Starting phenix.real_space_refine (version: dev)
on Thu Dec 22 09:05:03 2022 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6adq_9610/12_2022/6adq_9610.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6adq_9610/12_2022/6adq_9610.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6adq_9610/12_2022/6adq_9610.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6adq_9610/12_2022/6adq_9610.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6adq_9610/12_2022/6adq_9610.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6adq_9610/12_2022/6adq_9610.pdb"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "E ARG   47": "NH1" <-> "NH2"
    Residue "E ARG  119": "NH1" <-> "NH2"
    Residue "E ARG  163": "NH1" <-> "NH2"
    Residue "E ARG  170": "NH1" <-> "NH2"
    Residue "E ARG  289": "NH1" <-> "NH2"
    Residue "E ARG  303": "NH1" <-> "NH2"
    Residue "E ARG  331": "NH1" <-> "NH2"
    Residue "E ARG  332": "NH1" <-> "NH2"
    Residue "F ARG  205": "NH1" <-> "NH2"
    Residue "F ARG  459": "NH1" <-> "NH2"
    Residue "F ARG  527": "NH1" <-> "NH2"
    Residue "F ARG  535": "NH1" <-> "NH2"
    Residue "F ARG  540": "NH1" <-> "NH2"
    Residue "G ARG   15": "NH1" <-> "NH2"
    Residue "G ARG   21": "NH1" <-> "NH2"
    Residue "G ARG   51": "NH1" <-> "NH2"
    Residue "G ARG  100": "NH1" <-> "NH2"
    Residue "G ARG  164": "NH1" <-> "NH2"
    Residue "G ARG  203": "NH1" <-> "NH2"
    Residue "H ARG    6": "NH1" <-> "NH2"
    Residue "H ARG   57": "NH1" <-> "NH2"
    Residue "I ARG   55": "NH1" <-> "NH2"
    Residue "J ARG   60": "NH1" <-> "NH2"
    Residue "J ARG  117": "NH1" <-> "NH2"
    Residue "J ARG  148": "NH1" <-> "NH2"
    Residue "D ARG    7": "NH1" <-> "NH2"
    Residue "D ARG   24": "NH1" <-> "NH2"
    Residue "D ARG   96": "NH1" <-> "NH2"
    Residue "D ARG  100": "NH1" <-> "NH2"
    Residue "K PHE   75": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG   27": "NH1" <-> "NH2"
    Residue "B ARG  172": "NH1" <-> "NH2"
    Residue "B ARG  313": "NH1" <-> "NH2"
    Residue "B ARG  366": "NH1" <-> "NH2"
    Residue "B ARG  368": "NH1" <-> "NH2"
    Residue "B ARG  412": "NH1" <-> "NH2"
    Residue "B ARG  435": "NH1" <-> "NH2"
    Residue "B ARG  438": "NH1" <-> "NH2"
    Residue "C ARG   77": "NH1" <-> "NH2"
    Residue "C ARG  101": "NH1" <-> "NH2"
    Residue "C ARG  121": "NH1" <-> "NH2"
    Residue "C ARG  126": "NH1" <-> "NH2"
    Residue "C ARG  161": "NH1" <-> "NH2"
    Residue "C ARG  179": "NH1" <-> "NH2"
    Residue "C ARG  185": "NH1" <-> "NH2"
    Residue "C PHE  266": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  247": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  256": "NH1" <-> "NH2"
    Residue "A ARG  316": "NH1" <-> "NH2"
    Residue "A ARG  328": "NH1" <-> "NH2"
    Residue "A ARG  362": "NH1" <-> "NH2"
    Residue "Q ARG   47": "NH1" <-> "NH2"
    Residue "Q ARG  119": "NH1" <-> "NH2"
    Residue "Q ARG  163": "NH1" <-> "NH2"
    Residue "Q ARG  170": "NH1" <-> "NH2"
    Residue "Q ARG  289": "NH1" <-> "NH2"
    Residue "Q ARG  303": "NH1" <-> "NH2"
    Residue "Q ARG  331": "NH1" <-> "NH2"
    Residue "Q ARG  332": "NH1" <-> "NH2"
    Residue "R ARG  205": "NH1" <-> "NH2"
    Residue "R ARG  459": "NH1" <-> "NH2"
    Residue "R ARG  527": "NH1" <-> "NH2"
    Residue "R ARG  535": "NH1" <-> "NH2"
    Residue "R ARG  540": "NH1" <-> "NH2"
    Residue "S ARG   15": "NH1" <-> "NH2"
    Residue "S ARG   21": "NH1" <-> "NH2"
    Residue "S ARG   51": "NH1" <-> "NH2"
    Residue "S ARG  100": "NH1" <-> "NH2"
    Residue "S ARG  164": "NH1" <-> "NH2"
    Residue "S ARG  203": "NH1" <-> "NH2"
    Residue "T ARG    6": "NH1" <-> "NH2"
    Residue "T ARG   57": "NH1" <-> "NH2"
    Residue "U ARG   55": "NH1" <-> "NH2"
    Residue "V ARG   60": "NH1" <-> "NH2"
    Residue "V ARG  117": "NH1" <-> "NH2"
    Residue "V ARG  148": "NH1" <-> "NH2"
    Residue "P ARG    7": "NH1" <-> "NH2"
    Residue "P ARG   24": "NH1" <-> "NH2"
    Residue "P ARG   96": "NH1" <-> "NH2"
    Residue "P ARG  100": "NH1" <-> "NH2"
    Residue "W PHE   75": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N ARG   27": "NH1" <-> "NH2"
    Residue "N ARG  172": "NH1" <-> "NH2"
    Residue "N ARG  313": "NH1" <-> "NH2"
    Residue "N ARG  366": "NH1" <-> "NH2"
    Residue "N ARG  368": "NH1" <-> "NH2"
    Residue "N ARG  412": "NH1" <-> "NH2"
    Residue "N ARG  435": "NH1" <-> "NH2"
    Residue "N ARG  438": "NH1" <-> "NH2"
    Residue "O ARG   77": "NH1" <-> "NH2"
    Residue "O ARG  101": "NH1" <-> "NH2"
    Residue "O ARG  121": "NH1" <-> "NH2"
    Residue "O ARG  126": "NH1" <-> "NH2"
    Residue "O ARG  161": "NH1" <-> "NH2"
    Residue "O ARG  179": "NH1" <-> "NH2"
    Residue "O ARG  185": "NH1" <-> "NH2"
    Residue "O PHE  266": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M PHE  247": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M ARG  256": "NH1" <-> "NH2"
    Residue "M ARG  316": "NH1" <-> "NH2"
    Residue "M ARG  328": "NH1" <-> "NH2"
    Residue "M ARG  362": "NH1" <-> "NH2"
  Time to flip residues: 0.14s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib"
  Total number of atoms: 48946
  Number of models: 1
  Model: ""
    Number of chains: 44
    Chain: "E"
      Number of atoms: 2465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2465
          Classifications: {'peptide': 312}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 21, 'TRANS': 290}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "F"
      Number of atoms: 4373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 552, 4373
          Classifications: {'peptide': 552}
          Link IDs: {'PTRANS': 36, 'TRANS': 515}
    Chain: "G"
      Number of atoms: 1560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1560
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 7, 'TRANS': 195}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 4
    Chain: "H"
      Number of atoms: 1077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1077
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 5, 'TRANS': 133}
    Chain: "I"
      Number of atoms: 507
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 507
          Classifications: {'peptide': 67}
          Link IDs: {'PTRANS': 6, 'TRANS': 60}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 1041
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1041
          Classifications: {'peptide': 145}
          Link IDs: {'PTRANS': 10, 'TRANS': 134}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 736
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
          Chain breaks: 1
    Chain: "Y"
      Number of atoms: 1092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1092
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 131}
          Link IDs: {'PTRANS': 16, 'TRANS': 199}
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 427
          Unresolved non-hydrogen angles: 556
          Unresolved non-hydrogen dihedrals: 345
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 9, 'PHE:plan': 8, 'GLU:plan': 8, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 230
    Chain: "K"
      Number of atoms: 1072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1072
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 12, 'TRANS': 134}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 535, 4181
          Classifications: {'peptide': 535}
          Link IDs: {'PTRANS': 34, 'TRANS': 500}
    Chain: "C"
      Number of atoms: 1623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1623
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 16, 'TRANS': 206}
    Chain: "A"
      Number of atoms: 2977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 2977
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 26, 'TRANS': 355}
    Chain: "Q"
      Number of atoms: 2465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 2465
          Classifications: {'peptide': 312}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 21, 'TRANS': 290}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "R"
      Number of atoms: 4373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 552, 4373
          Classifications: {'peptide': 552}
          Link IDs: {'PTRANS': 36, 'TRANS': 515}
    Chain: "S"
      Number of atoms: 1560
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 203, 1560
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 7, 'TRANS': 195}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 4
    Chain: "T"
      Number of atoms: 1077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1077
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 5, 'TRANS': 133}
    Chain: "U"
      Number of atoms: 507
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 507
          Classifications: {'peptide': 67}
          Link IDs: {'PTRANS': 6, 'TRANS': 60}
          Chain breaks: 1
    Chain: "V"
      Number of atoms: 1041
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1041
          Classifications: {'peptide': 145}
          Link IDs: {'PTRANS': 10, 'TRANS': 134}
    Chain: "P"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 736
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
          Chain breaks: 1
    Chain: "Z"
      Number of atoms: 1092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1092
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 131}
          Link IDs: {'PTRANS': 16, 'TRANS': 199}
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 427
          Unresolved non-hydrogen angles: 556
          Unresolved non-hydrogen dihedrals: 345
          Unresolved non-hydrogen chiralities: 46
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 9, 'PHE:plan': 8, 'GLU:plan': 8, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 230
    Chain: "W"
      Number of atoms: 1072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1072
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 12, 'TRANS': 134}
          Chain breaks: 2
    Chain: "N"
      Number of atoms: 4181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 535, 4181
          Classifications: {'peptide': 535}
          Link IDs: {'PTRANS': 34, 'TRANS': 500}
    Chain: "O"
      Number of atoms: 1623
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1623
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 16, 'TRANS': 206}
    Chain: "M"
      Number of atoms: 2977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 382, 2977
          Classifications: {'peptide': 382}
          Link IDs: {'PTRANS': 26, 'TRANS': 355}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CU': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 279
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 279
          Unusual residues: {' CU': 2, 'CDL': 2, 'HEA': 2}
          Unexpected atoms: {'HEA,NA': 2, 'HEA,NB': 2, 'HEA,NC': 2, 'HEA,ND': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 111
          Unresolved non-hydrogen dihedrals: 69
          Unsupported chir.volume_sign: {'cros': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "G"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'9Y0': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 6
    Chain: "H"
      Number of atoms: 79
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 79
          Unusual residues: {'CDL': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 21
    Chain: "D"
      Number of atoms: 129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 129
          Unusual residues: {'9Y0': 1, 'CDL': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 20
    Chain: "Y"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 43
          Unusual residues: {'9XX': 1, 'PLM': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "K"
      Number of atoms: 155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 97
          Unknown residues: {'9YF': 1}
          Unusual residues: {'9XX': 1, '9Y0': 1, 'PLM': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 1}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 671
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 671
          Unusual residues: {'9Y0': 2, 'CDL': 4, 'HEM': 2, 'MQ9': 4}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
          Unresolved non-hydrogen bonds: 145
          Unresolved non-hydrogen angles: 153
          Unresolved non-hydrogen dihedrals: 137
          Planarities with less than four sites: {'MQ9:plan-6': 3, 'MQ9:plan-5': 3, 'MQ9:plan-4': 2}
          Unresolved non-hydrogen planarities: 40
    Chain: "C"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 144
          Unknown residues: {'9YF': 1}
          Unusual residues: {'HEC': 2, 'MQ9': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 1}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 215
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 99
          Unknown residues: {'9YF': 2}
          Unusual residues: {'CDL': 1, 'FES': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 5
    Chain: "Q"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CU': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "R"
      Number of atoms: 279
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 279
          Unusual residues: {' CU': 2, 'CDL': 2, 'HEA': 2}
          Unexpected atoms: {'HEA,NA': 2, 'HEA,NB': 2, 'HEA,NC': 2, 'HEA,ND': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 111
          Unresolved non-hydrogen dihedrals: 69
          Unsupported chir.volume_sign: {'cros': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "S"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'9Y0': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 6
    Chain: "T"
      Number of atoms: 79
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 79
          Unusual residues: {'CDL': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 21
    Chain: "P"
      Number of atoms: 129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 129
          Unusual residues: {'9Y0': 1, 'CDL': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 20
    Chain: "Z"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 43
          Unusual residues: {'9XX': 1, 'PLM': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "W"
      Number of atoms: 155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 97
          Unknown residues: {'9YF': 1}
          Unusual residues: {'9XX': 1, '9Y0': 1, 'PLM': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 1}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "N"
      Number of atoms: 573
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 573
          Unusual residues: {'CDL': 4, 'HEM': 2, 'MQ9': 4}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 145
          Unresolved non-hydrogen angles: 153
          Unresolved non-hydrogen dihedrals: 137
          Planarities with less than four sites: {'MQ9:plan-6': 3, 'MQ9:plan-5': 3, 'MQ9:plan-4': 2}
          Unresolved non-hydrogen planarities: 40
    Chain: "O"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 144
          Unknown residues: {'9YF': 1}
          Unusual residues: {'HEC': 2, 'MQ9': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 1}
          Chain breaks: 1
    Chain: "M"
      Number of atoms: 215
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 99
          Unknown residues: {'9YF': 2}
          Unusual residues: {'CDL': 1, 'FES': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 5

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1957  SG  CYS E 273      39.521  48.377  93.327  1.00 34.52           S
  ATOM   1987  SG  CYS E 277      42.970  51.319  92.746  1.00 34.50           S
  ATOM   1957  SG  CYS E 273      39.521  48.377  93.327  1.00 34.52           S
  ATOM   1987  SG  CYS E 277      42.970  51.319  92.746  1.00 34.50           S
  ATOM  24661  SG  CYS Q 273     173.682  86.823  93.331  1.00 34.15           S
  ATOM  24691  SG  CYS Q 277     170.235  83.887  92.739  1.00 34.44           S
  ATOM  24661  SG  CYS Q 273     173.682  86.823  93.331  1.00 34.15           S
  ATOM  24691  SG  CYS Q 277     170.235  83.887  92.739  1.00 34.44           S

  Number of atoms with unknown nonbonded energy type symbols: 480
    "HETATM45411  NB  HEA F 601 .*.     N  "
    "HETATM45412  ND  HEA F 601 .*.     N  "
    "HETATM45462  NA  HEA F 601 .*.     N  "
    "HETATM45463  NC  HEA F 601 .*.     N  "
    "HETATM45471  NB  HEA F 602 .*.     N  "
    "HETATM45472  ND  HEA F 602 .*.     N  "
    "HETATM45522  NA  HEA F 602 .*.     N  "
    "HETATM45523  NC  HEA F 602 .*.     N  "
    "HETATM46022  C   9YF K 202 .*.     C  "
    "HETATM46023  O   9YF K 202 .*.     O  "
    ... (remaining 470 not shown)
  Time building chain proxies: 25.90, per 1000 atoms: 0.53
  Number of scatterers: 48946
  At special positions: 0
  Unit cell: (214.5, 136.5, 183.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Cu      8     28.99
     Fe     16     26.01
     S     202     16.00
     P      52     15.00
     O    8644      8.00
     N    7706      7.00
     C   32318      6.00
    sf(0) = scattering factor at diffraction angle 0.
Sorry: Fatal problems interpreting model file:
  Number of atoms with unknown nonbonded energy type symbols: 480
    Please edit the model file to resolve the problems and/or supply a
    CIF file with matching restraint definitions, along with
    apply_cif_modification and apply_cif_link parameter definitions
    if necessary.