# Default parameters for subsequent refinement

refinement.crystal_symmetry {
  unit_cell = 68.52490234 68.75579834 74.6115036 90 90 90
  space_group = "P 21 21 21"
}
refinement.input {
  pdb {
    file_name = "/Users/francisreyes/Public/TTH071907-ATP_OXO-1/001-molrep1_refine_003.pdb"
  }
  neutron_data {
    file_name = None
    labels = None
  }
  neutron_r_free_flags {
    file_name = None
    label = None
    test_flag_value = None
    disable_suitability_test = False
  }
  xray_data {
    file_name = "ScalAveragedA.mtz"
    labels = "F,SIGF"
  }
  r_free_flags {
    file_name = "ScalAveragedA.mtz"
    label = "FreeR_flag"
    test_flag_value = 0
    disable_suitability_test = False
  }
  experimental_phases {
    file_name = None
    labels = None
  }
  monomers {
    file_name = None
  }
  symmetry_safety_check = *error warning
}
refinement.output {
  prefix = "001-molrep1_refine"
  serial = 4
  serial_format = "%03d"
  write_eff_file = True
  write_geo_file = True
  write_def_file = True
  export_final_f_model = mtz cns
  write_maps = True
  write_map_coefficients = True
}
refinement.electron_density_map {
  map_types = k*Fobs-n*Fmodel *2m*Fobs-D*Fmodel *m*Fobs-D*Fmodel
  k = 2
  n = 1
  map_format = *xplor
  map_coefficients_format = *mtz phs
  mtz_labels {
    map_type = "2m*Fobs-D*Fmodel"
    amplitudes = "2FOFCWT"
    phases = "PH2FOFCWT"
  }
  mtz_labels {
    map_type = "m*Fobs-D*Fmodel"
    amplitudes = "FOFCWT"
    phases = "PHFOFCWT"
  }
  mtz_labels {
    map_type = "k*Fobs-n*Fmodel"
    amplitudes = "oFOoFCWT"
    phases = "oPHFOoFCWT"
  }
  grid_resolution_factor = 0.3333333333
  region = *selection cell
  atom_selection = None
  atom_selection_buffer = 3
  apply_sigma_scaling = True
  apply_volume_scaling = False
}
refinement.refine {
  strategy = *individual_sites rigid_body *individual_adp group_adp tls \
             individual_occupancies group_occupancies group_anomalous none
  sites {
    individual = None
    rigid_body = None
  }
  adp {
    individual {
      isotropic = None
      anisotropic = None
    }
    group = None
    one_adp_group_per_residue = True
    tls =  None
    tls = None 
    tls = None 
  }
  occupancies {
    individual = None
    group = None
    one_occupancy_group_per_residue = False
  }
  anomalous_scatterers {
    group {
      selection = None
      f_prime = 0
      f_double_prime = 0
      refine = *f_prime *f_double_prime
    }
  }
}
refinement.main {
  high_resolution = 2.2
  low_resolution = 25
  bulk_solvent_and_scale = True
  simulated_annealing = True
  scale_adp = True
  ordered_solvent =  False
  ncs = False
  dbe = False
  ls_bulk_solvent_and_scale_if_r_greater_then = 0.99
  number_of_macro_cycles = 3
  max_number_of_iterations = 25
  generate_neutron_r_free_flags = False
  generate_r_free_flags = False
  r_free_flags_fraction = 0.1
  r_free_flags_max_free = 2000
  r_free_flags_lattice_symmetry_max_delta = 5
  r_free_flags_use_lattice_symmetry = True
  remove_test_set_memory = None
  use_form_factor_weights = False
  tan_u_iso = False
  use_convergence_test = False
  target = *ml mlhl ml_sad ls
  min_number_of_test_set_reflections_for_max_likelihood_target = 50
  max_number_of_resolution_bins = 30
  sigma_fobs_rejection_criterion = 0
  sigma_iobs_rejection_criterion = 0
  reference_xray_structure = None
  use_experimental_phases = None
  force_anomalous_flag_to_be_equal_to = None
  compute_optimal_errors = False
  random_seed = 2957036
  scattering_table = wk1995 it1992 *n_gaussian neutron
  use_normalized_geometry_target = True
  stop_refinement_if_resolution_higher_than = 0
  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
  twinning = True
  stir = None
  fft_vs_direct = False
  ignore_r_free_flags = False
  rigid_bond_test = False
}
refinement.modify_start_model {
  adp {
    randomize = None
    set_b_iso_to = None
    set_biso_to_wilson_b = None
    convert_to_isotropic = False
    shift_b_iso_by = None
  }
  sites {
    shake = None
    rigid_body {
      t = "0" "0" "0"
      r = "0" "0" "0"
    }
  }
  occupancies {
    randomize = None
  }
  selection = None
  remove_hydrogens = True
  remove_ordered_solvent = False
  write_modified = None
}
refinement.fake_f_obs {
  k_sol = 0
  b_sol = 0
  b_cart = "0" "0" "0" "0" "0" "0"
  scale = 1
}
refinement.hydrogens {
  mode = full riding
  refine = one_b_per_residue one_b_per_molecule
}
refinement.group_b_iso {
  number_of_macro_cycles = 3
  max_number_of_iterations = 25
  convergence_test = False
  run_finite_differences_test = False
}
refinement.adp {
  iso {
    max_number_of_iterations = 25
    automatic_randomization_if_all_equal = True
    scaling {
      scale_max = 3
      scale_min = 10
    }
  }
}
refinement.tls {
  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
}
refinement.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
    b_iso_max = None
  }
}
refinement.group_occupancy {
  number_of_macro_cycles = 3
  max_number_of_iterations = 25
  convergence_test = False
  run_finite_differences_test = False
}
refinement.group_anomalous {
  number_of_minimizer_cycles = 3
  lbfgs_max_iterations = 20
  number_of_finite_difference_tests = 0
}
refinement.rigid_body {
  protocol = one_zone *multiple_zones
  target = ls_wunit_k1 *ml
  refine_rotation = True
  refine_translation = True
  min_number_of_reflections = 500
  max_iterations = 25
  convergence_test = False
  convergence_delta = 1e-05
  bulk_solvent_and_scale = True
  euler_angle_convention = *xyz zyz
  high_resolution = 2
  low_high_res_limit = 6
  max_low_high_res_limit = 8
  lbfgs_line_search_max_function_evaluations = 10
}
refinement.ncs {
  find_ncs {
    temp_dir = ""
    min_length = 10
    njump = 1
    njump_recursion = 10
    min_length_recursion = 50
    min_percent = 95
    max_rmsd = 2
    quick = True
    max_rmsd_user = 3
    domain_finding_parameters {
      find_invariant_domains = True
      initial_rms = 0.5
      match_radius = 2
      similarity_threshold = 0.75
      smooth_length = 0
      min_contig_length = 3
      min_fraction_domain = 0.2
      max_rmsd_domain = 2
    }
    verbose = False
  }
  find_automatically = True
  coordinate_sigma = None
  b_factor_weight = None
  excessive_distance_limit = 1.5
  restraint_group {
    reference = None
    selection = None
    coordinate_sigma = 0.05
    b_factor_weight = 10
  }
}
refinement.pdb_interpretation {
  apply_cif_modification {
    data_mod = None
    residue_selection = None
  }
  apply_cif_link {
    data_link = None
    residue_selection_1 = None
    residue_selection_2 = None
  }
  link_distance_cutoff = 3
  disulfide_distance_cutoff = 3
  chir_volume_esd = 0.2
  peptide_link {
    cis_threshold = 45
    discard_psi_phi = True
    omega_esd_override_value = None
  }
  nonbonded_distance_cutoff = None
  default_vdw_distance = 1
  min_vdw_distance = 1
  nonbonded_buffer = 1
  vdw_1_4_factor = 0.6666666667
  translate_cns_dna_rna_residue_names = True
  clash_guard {
    nonbonded_distance_threshold = 0.5
    max_number_of_distances_below_threshold = 100
    max_fraction_of_distances_below_threshold = 0.1
  }
}
refinement.geometry_restraints.edits {
  bond {
    action = *add delete change
    atom_selection_1 = None
    atom_selection_2 = None
    symmetry_operation = None
    distance_ideal = None
    sigma = None
  }
  angle {
    action = *add delete change
    atom_selection_1 = None
    atom_selection_2 = None
    atom_selection_3 = None
    angle_ideal = None
    sigma = None
  }
}
refinement.geometry_restraints.remove {
  angles = None
  dihedrals = None
  chiralities = None
  planarities = None
}
refinement.ordered_solvent {
  low_resolution = 2.8
  mode = *auto filter_only every_macro_cycle
  output_residue_name = "HOH"
  output_chain_id = "S"
  output_atom_name = "O"
  b_iso_min = 1
  b_iso_max = 50
  b_iso = None
  scattering_type = "O"
  occupancy_min = 1
  occupancy_max = 1
  occupancy = 1
  bulk_solvent_mask_exclusions = True
  use_sigma_scaled_maps = True
  primary_map_type = "m*Fobs-D*Fmodel"
  primary_map_k = None
  primary_map_n = None
  primary_map_cutoff = 3
  secondary_map_type = "2m*Fobs-D*Fmodel"
  secondary_map_k = None
  secondary_map_n = None
  secondary_map_cutoff = 1
  peak_map_matching_tolerance = 2
  resolution_factor = 0.25
  min_solv_macromol_dist = 1.8
  max_solv_macromol_dist = 6
  min_solv_solv_dist = 1.8
  max_number_of_peaks = None
  verbose = 1
  peak_search {
    peak_search_level = 1
    max_peaks = 0
    interpolate = True
    min_distance_sym_equiv = 1e-06
    general_positions_only = False
    min_cross_distance = 2
  }
}
refinement.bulk_solvent_and_scale {
  bulk_solvent = True
  anisotropic_scaling = True
  statistical_solvent = False
  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 = 150
  b_sol_min = 10
  k_sol_grid_search_max = 0.6
  k_sol_grid_search_min = 0
  b_sol_grid_search_max = 100
  b_sol_grid_search_min = 10
  k_sol_step = 0.05
  b_sol_step = 5
  number_of_macro_cycles = 3
  number_of_minimization_macro_cycles = 3
  number_of_cycles_for_anisotropic_scaling = 3
  fix_k_sol = None
  fix_b_sol = None
  fix_b_cart {
    u11 = None
    u22 = None
    u33 = None
    u12 = None
    u13 = None
    u23 = None
  }
  apply_back_trace_of_b_cart = False
  start_minimization_from_k_sol = 0.35
  start_minimization_from_b_sol = 46
  start_minimization_from_b_cart {
    u11 = 0
    u22 = 0
    u33 = 0
    u12 = 0
    u13 = 0
    u23 = 0
  }
  nu_fix_n_atoms = None
  nu_fix_b_atoms = None
  verbose = 1
}
refinement.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
  fix_scale_for_calc_option = None
  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
  }
}
refinement.mask {
  solvent_radius = 1.11
  shrink_truncation_radius = 0.9
  grid_step_factor = 4
  verbose = -1
  mean_shift_for_mask_update = 0.1
}
refinement.cartesian_dynamics {
  temperature = 300
  number_of_steps = 200
  time_step = 0.0005
  n_print = 100
  verbose = -1
}
refinement.simulated_annealing {
  start_temperature = 5000
  final_temperature = 300
  cool_rate = 100
  number_of_steps = 25
  time_step = 0.0005
  n_print = 100
  update_grads_shift = 0.3
  refine_sites = True
  refine_adp = False
  max_number_of_iterations = 25
  mode = every_macro_cycle *second_and_before_last once first
  verbose = -1
}
refinement.target_weights {
  wxc_scale = 0.5
  wxu_scale = 1
  wc = 1
  wu = 1
  fix_wxc = None
  fix_wxu = None
  allow_automatic_adjustment = False
  delta_r_free_r_work = 6
  wxc_scale_drop = 3
  wxu_scale_drop = 3
  max_number_of_macro_cycles = 12
  optimize_wxc = False
  optimization_criterion = *r_free gradient_angle
  optimize_wxu = False
  shake_sites = True
  shake_adp = 10
  regularize_ncycles = 50
  gradient_filtering = True
  gradient_filtering_method = *cns new
  rmsd_cutoff_for_gradient_filtering = 3
  verbose = 1
  neutrons {
    wxnc_scale = 1
    wxnu_scale = 1
  }
}
refinement.dbe {
  b_iso_max = 10
  occupancy_min = 0.7
  occupancy_max = 1.5
  initial_dbe_occupancy = 1
  build_dbe_types = L R B BH
  number_of_macro_cycles = 10
  use_map = True
  resolution_factor = 0.1
  restraints {
    selection = D1 D2 D3 D4 D5 D6 D7 D8 D9 D10
    weight_scale = 10
  }
}
refinement.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
}
refinement.neutron {
  low_resolution = None
  high_resolution = None
}
refinement.twinning {
  twin_law = "k,h,-l"
  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 = True
    }
  }
}
refinement.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
}
