refinement {
  crystal_symmetry {
    unit_cell = None
    space_group = None
  }
  input {
    pdb {
      file_name = None
    }
    xray_data {
      file_name = None
      labels = None
      high_resolution = None
      low_resolution = 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
      r_free_flags {
        file_name = None
        label = None
        test_flag_value = 1
        ignore_r_free_flags = False
        generate = True
        fraction = 0.1
        use_lattice_symmetry = True
        use_dataman_shells = False
        n_shells = 20
      }
    }
    experimental_phases {
      file_name = None
      labels = None
    }
    monomers {
      file_name = None
    }
    sequence {
      file_name = None
    }
  }
  output {
    prefix = None
    serial = None
    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_reflection_cif_file = False
    export_final_f_model = False
    write_maps = False
    write_map_coefficients = True
    write_map_coefficients_only = False
    pickle_fmodel = False
  }
  electron_density_maps {
    apply_default_maps = None
    map_coefficients {
      map_type = None
      format = *mtz phs
      mtz_label_amplitudes = None
      mtz_label_phases = None
      fill_missing_f_obs = False
      sharpening = False
      sharpening_b_factor = None
      exclude_free_r_reflections = False
      isotropize = True
    }
    map {
      map_type = None
      format = xplor *ccp4
      file_name = None
      fill_missing_f_obs = False
      grid_resolution_factor = 1/4.
      region = *selection cell
      atom_selection = None
      atom_selection_buffer = 3
      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
    sites {
      individual = (altloc C or altloc D)  
      torsion_angles = None
      rigid_body = None
    }
    adp {
      individual {
        isotropic = (altloc C or altloc D)
        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
      
    }
    anomalous_scatterers {
      group {
        selection = None
        f_prime = 0
        f_double_prime = 0
        refine = *f_prime *f_double_prime
      }
    }
  }
  custom_scattering_factors = None
  main {
    stop_for_unknowns = True
    flip_peptides = False
    nqh_flips = False
    simulated_annealing = False
    simulated_annealing_torsion = False
    ordered_solvent = False
    real_space_refinement = *local global
    rotamer_restraints = False
    place_ions = None
    ias = False
    number_of_macro_cycles = 2
    target = *auto ml mlhl ml_sad ls mli
    max_number_of_resolution_bins = 30
    use_experimental_phases = None
    scattering_table = wk1995 it1992 *n_gaussian electron neutron
    wavelength = None
    switch_to_isotropic_high_res_limit = 1.5
  }
  statistical_model_for_missing_atoms {
    solvent_content = 0.0
    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
      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
    }
  }
  group_b_iso {
    use_restraints = True
    restraints_weight = None
  }
  adp {
    iso {
      max_number_of_iterations = 25
      scaling {
        scale_max = 3.0
        scale_min = 10.0
      }
    }
  }
  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
    min_tls_group_size = 5
    verbose = True
  }
  adp_restraints {
    iso {
      use_u_local_only = False
      sphere_radius = 5.0
      distance_power = 1.69
      average_power = 1.03
      wilson_b_weight_auto = False
      wilson_b_weight = None
      plain_pairs_radius = 5.0
      refine_ap_and_dp = False
    }
  }
  rigid_body {
    mode = *first_macro_cycle_only every_macro_cycle
    target = ls_wunit_k1 ml *auto
    target_auto_switch_resolution = 6.0
    refine_rotation = True
    refine_translation = True
    max_iterations = 25
    bulk_solvent_and_scale = False
    min_number_of_reflections = 200
    multi_body_factor = 1
    zone_exponent = 3.0
    high_resolution = 3.0
    number_of_zones = 5
  }
  ncs {
    type = *torsion cartesian constraints
    restrain_b_factors = False
    b_factor_weight = 10
    excessive_distance_limit = 1.5
    torsion {
      sigma = 2.5
      limit = 15.0
      fix_outliers = False
      check_rotamer_consistency = Auto
    }
  }
  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
  }
  ias {
    b_iso_max = 100.0
    occupancy_min = -1.0
    occupancy_max = 1.5
    ias_b_iso_max = 100.0
    ias_b_iso_min = 0.0
    ias_occupancy_min = 0.01
    ias_occupancy_max = 3.0
    initial_ias_occupancy = 1.0
    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
    }
  }
  twinning {
    twin_law = None
    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
      }
    }
  }
  reference_model {
    enabled = True
    file = None
    use_starting_model_as_reference = True
    sigma = 1.0
    limit = 15.0
    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 = all
      selection = all
      file_name = None
    }
    search_options {
      chain_similarity_threshold = 0.85
      chain_max_rmsd = 100.
      residue_match_radius = 1000
      try_shortcuts = False
    }
  }
}