# Default parameters for subsequent refinement
# Date 2024-12-29 Time 09:19:02 PST -0800 (1735492742.03 s)

# Command to extract only non-defaults:
#   phenix.refine --diff_params "shake_3337960_refine_002.def"

data_manager {
  phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff"
  default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff"
  restraint_files = None
  default_restraint = None
  miller_array {
    file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.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 = 3
      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 = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz"
  model {
    file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3337960.pdb"
    type = *x_ray neutron electron reference
  }
  default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3337960.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 = (chain A and resseq 15 and (name OE2 or name OE1)) or \
                   (chain A and resseq 24 and (name OD2 or name OD1))
      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 {
    fit_altlocs_method = masking sampling
    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 = True
    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 = 1
    update_f_part1 = True
    tncs_correction = False
    ddr {
      enable = False
      weighting_factor = 0.5
      cc_minimum = 0
      map_value_minimum = 0.5
      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
      keep_occupancy = False
      altloc_to_keep = None
      average_alt_confs = 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
    }
  }
  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
      include_modified_amino_acid_in_cdl = False
      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
    use_ncs_to_build_restraints = True
    show_restraints_histograms = 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 = None
          helix_identifier = None
          enabled = True
          selection = None
          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 = None
          sheet_id = None
          strand {
            selection = None
            sense = parallel antiparallel *unknown
            bond_start_current = None
            bond_start_previous = None
          }
          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
        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 = False
    }
    c_beta_restraints = True
    reference_coordinate_restraints {
      enabled = False
      exclude_outliers = True
      selection = all
      sigma = 0.2
      limit = 1
      top_out = False
      reference_is_average_alt_confs = False
    }
    automatic_restraints {
      side_chain_parallelity = False
    }
    automatic_linking {
      link_all = False
      link_none = False
      link_metals = Auto
      link_residues = True
      link_amino_acid_rna_dna = False
      link_carbohydrates = True
      link_ligands = True
      link_small_molecules = False
      metal_coordination_cutoff = 3
      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 = False
      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 = None
    const_shrink_donor_acceptor = 0
    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
      enable = True
    }
    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 = 4
    mode = second_half filter_only every_macro_cycle \
           *every_macro_cycle_after_first
    mask_atoms_selection = "protein and (name CA or name CB or name N or name C or name O)"
    include_altlocs = False
    n_cycles = 1
    output_residue_name = "HOH"
    output_chain_id = "S"
    output_atom_name = "O"
    scattering_type = "O"
    primary_map_type = "mFobs-DFmodel"
    primary_map_cutoff = 2.5
    secondary_map_and_map_cc_filter {
      cc_map_1_type = "Fmodel"
      cc_map_2_type = "2mFobs-DFmodel"
      poor_cc_threshold = 0.7
      poor_map_value_threshold = 0.7
    }
    dist_min = 1.8
    dist_max = 3.2
    dist_min_altloc = 0.5
    refine_oat = False
    refine_adp = True
    refine_occupancies = True
    new_solvent = *isotropic anisotropic
    b_iso_min = 1
    b_iso_max = 80
    anisotropy_min = 0.1
    occupancy_min = 0.2
    occupancy_max = 1
    occupancy = 1
    filter_at_start = True
    ignore_final_filtering_step = True
    correct_drifted_waters = False
  }
  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 = 3.2
      min_peak_peak_dist = 3.2
      use_hydrogens = False
    }
    max_number_of_peaks = 3273
    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 = False
    optimize_adp_weight = False
    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
          }
        }
      }
    }
  }
  amber {
    use_amber = False
    topology_file_name = None
    coordinate_file_name = None
    order_file_name = None
    wxc_factor = 1
    restraint_wt = 0
    restraintmask = ""
    reference_file_name = ""
    bellymask = ""
    qmmask = ""
    qmcharge = 0
    netcdf_trajectory_file_name = ""
    print_amber_energies = False
  }
  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
      }
      specific_atom_multiplicities {
        atom_selection = None
        multiplicity = None
      }
      calculate = *in_situ_opt starting_energy final_energy starting_strain \
                  final_strain starting_bound final_bound starting_binding \
                  final_binding 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
      ignore_lack_of_h_on_ligand = 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 = "shake_3337960_refine"
  suffix = None
  serial = 2
  serial_format = "%03d"
  target_output_format = None *pdb mmcif
  overwrite = False
}
