max = 162 delta_range_3p_min = 65 delta_range_3p_max = 104 p_distance_c1p_outbound_line_2p_max = 2.9 o3p_distance_c1p_outbound_line_2p_max = 2.4 bond_detection_distance_tolerance = 0.5 } show_histogram_slots { bond_lengths = 5 nonbonded_interaction_distances = 5 bond_angle_deviations_from_ideal = 5 dihedral_angle_deviations_from_ideal = 5 chiral_volume_deviations_from_ideal = 5 } show_max_items { not_linked = 5 bond_restraints_sorted_by_residual = 5 nonbonded_interactions_sorted_by_model_distance = 5 bond_angle_restraints_sorted_by_residual = 5 dihedral_angle_restraints_sorted_by_residual = 3 chirality_restraints_sorted_by_residual = 3 planarity_restraints_sorted_by_residual = 3 residues_with_excluded_nonbonded_symmetry_interactions = 12 fatal_problem_max_lines = 10 } ncs_group { reference = None selection = None } ncs_search { enabled = False exclude_selection = element H or element D or water chain_similarity_threshold = 0.85 chain_max_rmsd = 2 residue_match_radius = 4 try_shortcuts = False minimum_number_of_atoms_in_copy = 3 validate_user_supplied_groups = True } clash_guard { nonbonded_distance_threshold = 0.5 max_number_of_distances_below_threshold = 100 max_fraction_of_distances_below_threshold = 0.1 } } geometry_restraints.edits { excessive_bond_distance_limit = 10 bond { action = *add delete change atom_selection_1 = None atom_selection_2 = None symmetry_operation = None distance_ideal = None sigma = None slack = None limit = -1.0 top_out = False } angle { action = *add delete change atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None angle_ideal = None sigma = None } dihedral { action = *add delete change atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None angle_ideal = None alt_angle_ideals = None sigma = None periodicity = 1 } planarity { action = *add delete change atom_selection = None sigma = None } parallelity { action = *add delete change atom_selection_1 = None atom_selection_2 = None sigma = 0.027 target_angle_deg = 0 } } geometry_restraints.remove { angles = None dihedrals = None chiralities = None planarities = None parallelities = None } ordered_solvent { low_resolution = 2.8 mode = *second_half filter_only every_macro_cycle \ every_macro_cycle_after_first keep_existing = False n_cycles = 3 output_residue_name = "HOH" output_chain_id = "S" output_atom_name = "O" scattering_type = "O" primary_map_type = "mFobs-DFmodel" primary_map_cutoff = 3 secondary_map_and_map_cc_filter { cc_map_1_type = "Fmodel" cc_map_2_type = "2mFo-DFmodel" poor_cc_threshold = 0.7 poor_map_value_threshold = 0.7 } h_bond_min_mac = 1.8 h_bond_min_sol = 1.8 h_bond_max = 3.2 refine_adp = True refine_occupancies = False new_solvent = *isotropic anisotropic b_iso_min = 1 b_iso_max = 80 anisotropy_min = 0.1 b_iso = None occupancy_min = 0.1 occupancy_max = 1 occupancy = 1 filter_at_start = True ignore_final_filtering_step = False correct_drifted_waters = True } peak_search { use_sigma_scaled_maps = True grid_step = 0.6 map_next_to_model { min_model_peak_dist = 1.8 max_model_peak_dist = 6 min_peak_peak_dist = 1.8 use_hydrogens = False } max_number_of_peaks = None peak_search { peak_search_level = 1 max_peaks = 0 interpolate = True min_distance_sym_equiv = None general_positions_only = False min_cross_distance = 1.8 min_cubicle_edge = 5 } } bulk_solvent_and_scale { mode = slow *fast apply_back_trace = True bulk_solvent = True anisotropic_scaling = True k_sol_b_sol_grid_search = True minimization_k_sol_b_sol = True minimization_b_cart = True target = ls_wunit_k1 *ml symmetry_constraints_on_b_cart = True k_sol_max = 0.6 k_sol_min = 0 b_sol_max = 300 b_sol_min = 0 k_sol_grid_search_max = 0.6 k_sol_grid_search_min = 0 b_sol_grid_search_max = 80 b_sol_grid_search_min = 20 k_sol_step = 0.2 b_sol_step = 20 number_of_macro_cycles = 1 max_iterations = 25 min_iterations = 25 fix_k_sol = None fix_b_sol = None fix_b_cart { b11 = None b22 = None b33 = None b12 = None b13 = None b23 = None } } alpha_beta { free_reflections_per_bin = 140 number_of_macromolecule_atoms_absent = 225 n_atoms_included = 0 bf_atoms_absent = 15 final_error = 0 absent_atom_type = "O" method = *est calc estimation_algorithm = *analytical iterative verbose = -1 interpolation = True number_of_waters_absent = 613 sigmaa_estimator { kernel_width_free_reflections = 100 kernel_on_chebyshev_nodes = True number_of_sampling_points = 20 number_of_chebyshev_terms = 10 use_sampling_sum_weights = True } } mask { use_asu_masks = True solvent_radius = 1.1 shrink_truncation_radius = 0.9 use_resolution_based_gridding = False step = 0.6 n_real = None grid_step_factor = 4 verbose = 1 mean_shift_for_mask_update = 0.1 ignore_zero_occupancy_atoms = True ignore_hydrogens = True n_radial_shells = 1 radial_shell_width = 1.3 Fmask_res_high = 3 } tardy { mode = every_macro_cycle *second_and_before_last once first first_half xray_weight_factor = 10 start_temperature_kelvin = 2500 final_temperature_kelvin = 300 velocity_scaling = True temperature_cap_factor = 1.5 excessive_temperature_factor = 5 number_of_cooling_steps = 500 number_of_time_steps = 1 time_step_pico_seconds = 0.001 temperature_degrees_of_freedom = *cartesian constrained minimization_max_iterations = 0 prolsq_repulsion_function_changes { c_rep = None k_rep = 0.75 irexp = None rexp = None } omit_bonds_with_slack_greater_than = 0 constrain_dihedrals_with_sigma_less_than = 10 near_singular_hinges_angular_tolerance_deg = 5 emulate_cartesian = False trajectory_directory = None } cartesian_dynamics { temperature = 300 number_of_steps = 200 time_step = 0.0005 initial_velocities_zero_fraction = 0 n_print = 100 verbose = -1 random_seed = None n_collect = 10 stop_cm_motion = True } simulated_annealing { start_temperature = 5000 final_temperature = 300 cool_rate = 100 number_of_steps = 50 time_step = 0.0005 initial_velocities_zero_fraction = 0 interleave_minimization = False verbose = -1 n_print = 100 update_grads_shift = 0.3 random_seed = None refine_sites = True refine_adp = False max_number_of_iterations = 25 mode = every_macro_cycle *second_and_before_last once first first_half } target_weights { optimize_xyz_weight = True optimize_adp_weight = True wxc_scale = 0.5 wxu_scale = 1 wc = 1 wu = 1 fix_wxc = None fix_wxu = None shake_sites = True shake_adp = 10 regularize_ncycles = 50 verbose = 1 wnc_scale = 0.5 wnu_scale = 1 rmsd_cutoff_for_gradient_filtering = 3 force_optimize_weights = False weight_selection_criteria { bonds_rmsd = None angles_rmsd = None r_free_minus_r_work = None r_free_range_width = None mean_diff_b_iso_bonded_fraction = None min_diff_b_iso_bonded = None } } ias { b_iso_max = 100 occupancy_min = -1 occupancy_max = 1.5 ias_b_iso_max = 100 ias_b_iso_min = 0 ias_occupancy_min = 0.01 ias_occupancy_max = 3 initial_ias_occupancy = 1 build_ias_types = L R B BH ring_atoms = None lone_pair { atom_x = CA atom_xo = C atom_o = O } use_map = True build_only = False file_prefix = None peak_search_map { map_type = *Fobs-Fmodel mFobs-DFmodel grid_step = 0.25 scaling = *volume sigma } } ls_target_names { target_name = *ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed \ ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit \ ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed \ ls_wff_k1ask3_fixed lsm_kunit lsm_k1 lsm_k2 lsm_k1_fixed \ lsm_k1ask3_fixed } twinning { twin_target = *twin_lsq_f detwin { mode = algebraic proportional *auto map_types { twofofc = *two_m_dtfo_d_fc two_dtfo_fc fofc = *m_dtfo_d_fc gradient m_gradient aniso_correct = False } } } structure_factors_and_gradients_accuracy { algorithm = *fft direct cos_sin_table = False grid_resolution_factor = 0.3333333333 quality_factor = None u_base = None b_base = None wing_cutoff = None exp_table_one_over_step_size = None } r_free_flags { fraction = 0.1 max_free = 2000 lattice_symmetry_max_delta = 5 use_lattice_symmetry = True } reference_model { enabled = False file = None use_starting_model_as_reference = False sigma = 1 limit = 15 hydrogens = False main_chain = True side_chain = True fix_outliers = True strict_rotamer_matching = False auto_shutoff_for_ncs = False secondary_structure_only = False reference_group { reference = None selection = None file_name = None } search_options { exclude_selection = element H or element D or water chain_similarity_threshold = 0.85 chain_max_rmsd = 100 residue_match_radius = 1000 try_shortcuts = False minimum_number_of_atoms_in_copy = 3 validate_user_supplied_groups = True } } ion_placement { debug = False ion_chain_id = "X" initial_occupancy = 1 initial_b_iso = Auto refine_ion_occupancies = True refine_ion_adp = *Auto isotropic anisotropic none refine_anomalous = True max_distance_between_like_charges = 3.5 use_svm = True svm { svm_name = *Auto heavy merged_high_res filtered_outputs = True min_score = 0.2 min_score_above = 0.1 min_fraction_of_next = 2 } require_valence = False ambiguous_valence_cutoff = 0.5 d_min_strict_valence = 1.5 anom_map_type = *residual simple llg find_anomalous_substructure = Auto use_phaser = True aggressive = False map_sampling_radius = 2 water { min_2fofc_level = 1.8 max_fofc_level = 3 max_anom_level = 3 max_occ = 1 min_b_iso = 1 fp_max = 1 fpp_max = 0 max_stddev_b_iso = 5 min_frac_b_iso = 0.2 min_frac_calpha_b_iso = 0.75 max_frac_calpha_2fofc = 1.2 min_2fofc_coordinating = 0.9 } phaser { llgc_ncycles = None distance_cutoff = 1.5 distance_cutoff_same_site = 0.7 fpp_ratio_min = 0.2 fpp_ratio_max = 1.1 } chloride { max_distance_to_amide_n = 3.5 max_distance_to_cation = 3.5 min_distance_to_anion = 3.5 min_distance_to_other_sites = 2.1 max_distance_to_hydroxyl = 3.5 delta_amide_h_angle = 20 delta_planar_angle = 10 max_deviation_from_plane = 0.8 } } gui { base_output_dir = None tmp_dir = None send_notification = False notify_email = None add_hydrogens = False skip_rsr = False skip_kinemage = False phil_file = None ready_set_hydrogens { neutron_option = *all_h all_d hd_and_h hd_and_d all_hd add_h_to_water = False add_d_to_water = False neutron_exchange_hydrogens = False perdeuterate = False } migration { refinement { input { experimental_phases { file_name = None labels = None } monomers { file_name = None } electron_data { file_name = None labels = None r_free_flags { file_name = None label = None } } neutron_data { file_name = None labels = None r_free_flags { file_name = None label = None } } pdb { file_name = None neutron_file_name = None electron_file_name = None } xray_data { file_name = None labels = None r_free_flags { file_name = None label = None } } sequence { file_name = None } } } } } qi { working_directory = None qm_restraints { selection = None run_in_macro_cycles = *first_only first_and_last all last_only test buffer = 3.5 specific_atom_charges { atom_selection = None charge = None } calculate = *in_situ_opt starting_energy final_energy starting_strain \ final_strain starting_bound final_bound \ starting_higher_single_point final_higher_single_point write_files = *restraints pdb_core pdb_buffer pdb_final_core \ pdb_final_buffer protein_optimisation_freeze = *all None main_chain main_chain_to_beta \ main_chain_to_delta torsions remove_water = False restraints_filename = Auto cleanup = all *most None ignore_x_h_distance_protein = False capping_groups = True freeze_specific_atoms { atom_selection = None } include_nearest_neighbours_in_optimisation = False include_inter_residue_restraints = False do_not_update_restraints = False buffer_selection = None package { program = *mopac test charge = Auto multiplicity = Auto method = Auto basis_set = Auto solvent_model = None nproc = 1 read_output_to_skip_opt_if_available = False ignore_input_differences = False view_output = None } } } den { reference_file = None gamma = 0.5 kappa = 0.1 weight = 30 sigma = 0.44 optimize = True opt_gamma_values = 0 0.2 0.4 0.6 0.8 1 opt_weight_values = 3 10 30 100 300 num_cycles = 10 kappa_burn_in_cycles = 2 bulk_solvent_and_scale = True refine_adp = True final_refinement_cycle = False verbose = False annealing_type = *torsion cartesian minimize_c_alpha_only = False output_kinemage = False restraint_network { lower_distance_cutoff = 3 upper_distance_cutoff = 15 sequence_separation_low = 0 sequence_separation_limit = 10 exclude_hydrogens = True ndistance_ratio = 1 export_den_pairs = False den_network_file = None } } } output { filename = None file_name = None prefix = "1OTH_ref.pdb_fitted_modified_refine" suffix = None serial = 2 serial_format = "%03d" target_output_format = None *pdb mmcif overwrite = True }