346 lines
8.2 KiB
Plaintext
346 lines
8.2 KiB
Plaintext
refinement {
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crystal_symmetry {
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unit_cell = None
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space_group = None
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}
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input {
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pdb {
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file_name = None
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}
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xray_data {
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file_name = None
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labels = None
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high_resolution = None
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low_resolution = None
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outliers_rejection = True
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french_wilson_scale = True
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french_wilson {
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max_bins = 60
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min_bin_size = 40
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}
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sigma_fobs_rejection_criterion = None
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sigma_iobs_rejection_criterion = None
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r_free_flags {
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file_name = None
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label = None
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test_flag_value = 1
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ignore_r_free_flags = False
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generate = True
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fraction = 0.1
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use_lattice_symmetry = True
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use_dataman_shells = False
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n_shells = 20
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}
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}
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experimental_phases {
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file_name = None
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labels = None
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}
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monomers {
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file_name = None
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}
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sequence {
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file_name = None
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}
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}
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output {
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prefix = None
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serial = None
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job_title = None
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write_eff_file = True
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write_geo_file = True
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write_final_geo_file = False
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write_def_file = True
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write_model_cif_file = True
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write_reflection_cif_file = False
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export_final_f_model = False
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write_maps = False
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write_map_coefficients = True
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write_map_coefficients_only = False
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pickle_fmodel = False
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}
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electron_density_maps {
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apply_default_maps = None
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map_coefficients {
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map_type = None
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format = *mtz phs
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mtz_label_amplitudes = None
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mtz_label_phases = None
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fill_missing_f_obs = False
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sharpening = False
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sharpening_b_factor = None
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exclude_free_r_reflections = False
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isotropize = True
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}
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map {
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map_type = None
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format = xplor *ccp4
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file_name = None
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fill_missing_f_obs = False
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grid_resolution_factor = 1/4.
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region = *selection cell
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atom_selection = None
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atom_selection_buffer = 3
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sharpening = False
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sharpening_b_factor = None
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exclude_free_r_reflections = False
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isotropize = True
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}
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}
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refine {
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strategy = individual_sites individual_sites_real_space *rigid_body \
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individual_adp *group_adp tls occupancies group_anomalous
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sites {
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individual = (altloc C or altloc D)
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torsion_angles = None
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rigid_body = None
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}
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adp {
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individual {
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isotropic = (altloc C or altloc D)
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anisotropic = None
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}
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group_adp_refinement_mode = *one_adp_group_per_residue \
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two_adp_groups_per_residue group_selection
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group = None
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tls = None
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}
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occupancies {
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individual = None
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remove_selection = None
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}
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anomalous_scatterers {
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group {
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selection = None
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f_prime = 0
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f_double_prime = 0
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refine = *f_prime *f_double_prime
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}
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}
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}
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custom_scattering_factors = None
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main {
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stop_for_unknowns = True
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flip_peptides = False
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nqh_flips = False
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simulated_annealing = False
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simulated_annealing_torsion = False
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ordered_solvent = False
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real_space_refinement = *local global
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rotamer_restraints = False
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place_ions = None
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ias = False
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number_of_macro_cycles = 2
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target = *auto ml mlhl ml_sad ls mli
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max_number_of_resolution_bins = 30
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use_experimental_phases = None
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scattering_table = wk1995 it1992 *n_gaussian electron neutron
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wavelength = None
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switch_to_isotropic_high_res_limit = 1.5
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}
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statistical_model_for_missing_atoms {
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solvent_content = 0.0
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map_type = *2mFo-DFc
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resolution_factor = 0.25
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probability_mask = True
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diff_map_cutoff = 1.5
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output_all_masks = False
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use_dm_map = False
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}
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modify_start_model {
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modify {
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remove = None
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keep = None
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put_into_box_with_buffer = None
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selection = None
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flip_symmetric_amino_acids = False
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adp {
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atom_selection = None
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randomize = False
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set_b_iso = None
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convert_to_isotropic = False
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convert_to_anisotropic = False
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shift_b_iso = None
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scale_adp = None
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}
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sites {
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atom_selection = None
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shake = None
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switch_rotamers = max_distant min_distant exact_match fix_outliers
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translate = 0 0 0
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rotate = 0 0 0
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euler_angle_convention = *xyz zyz
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}
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occupancies {
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atom_selection = None
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randomize = False
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set = None
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}
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rotate_about_axis {
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axis = None
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angle = None
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atom_selection = None
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}
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change_of_basis = None
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renumber_residues = False
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increment_resseq = None
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truncate_to_polyala = False
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truncate_to_polygly = False
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remove_alt_confs = False
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always_keep_one_conformer = False
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set_chemical_element_simple_if_necessary = None
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set_seg_id_to_chain_id = False
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clear_seg_id = False
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convert_semet_to_met = False
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convert_met_to_semet = False
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rename_chain_id {
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old_id = None
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new_id = None
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}
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set_charge {
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charge_selection = None
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charge = None
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}
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neutralize_scatterers = False
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remove_fraction = None
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random_seed = None
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move_waters_last = False
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}
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output {
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file_name = None
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format = *pdb mmcif
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}
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}
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group_b_iso {
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use_restraints = True
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restraints_weight = None
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}
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adp {
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iso {
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max_number_of_iterations = 25
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scaling {
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scale_max = 3.0
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scale_min = 10.0
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}
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}
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}
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tls {
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find_automatically = None
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one_residue_one_group = None
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refine_T = True
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refine_L = True
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refine_S = True
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number_of_macro_cycles = 2
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max_number_of_iterations = 25
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start_tls_value = None
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min_tls_group_size = 5
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verbose = True
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}
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adp_restraints {
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iso {
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use_u_local_only = False
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sphere_radius = 5.0
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distance_power = 1.69
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average_power = 1.03
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wilson_b_weight_auto = False
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wilson_b_weight = None
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plain_pairs_radius = 5.0
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refine_ap_and_dp = False
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}
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}
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rigid_body {
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mode = *first_macro_cycle_only every_macro_cycle
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target = ls_wunit_k1 ml *auto
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target_auto_switch_resolution = 6.0
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refine_rotation = True
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refine_translation = True
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max_iterations = 25
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bulk_solvent_and_scale = False
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min_number_of_reflections = 200
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multi_body_factor = 1
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zone_exponent = 3.0
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high_resolution = 3.0
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number_of_zones = 5
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}
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ncs {
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type = *torsion cartesian constraints
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restrain_b_factors = False
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b_factor_weight = 10
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excessive_distance_limit = 1.5
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torsion {
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sigma = 2.5
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limit = 15.0
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fix_outliers = False
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check_rotamer_consistency = Auto
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}
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}
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modify_f_obs {
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remove = random strong weak strong_and_weak low other
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remove_fraction = 0.1
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fill_mode = fobs_mean_mixed_with_dfmodel random fobs_mean *dfmodel
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}
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ias {
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b_iso_max = 100.0
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occupancy_min = -1.0
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occupancy_max = 1.5
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ias_b_iso_max = 100.0
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ias_b_iso_min = 0.0
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ias_occupancy_min = 0.01
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ias_occupancy_max = 3.0
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initial_ias_occupancy = 1.0
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build_ias_types = L R B BH
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ring_atoms = None
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lone_pair {
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atom_x = CA
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atom_xo = C
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atom_o = O
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}
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use_map = True
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build_only = False
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file_prefix = None
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peak_search_map {
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map_type = *Fobs-Fmodel mFobs-DFmodel
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grid_step = 0.25
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scaling = *volume sigma
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}
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}
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twinning {
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twin_law = None
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twin_target = *twin_lsq_f
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detwin {
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mode = algebraic proportional *auto
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map_types {
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twofofc = *two_m_dtfo_d_fc two_dtfo_fc
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fofc = *m_dtfo_d_fc gradient m_gradient
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aniso_correct = False
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}
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}
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}
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reference_model {
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enabled = True
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file = None
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use_starting_model_as_reference = True
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sigma = 1.0
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limit = 15.0
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hydrogens = False
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main_chain = True
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side_chain = True
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fix_outliers = True
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strict_rotamer_matching = False
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auto_shutoff_for_ncs = False
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secondary_structure_only = False
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reference_group {
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reference = all
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selection = all
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file_name = None
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}
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search_options {
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chain_similarity_threshold = 0.85
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chain_max_rmsd = 100.
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residue_match_radius = 1000
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try_shortcuts = False
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}
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}
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}
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