Starting phenix.real_space_refine (version: 1.21rc1)
on Wed Oct 18 11:38:59 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/10_2023/6sht_10205_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/10_2023/6sht_10205.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/10_2023/6sht_10205.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/10_2023/6sht_10205.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/10_2023/6sht_10205_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/10_2023/6sht_10205_neut.pdb"
  }
  resolution = 2.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
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=   0.001 sd=   0.015
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
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Fe     24      7.16       5
     Mg     24      5.21       5
     S     192      5.16       5
     C   22296      2.51       5
     N    6264      2.21       5
     O    8352      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG   60": "NH1" <-> "NH2"
    Residue "A ARG   60": "NH1" <-> "NH2"
    Residue "A ASP   89": "OD1" <-> "OD2"
    Residue "B PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG   60": "NH1" <-> "NH2"
    Residue "B ARG   60": "NH1" <-> "NH2"
    Residue "B ASP   89": "OD1" <-> "OD2"
    Residue "C PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG   60": "NH1" <-> "NH2"
    Residue "C ARG   60": "NH1" <-> "NH2"
    Residue "C ASP   89": "OD1" <-> "OD2"
    Residue "D PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG   60": "NH1" <-> "NH2"
    Residue "D ARG   60": "NH1" <-> "NH2"
    Residue "D ASP   89": "OD1" <-> "OD2"
    Residue "E PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG   60": "NH1" <-> "NH2"
    Residue "E ARG   60": "NH1" <-> "NH2"
    Residue "E ASP   89": "OD1" <-> "OD2"
    Residue "F PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ARG   60": "NH1" <-> "NH2"
    Residue "F ARG   60": "NH1" <-> "NH2"
    Residue "F ASP   89": "OD1" <-> "OD2"
    Residue "G PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G ARG   60": "NH1" <-> "NH2"
    Residue "G ARG   60": "NH1" <-> "NH2"
    Residue "G ASP   89": "OD1" <-> "OD2"
    Residue "H PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ARG   60": "NH1" <-> "NH2"
    Residue "H ARG   60": "NH1" <-> "NH2"
    Residue "H ASP   89": "OD1" <-> "OD2"
    Residue "I PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ARG   60": "NH1" <-> "NH2"
    Residue "I ARG   60": "NH1" <-> "NH2"
    Residue "I ASP   89": "OD1" <-> "OD2"
    Residue "J PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "J ARG   60": "NH1" <-> "NH2"
    Residue "J ARG   60": "NH1" <-> "NH2"
    Residue "J ASP   89": "OD1" <-> "OD2"
    Residue "K PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K ARG   60": "NH1" <-> "NH2"
    Residue "K ARG   60": "NH1" <-> "NH2"
    Residue "K ASP   89": "OD1" <-> "OD2"
    Residue "L PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L ARG   60": "NH1" <-> "NH2"
    Residue "L ARG   60": "NH1" <-> "NH2"
    Residue "L ASP   89": "OD1" <-> "OD2"
    Residue "M PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M ARG   60": "NH1" <-> "NH2"
    Residue "M ARG   60": "NH1" <-> "NH2"
    Residue "M ASP   89": "OD1" <-> "OD2"
    Residue "N PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N ARG   60": "NH1" <-> "NH2"
    Residue "N ARG   60": "NH1" <-> "NH2"
    Residue "N ASP   89": "OD1" <-> "OD2"
    Residue "O PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O ARG   60": "NH1" <-> "NH2"
    Residue "O ARG   60": "NH1" <-> "NH2"
    Residue "O ASP   89": "OD1" <-> "OD2"
    Residue "P PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P ARG   60": "NH1" <-> "NH2"
    Residue "P ARG   60": "NH1" <-> "NH2"
    Residue "P ASP   89": "OD1" <-> "OD2"
    Residue "Q PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "Q ARG   60": "NH1" <-> "NH2"
    Residue "Q ARG   60": "NH1" <-> "NH2"
    Residue "Q ASP   89": "OD1" <-> "OD2"
    Residue "R PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R ARG   60": "NH1" <-> "NH2"
    Residue "R ARG   60": "NH1" <-> "NH2"
    Residue "R ASP   89": "OD1" <-> "OD2"
    Residue "S PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "S ARG   60": "NH1" <-> "NH2"
    Residue "S ARG   60": "NH1" <-> "NH2"
    Residue "S ASP   89": "OD1" <-> "OD2"
    Residue "T PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T ARG   60": "NH1" <-> "NH2"
    Residue "T ARG   60": "NH1" <-> "NH2"
    Residue "T ASP   89": "OD1" <-> "OD2"
    Residue "U PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "U ARG   60": "NH1" <-> "NH2"
    Residue "U ARG   60": "NH1" <-> "NH2"
    Residue "U ASP   89": "OD1" <-> "OD2"
    Residue "V PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "V ARG   60": "NH1" <-> "NH2"
    Residue "V ARG   60": "NH1" <-> "NH2"
    Residue "V ASP   89": "OD1" <-> "OD2"
    Residue "W PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "W ARG   60": "NH1" <-> "NH2"
    Residue "W ARG   60": "NH1" <-> "NH2"
    Residue "W ASP   89": "OD1" <-> "OD2"
    Residue "X PHE   48": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X ARG   60": "NH1" <-> "NH2"
    Residue "X ARG   60": "NH1" <-> "NH2"
    Residue "X ASP   89": "OD1" <-> "OD2"
  Time to flip residues: 0.12s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib"
  Total number of atoms: 37152
  Number of models: 1
  Model: ""
    Number of chains: 24
    Chain: "A"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS A 174 "
              pdbres=" FE A 201 "
            Not linked:
              pdbres=" FE A 201 "
              pdbres=" MG A 202 "
            Not linked:
              pdbres=" MG A 202 "
              pdbres="HOH A 301 "
            Not linked:
              pdbres="HOH A 301 "
              pdbres="HOH A 302 "
            Not linked:
              pdbres="HOH A 302 "
              pdbres="HOH A 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS A 174 "
              pdbres=" FE A 201 "
            Not linked:
              pdbres=" FE A 201 "
              pdbres=" MG A 202 "
            Not linked:
              pdbres=" MG A 202 "
              pdbres="HOH A 301 "
            Not linked:
              pdbres="HOH A 301 "
              pdbres="HOH A 302 "
            Not linked:
              pdbres="HOH A 302 "
              pdbres="HOH A 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "B"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS B 174 "
              pdbres=" FE B 201 "
            Not linked:
              pdbres=" FE B 201 "
              pdbres=" MG B 202 "
            Not linked:
              pdbres=" MG B 202 "
              pdbres="HOH B 301 "
            Not linked:
              pdbres="HOH B 301 "
              pdbres="HOH B 302 "
            Not linked:
              pdbres="HOH B 302 "
              pdbres="HOH B 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS B 174 "
              pdbres=" FE B 201 "
            Not linked:
              pdbres=" FE B 201 "
              pdbres=" MG B 202 "
            Not linked:
              pdbres=" MG B 202 "
              pdbres="HOH B 301 "
            Not linked:
              pdbres="HOH B 301 "
              pdbres="HOH B 302 "
            Not linked:
              pdbres="HOH B 302 "
              pdbres="HOH B 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "C"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS C 174 "
              pdbres=" FE C 201 "
            Not linked:
              pdbres=" FE C 201 "
              pdbres=" MG C 202 "
            Not linked:
              pdbres=" MG C 202 "
              pdbres="HOH C 301 "
            Not linked:
              pdbres="HOH C 301 "
              pdbres="HOH C 302 "
            Not linked:
              pdbres="HOH C 302 "
              pdbres="HOH C 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS C 174 "
              pdbres=" FE C 201 "
            Not linked:
              pdbres=" FE C 201 "
              pdbres=" MG C 202 "
            Not linked:
              pdbres=" MG C 202 "
              pdbres="HOH C 301 "
            Not linked:
              pdbres="HOH C 301 "
              pdbres="HOH C 302 "
            Not linked:
              pdbres="HOH C 302 "
              pdbres="HOH C 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "D"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS D 174 "
              pdbres=" FE D 201 "
            Not linked:
              pdbres=" FE D 201 "
              pdbres=" MG D 202 "
            Not linked:
              pdbres=" MG D 202 "
              pdbres="HOH D 301 "
            Not linked:
              pdbres="HOH D 301 "
              pdbres="HOH D 302 "
            Not linked:
              pdbres="HOH D 302 "
              pdbres="HOH D 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS D 174 "
              pdbres=" FE D 201 "
            Not linked:
              pdbres=" FE D 201 "
              pdbres=" MG D 202 "
            Not linked:
              pdbres=" MG D 202 "
              pdbres="HOH D 301 "
            Not linked:
              pdbres="HOH D 301 "
              pdbres="HOH D 302 "
            Not linked:
              pdbres="HOH D 302 "
              pdbres="HOH D 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "E"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS E 174 "
              pdbres=" FE E 201 "
            Not linked:
              pdbres=" FE E 201 "
              pdbres=" MG E 202 "
            Not linked:
              pdbres=" MG E 202 "
              pdbres="HOH E 301 "
            Not linked:
              pdbres="HOH E 301 "
              pdbres="HOH E 302 "
            Not linked:
              pdbres="HOH E 302 "
              pdbres="HOH E 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS E 174 "
              pdbres=" FE E 201 "
            Not linked:
              pdbres=" FE E 201 "
              pdbres=" MG E 202 "
            Not linked:
              pdbres=" MG E 202 "
              pdbres="HOH E 301 "
            Not linked:
              pdbres="HOH E 301 "
              pdbres="HOH E 302 "
            Not linked:
              pdbres="HOH E 302 "
              pdbres="HOH E 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "F"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS F 174 "
              pdbres=" FE F 201 "
            Not linked:
              pdbres=" FE F 201 "
              pdbres=" MG F 202 "
            Not linked:
              pdbres=" MG F 202 "
              pdbres="HOH F 301 "
            Not linked:
              pdbres="HOH F 301 "
              pdbres="HOH F 302 "
            Not linked:
              pdbres="HOH F 302 "
              pdbres="HOH F 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS F 174 "
              pdbres=" FE F 201 "
            Not linked:
              pdbres=" FE F 201 "
              pdbres=" MG F 202 "
            Not linked:
              pdbres=" MG F 202 "
              pdbres="HOH F 301 "
            Not linked:
              pdbres="HOH F 301 "
              pdbres="HOH F 302 "
            Not linked:
              pdbres="HOH F 302 "
              pdbres="HOH F 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "G"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS G 174 "
              pdbres=" FE G 201 "
            Not linked:
              pdbres=" FE G 201 "
              pdbres=" MG G 202 "
            Not linked:
              pdbres=" MG G 202 "
              pdbres="HOH G 301 "
            Not linked:
              pdbres="HOH G 301 "
              pdbres="HOH G 302 "
            Not linked:
              pdbres="HOH G 302 "
              pdbres="HOH G 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS G 174 "
              pdbres=" FE G 201 "
            Not linked:
              pdbres=" FE G 201 "
              pdbres=" MG G 202 "
            Not linked:
              pdbres=" MG G 202 "
              pdbres="HOH G 301 "
            Not linked:
              pdbres="HOH G 301 "
              pdbres="HOH G 302 "
            Not linked:
              pdbres="HOH G 302 "
              pdbres="HOH G 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "H"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS H 174 "
              pdbres=" FE H 201 "
            Not linked:
              pdbres=" FE H 201 "
              pdbres=" MG H 202 "
            Not linked:
              pdbres=" MG H 202 "
              pdbres="HOH H 301 "
            Not linked:
              pdbres="HOH H 301 "
              pdbres="HOH H 302 "
            Not linked:
              pdbres="HOH H 302 "
              pdbres="HOH H 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS H 174 "
              pdbres=" FE H 201 "
            Not linked:
              pdbres=" FE H 201 "
              pdbres=" MG H 202 "
            Not linked:
              pdbres=" MG H 202 "
              pdbres="HOH H 301 "
            Not linked:
              pdbres="HOH H 301 "
              pdbres="HOH H 302 "
            Not linked:
              pdbres="HOH H 302 "
              pdbres="HOH H 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "I"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS I 174 "
              pdbres=" FE I 201 "
            Not linked:
              pdbres=" FE I 201 "
              pdbres=" MG I 202 "
            Not linked:
              pdbres=" MG I 202 "
              pdbres="HOH I 301 "
            Not linked:
              pdbres="HOH I 301 "
              pdbres="HOH I 302 "
            Not linked:
              pdbres="HOH I 302 "
              pdbres="HOH I 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS I 174 "
              pdbres=" FE I 201 "
            Not linked:
              pdbres=" FE I 201 "
              pdbres=" MG I 202 "
            Not linked:
              pdbres=" MG I 202 "
              pdbres="HOH I 301 "
            Not linked:
              pdbres="HOH I 301 "
              pdbres="HOH I 302 "
            Not linked:
              pdbres="HOH I 302 "
              pdbres="HOH I 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "J"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS J 174 "
              pdbres=" FE J 201 "
            Not linked:
              pdbres=" FE J 201 "
              pdbres=" MG J 202 "
            Not linked:
              pdbres=" MG J 202 "
              pdbres="HOH J 301 "
            Not linked:
              pdbres="HOH J 301 "
              pdbres="HOH J 302 "
            Not linked:
              pdbres="HOH J 302 "
              pdbres="HOH J 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS J 174 "
              pdbres=" FE J 201 "
            Not linked:
              pdbres=" FE J 201 "
              pdbres=" MG J 202 "
            Not linked:
              pdbres=" MG J 202 "
              pdbres="HOH J 301 "
            Not linked:
              pdbres="HOH J 301 "
              pdbres="HOH J 302 "
            Not linked:
              pdbres="HOH J 302 "
              pdbres="HOH J 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "K"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS K 174 "
              pdbres=" FE K 201 "
            Not linked:
              pdbres=" FE K 201 "
              pdbres=" MG K 202 "
            Not linked:
              pdbres=" MG K 202 "
              pdbres="HOH K 301 "
            Not linked:
              pdbres="HOH K 301 "
              pdbres="HOH K 302 "
            Not linked:
              pdbres="HOH K 302 "
              pdbres="HOH K 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS K 174 "
              pdbres=" FE K 201 "
            Not linked:
              pdbres=" FE K 201 "
              pdbres=" MG K 202 "
            Not linked:
              pdbres=" MG K 202 "
              pdbres="HOH K 301 "
            Not linked:
              pdbres="HOH K 301 "
              pdbres="HOH K 302 "
            Not linked:
              pdbres="HOH K 302 "
              pdbres="HOH K 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "L"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS L 174 "
              pdbres=" FE L 201 "
            Not linked:
              pdbres=" FE L 201 "
              pdbres=" MG L 202 "
            Not linked:
              pdbres=" MG L 202 "
              pdbres="HOH L 301 "
            Not linked:
              pdbres="HOH L 301 "
              pdbres="HOH L 302 "
            Not linked:
              pdbres="HOH L 302 "
              pdbres="HOH L 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS L 174 "
              pdbres=" FE L 201 "
            Not linked:
              pdbres=" FE L 201 "
              pdbres=" MG L 202 "
            Not linked:
              pdbres=" MG L 202 "
              pdbres="HOH L 301 "
            Not linked:
              pdbres="HOH L 301 "
              pdbres="HOH L 302 "
            Not linked:
              pdbres="HOH L 302 "
              pdbres="HOH L 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "M"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS M 174 "
              pdbres=" FE M 201 "
            Not linked:
              pdbres=" FE M 201 "
              pdbres=" MG M 202 "
            Not linked:
              pdbres=" MG M 202 "
              pdbres="HOH M 301 "
            Not linked:
              pdbres="HOH M 301 "
              pdbres="HOH M 302 "
            Not linked:
              pdbres="HOH M 302 "
              pdbres="HOH M 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS M 174 "
              pdbres=" FE M 201 "
            Not linked:
              pdbres=" FE M 201 "
              pdbres=" MG M 202 "
            Not linked:
              pdbres=" MG M 202 "
              pdbres="HOH M 301 "
            Not linked:
              pdbres="HOH M 301 "
              pdbres="HOH M 302 "
            Not linked:
              pdbres="HOH M 302 "
              pdbres="HOH M 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "N"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS N 174 "
              pdbres=" FE N 201 "
            Not linked:
              pdbres=" FE N 201 "
              pdbres=" MG N 202 "
            Not linked:
              pdbres=" MG N 202 "
              pdbres="HOH N 301 "
            Not linked:
              pdbres="HOH N 301 "
              pdbres="HOH N 302 "
            Not linked:
              pdbres="HOH N 302 "
              pdbres="HOH N 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS N 174 "
              pdbres=" FE N 201 "
            Not linked:
              pdbres=" FE N 201 "
              pdbres=" MG N 202 "
            Not linked:
              pdbres=" MG N 202 "
              pdbres="HOH N 301 "
            Not linked:
              pdbres="HOH N 301 "
              pdbres="HOH N 302 "
            Not linked:
              pdbres="HOH N 302 "
              pdbres="HOH N 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "O"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS O 174 "
              pdbres=" FE O 201 "
            Not linked:
              pdbres=" FE O 201 "
              pdbres=" MG O 202 "
            Not linked:
              pdbres=" MG O 202 "
              pdbres="HOH O 301 "
            Not linked:
              pdbres="HOH O 301 "
              pdbres="HOH O 302 "
            Not linked:
              pdbres="HOH O 302 "
              pdbres="HOH O 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS O 174 "
              pdbres=" FE O 201 "
            Not linked:
              pdbres=" FE O 201 "
              pdbres=" MG O 202 "
            Not linked:
              pdbres=" MG O 202 "
              pdbres="HOH O 301 "
            Not linked:
              pdbres="HOH O 301 "
              pdbres="HOH O 302 "
            Not linked:
              pdbres="HOH O 302 "
              pdbres="HOH O 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "P"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS P 174 "
              pdbres=" FE P 201 "
            Not linked:
              pdbres=" FE P 201 "
              pdbres=" MG P 202 "
            Not linked:
              pdbres=" MG P 202 "
              pdbres="HOH P 301 "
            Not linked:
              pdbres="HOH P 301 "
              pdbres="HOH P 302 "
            Not linked:
              pdbres="HOH P 302 "
              pdbres="HOH P 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS P 174 "
              pdbres=" FE P 201 "
            Not linked:
              pdbres=" FE P 201 "
              pdbres=" MG P 202 "
            Not linked:
              pdbres=" MG P 202 "
              pdbres="HOH P 301 "
            Not linked:
              pdbres="HOH P 301 "
              pdbres="HOH P 302 "
            Not linked:
              pdbres="HOH P 302 "
              pdbres="HOH P 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "Q"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS Q 174 "
              pdbres=" FE Q 201 "
            Not linked:
              pdbres=" FE Q 201 "
              pdbres=" MG Q 202 "
            Not linked:
              pdbres=" MG Q 202 "
              pdbres="HOH Q 301 "
            Not linked:
              pdbres="HOH Q 301 "
              pdbres="HOH Q 302 "
            Not linked:
              pdbres="HOH Q 302 "
              pdbres="HOH Q 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS Q 174 "
              pdbres=" FE Q 201 "
            Not linked:
              pdbres=" FE Q 201 "
              pdbres=" MG Q 202 "
            Not linked:
              pdbres=" MG Q 202 "
              pdbres="HOH Q 301 "
            Not linked:
              pdbres="HOH Q 301 "
              pdbres="HOH Q 302 "
            Not linked:
              pdbres="HOH Q 302 "
              pdbres="HOH Q 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "R"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS R 174 "
              pdbres=" FE R 201 "
            Not linked:
              pdbres=" FE R 201 "
              pdbres=" MG R 202 "
            Not linked:
              pdbres=" MG R 202 "
              pdbres="HOH R 301 "
            Not linked:
              pdbres="HOH R 301 "
              pdbres="HOH R 302 "
            Not linked:
              pdbres="HOH R 302 "
              pdbres="HOH R 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS R 174 "
              pdbres=" FE R 201 "
            Not linked:
              pdbres=" FE R 201 "
              pdbres=" MG R 202 "
            Not linked:
              pdbres=" MG R 202 "
              pdbres="HOH R 301 "
            Not linked:
              pdbres="HOH R 301 "
              pdbres="HOH R 302 "
            Not linked:
              pdbres="HOH R 302 "
              pdbres="HOH R 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "S"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS S 174 "
              pdbres=" FE S 201 "
            Not linked:
              pdbres=" FE S 201 "
              pdbres=" MG S 202 "
            Not linked:
              pdbres=" MG S 202 "
              pdbres="HOH S 301 "
            Not linked:
              pdbres="HOH S 301 "
              pdbres="HOH S 302 "
            Not linked:
              pdbres="HOH S 302 "
              pdbres="HOH S 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS S 174 "
              pdbres=" FE S 201 "
            Not linked:
              pdbres=" FE S 201 "
              pdbres=" MG S 202 "
            Not linked:
              pdbres=" MG S 202 "
              pdbres="HOH S 301 "
            Not linked:
              pdbres="HOH S 301 "
              pdbres="HOH S 302 "
            Not linked:
              pdbres="HOH S 302 "
              pdbres="HOH S 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "T"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS T 174 "
              pdbres=" FE T 201 "
            Not linked:
              pdbres=" FE T 201 "
              pdbres=" MG T 202 "
            Not linked:
              pdbres=" MG T 202 "
              pdbres="HOH T 301 "
            Not linked:
              pdbres="HOH T 301 "
              pdbres="HOH T 302 "
            Not linked:
              pdbres="HOH T 302 "
              pdbres="HOH T 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS T 174 "
              pdbres=" FE T 201 "
            Not linked:
              pdbres=" FE T 201 "
              pdbres=" MG T 202 "
            Not linked:
              pdbres=" MG T 202 "
              pdbres="HOH T 301 "
            Not linked:
              pdbres="HOH T 301 "
              pdbres="HOH T 302 "
            Not linked:
              pdbres="HOH T 302 "
              pdbres="HOH T 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "U"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS U 174 "
              pdbres=" FE U 201 "
            Not linked:
              pdbres=" FE U 201 "
              pdbres=" MG U 202 "
            Not linked:
              pdbres=" MG U 202 "
              pdbres="HOH U 301 "
            Not linked:
              pdbres="HOH U 301 "
              pdbres="HOH U 302 "
            Not linked:
              pdbres="HOH U 302 "
              pdbres="HOH U 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS U 174 "
              pdbres=" FE U 201 "
            Not linked:
              pdbres=" FE U 201 "
              pdbres=" MG U 202 "
            Not linked:
              pdbres=" MG U 202 "
              pdbres="HOH U 301 "
            Not linked:
              pdbres="HOH U 301 "
              pdbres="HOH U 302 "
            Not linked:
              pdbres="HOH U 302 "
              pdbres="HOH U 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "V"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS V 174 "
              pdbres=" FE V 201 "
            Not linked:
              pdbres=" FE V 201 "
              pdbres=" MG V 202 "
            Not linked:
              pdbres=" MG V 202 "
              pdbres="HOH V 301 "
            Not linked:
              pdbres="HOH V 301 "
              pdbres="HOH V 302 "
            Not linked:
              pdbres="HOH V 302 "
              pdbres="HOH V 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS V 174 "
              pdbres=" FE V 201 "
            Not linked:
              pdbres=" FE V 201 "
              pdbres=" MG V 202 "
            Not linked:
              pdbres=" MG V 202 "
              pdbres="HOH V 301 "
            Not linked:
              pdbres="HOH V 301 "
              pdbres="HOH V 302 "
            Not linked:
              pdbres="HOH V 302 "
              pdbres="HOH V 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "W"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS W 174 "
              pdbres=" FE W 201 "
            Not linked:
              pdbres=" FE W 201 "
              pdbres=" MG W 202 "
            Not linked:
              pdbres=" MG W 202 "
              pdbres="HOH W 301 "
            Not linked:
              pdbres="HOH W 301 "
              pdbres="HOH W 302 "
            Not linked:
              pdbres="HOH W 302 "
              pdbres="HOH W 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS W 174 "
              pdbres=" FE W 201 "
            Not linked:
              pdbres=" FE W 201 "
              pdbres=" MG W 202 "
            Not linked:
              pdbres=" MG W 202 "
              pdbres="HOH W 301 "
            Not linked:
              pdbres="HOH W 301 "
              pdbres="HOH W 302 "
            Not linked:
              pdbres="HOH W 302 "
              pdbres="HOH W 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
    Chain: "X"
      Number of atoms: 1548
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS X 174 "
              pdbres=" FE X 201 "
            Not linked:
              pdbres=" FE X 201 "
              pdbres=" MG X 202 "
            Not linked:
              pdbres=" MG X 202 "
              pdbres="HOH X 301 "
            Not linked:
              pdbres="HOH X 301 "
              pdbres="HOH X 302 "
            Not linked:
              pdbres="HOH X 302 "
              pdbres="HOH X 303 "
            ... (remaining 69 not shown)
      Conformer: "B"
        Number of residues, atoms: 248, 1499
          Unusual residues: {' FE': 1, ' MG': 1}
          Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74}
            Not linked:
              pdbres="HIS X 174 "
              pdbres=" FE X 201 "
            Not linked:
              pdbres=" FE X 201 "
              pdbres=" MG X 202 "
            Not linked:
              pdbres=" MG X 202 "
              pdbres="HOH X 301 "
            Not linked:
              pdbres="HOH X 301 "
              pdbres="HOH X 302 "
            Not linked:
              pdbres="HOH X 302 "
              pdbres="HOH X 303 "
            ... (remaining 69 not shown)
          bond proxies already assigned to first conformer: 1397
  Residues with excluded nonbonded symmetry interactions: 48
    residue:
      pdb="FE    FE A 201 " occ=0.25
    residue:
      pdb=" O   HOH A 359 " occ=0.33
    residue:
      pdb="FE    FE B 201 " occ=0.25
    residue:
      pdb=" O   HOH B 359 " occ=0.33
    residue:
      pdb="FE    FE C 201 " occ=0.25
    residue:
      pdb=" O   HOH C 359 " occ=0.33
    residue:
      pdb="FE    FE D 201 " occ=0.25
    residue:
      pdb=" O   HOH D 359 " occ=0.33
    residue:
      pdb="FE    FE E 201 " occ=0.25
    residue:
      pdb=" O   HOH E 359 " occ=0.33
    residue:
      pdb="FE    FE F 201 " occ=0.25
    residue:
      pdb=" O   HOH F 359 " occ=0.33
    ... (remaining 36 not shown)
  Time building chain proxies: 36.39, per 1000 atoms: 0.98
  Number of scatterers: 37152
  At special positions: 0
  Unit cell: (135.36, 135.36, 135.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe     24     26.01
     S     192     16.00
     Mg     24     11.99
     O    8352      8.00
     N    6264      7.00
     C   22296      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 15.42
  Conformation dependent library (CDL) restraints added in 10.1 seconds
  

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  8400

  Finding SS restraints...
    Secondary structure from input PDB file:
      144 helices and 0 sheets defined
      77.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 40
    Processing helix  chain 'A' and resid 45 through 73
    Processing helix  chain 'A' and resid 92 through 120
    Processing helix  chain 'A' and resid 123 through 134
    Processing helix  chain 'A' and resid 134 through 156
    Processing helix  chain 'A' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR A 165 " --> pdb=" O   GLY A 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 40
    Processing helix  chain 'B' and resid 45 through 73
    Processing helix  chain 'B' and resid 92 through 120
    Processing helix  chain 'B' and resid 123 through 134
    Processing helix  chain 'B' and resid 134 through 156
    Processing helix  chain 'B' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR B 165 " --> pdb=" O   GLY B 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 10 through 40
    Processing helix  chain 'C' and resid 45 through 73
    Processing helix  chain 'C' and resid 92 through 120
    Processing helix  chain 'C' and resid 123 through 134
    Processing helix  chain 'C' and resid 134 through 156
    Processing helix  chain 'C' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR C 165 " --> pdb=" O   GLY C 161 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 10 through 40
    Processing helix  chain 'D' and resid 45 through 73
    Processing helix  chain 'D' and resid 92 through 120
    Processing helix  chain 'D' and resid 123 through 134
    Processing helix  chain 'D' and resid 134 through 156
    Processing helix  chain 'D' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR D 165 " --> pdb=" O   GLY D 161 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 10 through 40
    Processing helix  chain 'E' and resid 45 through 73
    Processing helix  chain 'E' and resid 92 through 120
    Processing helix  chain 'E' and resid 123 through 134
    Processing helix  chain 'E' and resid 134 through 156
    Processing helix  chain 'E' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR E 165 " --> pdb=" O   GLY E 161 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 10 through 40
    Processing helix  chain 'F' and resid 45 through 73
    Processing helix  chain 'F' and resid 92 through 120
    Processing helix  chain 'F' and resid 123 through 134
    Processing helix  chain 'F' and resid 134 through 156
    Processing helix  chain 'F' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR F 165 " --> pdb=" O   GLY F 161 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 10 through 40
    Processing helix  chain 'G' and resid 45 through 73
    Processing helix  chain 'G' and resid 92 through 120
    Processing helix  chain 'G' and resid 123 through 134
    Processing helix  chain 'G' and resid 134 through 156
    Processing helix  chain 'G' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR G 165 " --> pdb=" O   GLY G 161 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 10 through 40
    Processing helix  chain 'H' and resid 45 through 73
    Processing helix  chain 'H' and resid 92 through 120
    Processing helix  chain 'H' and resid 123 through 134
    Processing helix  chain 'H' and resid 134 through 156
    Processing helix  chain 'H' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR H 165 " --> pdb=" O   GLY H 161 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 10 through 40
    Processing helix  chain 'I' and resid 45 through 73
    Processing helix  chain 'I' and resid 92 through 120
    Processing helix  chain 'I' and resid 123 through 134
    Processing helix  chain 'I' and resid 134 through 156
    Processing helix  chain 'I' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR I 165 " --> pdb=" O   GLY I 161 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 10 through 40
    Processing helix  chain 'J' and resid 45 through 73
    Processing helix  chain 'J' and resid 92 through 120
    Processing helix  chain 'J' and resid 123 through 134
    Processing helix  chain 'J' and resid 134 through 156
    Processing helix  chain 'J' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR J 165 " --> pdb=" O   GLY J 161 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 10 through 40
    Processing helix  chain 'K' and resid 45 through 73
    Processing helix  chain 'K' and resid 92 through 120
    Processing helix  chain 'K' and resid 123 through 134
    Processing helix  chain 'K' and resid 134 through 156
    Processing helix  chain 'K' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR K 165 " --> pdb=" O   GLY K 161 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 10 through 40
    Processing helix  chain 'L' and resid 45 through 73
    Processing helix  chain 'L' and resid 92 through 120
    Processing helix  chain 'L' and resid 123 through 134
    Processing helix  chain 'L' and resid 134 through 156
    Processing helix  chain 'L' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR L 165 " --> pdb=" O   GLY L 161 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 10 through 40
    Processing helix  chain 'M' and resid 45 through 73
    Processing helix  chain 'M' and resid 92 through 120
    Processing helix  chain 'M' and resid 123 through 134
    Processing helix  chain 'M' and resid 134 through 156
    Processing helix  chain 'M' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR M 165 " --> pdb=" O   GLY M 161 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 10 through 40
    Processing helix  chain 'N' and resid 45 through 73
    Processing helix  chain 'N' and resid 92 through 120
    Processing helix  chain 'N' and resid 123 through 134
    Processing helix  chain 'N' and resid 134 through 156
    Processing helix  chain 'N' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR N 165 " --> pdb=" O   GLY N 161 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 10 through 40
    Processing helix  chain 'O' and resid 45 through 73
    Processing helix  chain 'O' and resid 92 through 120
    Processing helix  chain 'O' and resid 123 through 134
    Processing helix  chain 'O' and resid 134 through 156
    Processing helix  chain 'O' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR O 165 " --> pdb=" O   GLY O 161 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 10 through 40
    Processing helix  chain 'P' and resid 45 through 73
    Processing helix  chain 'P' and resid 92 through 120
    Processing helix  chain 'P' and resid 123 through 134
    Processing helix  chain 'P' and resid 134 through 156
    Processing helix  chain 'P' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR P 165 " --> pdb=" O   GLY P 161 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 10 through 40
    Processing helix  chain 'Q' and resid 45 through 73
    Processing helix  chain 'Q' and resid 92 through 120
    Processing helix  chain 'Q' and resid 123 through 134
    Processing helix  chain 'Q' and resid 134 through 156
    Processing helix  chain 'Q' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR Q 165 " --> pdb=" O   GLY Q 161 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 10 through 40
    Processing helix  chain 'R' and resid 45 through 73
    Processing helix  chain 'R' and resid 92 through 120
    Processing helix  chain 'R' and resid 123 through 134
    Processing helix  chain 'R' and resid 134 through 156
    Processing helix  chain 'R' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR R 165 " --> pdb=" O   GLY R 161 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 10 through 40
    Processing helix  chain 'S' and resid 45 through 73
    Processing helix  chain 'S' and resid 92 through 120
    Processing helix  chain 'S' and resid 123 through 134
    Processing helix  chain 'S' and resid 134 through 156
    Processing helix  chain 'S' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR S 165 " --> pdb=" O   GLY S 161 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 10 through 40
    Processing helix  chain 'T' and resid 45 through 73
    Processing helix  chain 'T' and resid 92 through 120
    Processing helix  chain 'T' and resid 123 through 134
    Processing helix  chain 'T' and resid 134 through 156
    Processing helix  chain 'T' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR T 165 " --> pdb=" O   GLY T 161 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 10 through 40
    Processing helix  chain 'U' and resid 45 through 73
    Processing helix  chain 'U' and resid 92 through 120
    Processing helix  chain 'U' and resid 123 through 134
    Processing helix  chain 'U' and resid 134 through 156
    Processing helix  chain 'U' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR U 165 " --> pdb=" O   GLY U 161 " (cutoff:3.500A)
    Processing helix  chain 'V' and resid 10 through 40
    Processing helix  chain 'V' and resid 45 through 73
    Processing helix  chain 'V' and resid 92 through 120
    Processing helix  chain 'V' and resid 123 through 134
    Processing helix  chain 'V' and resid 134 through 156
    Processing helix  chain 'V' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR V 165 " --> pdb=" O   GLY V 161 " (cutoff:3.500A)
    Processing helix  chain 'W' and resid 10 through 40
    Processing helix  chain 'W' and resid 45 through 73
    Processing helix  chain 'W' and resid 92 through 120
    Processing helix  chain 'W' and resid 123 through 134
    Processing helix  chain 'W' and resid 134 through 156
    Processing helix  chain 'W' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR W 165 " --> pdb=" O   GLY W 161 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 10 through 40
    Processing helix  chain 'X' and resid 45 through 73
    Processing helix  chain 'X' and resid 92 through 120
    Processing helix  chain 'X' and resid 123 through 134
    Processing helix  chain 'X' and resid 134 through 156
    Processing helix  chain 'X' and resid 161 through 171
      removed outlier: 3.872A  pdb=" N   TYR X 165 " --> pdb=" O   GLY X 161 " (cutoff:3.500A)

    2640 hydrogen bonds defined for protein.
    7776 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 11.64

  Time building geometry restraints manager: 16.14 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.20 -     1.33: 9888
        1.33 -     1.46: 8088
        1.46 -     1.58: 17976
        1.58 -     1.71: 48
        1.71 -     1.84: 312
  Bond restraints: 36312
  Sorted by residual:
  bond pdb=" CA  ALA D 157 "
       pdb=" CB  ALA D 157 "
    ideal  model  delta    sigma   weight residual
    1.530  1.465  0.064 1.46e-02 4.69e+03 1.94e+01
  bond pdb=" CA  ALA M 157 "
       pdb=" CB  ALA M 157 "
    ideal  model  delta    sigma   weight residual
    1.530  1.465  0.064 1.46e-02 4.69e+03 1.94e+01
  bond pdb=" CA  ALA B 157 "
       pdb=" CB  ALA B 157 "
    ideal  model  delta    sigma   weight residual
    1.530  1.465  0.064 1.46e-02 4.69e+03 1.94e+01
  bond pdb=" CA  ALA E 157 "
       pdb=" CB  ALA E 157 "
    ideal  model  delta    sigma   weight residual
    1.530  1.465  0.064 1.46e-02 4.69e+03 1.94e+01
  bond pdb=" CA  ALA K 157 "
       pdb=" CB  ALA K 157 "
    ideal  model  delta    sigma   weight residual
    1.530  1.465  0.064 1.46e-02 4.69e+03 1.94e+01
  ... (remaining 36307 not shown)

  Histogram of bond angle deviations from ideal:
       99.84 -   106.68: 1032
      106.68 -   113.53: 18624
      113.53 -   120.37: 16008
      120.37 -   127.21: 13080
      127.21 -   134.06: 360
  Bond angle restraints: 49104
  Sorted by residual:
  angle pdb=" N   HIS B 170 "
        pdb=" CA  HIS B 170 "
        pdb=" C   HIS B 170 "
      ideal   model   delta    sigma   weight residual
     111.69  118.63   -6.94 1.23e+00 6.61e-01 3.18e+01
  angle pdb=" N   HIS D 170 "
        pdb=" CA  HIS D 170 "
        pdb=" C   HIS D 170 "
      ideal   model   delta    sigma   weight residual
     111.69  118.63   -6.94 1.23e+00 6.61e-01 3.18e+01
  angle pdb=" N   HIS Q 170 "
        pdb=" CA  HIS Q 170 "
        pdb=" C   HIS Q 170 "
      ideal   model   delta    sigma   weight residual
     111.69  118.63   -6.94 1.23e+00 6.61e-01 3.18e+01
  angle pdb=" N   HIS U 170 "
        pdb=" CA  HIS U 170 "
        pdb=" C   HIS U 170 "
      ideal   model   delta    sigma   weight residual
     111.69  118.63   -6.94 1.23e+00 6.61e-01 3.18e+01
  angle pdb=" N   HIS J 170 "
        pdb=" CA  HIS J 170 "
        pdb=" C   HIS J 170 "
      ideal   model   delta    sigma   weight residual
     111.69  118.63   -6.94 1.23e+00 6.61e-01 3.18e+01
  ... (remaining 49099 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.95: 21504
       35.95 -    71.90: 1032
       71.90 -   107.85: 24
      107.85 -   143.80: 0
      143.80 -   179.75: 24
  Dihedral angle restraints: 22584
    sinusoidal: 9456
      harmonic: 13128
  Sorted by residual:
  dihedral pdb=" CD BARG A  60 "
           pdb=" NE BARG A  60 "
           pdb=" CZ BARG A  60 "
           pdb=" NH1BARG A  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  179.75 -179.75     1      1.00e+01 1.00e-02 1.92e+02
  dihedral pdb=" CD BARG C  60 "
           pdb=" NE BARG C  60 "
           pdb=" CZ BARG C  60 "
           pdb=" NH1BARG C  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  179.75 -179.75     1      1.00e+01 1.00e-02 1.92e+02
  dihedral pdb=" CD BARG D  60 "
           pdb=" NE BARG D  60 "
           pdb=" CZ BARG D  60 "
           pdb=" NH1BARG D  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  179.75 -179.75     1      1.00e+01 1.00e-02 1.92e+02
  ... (remaining 22581 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.054: 2664
       0.054 -    0.105: 1848
       0.105 -    0.157: 504
       0.157 -    0.209: 72
       0.209 -    0.261: 24
  Chirality restraints: 5112
  Sorted by residual:
  chirality pdb=" CA  VAL I  43 "
            pdb=" N   VAL I  43 "
            pdb=" C   VAL I  43 "
            pdb=" CB  VAL I  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CA  VAL C  43 "
            pdb=" N   VAL C  43 "
            pdb=" C   VAL C  43 "
            pdb=" CB  VAL C  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CA  VAL K  43 "
            pdb=" N   VAL K  43 "
            pdb=" C   VAL K  43 "
            pdb=" CB  VAL K  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.26 2.00e-01 2.50e+01 1.70e+00
  ... (remaining 5109 not shown)

  Planarity restraints: 6480
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 134 "   -0.038 2.00e-02 2.50e+03   1.99e-02 7.93e+00
        pdb=" CG  TYR F 134 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 134 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 134 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 134 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 134 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 134 "   -0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR F 134 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L 134 "   -0.038 2.00e-02 2.50e+03   1.99e-02 7.93e+00
        pdb=" CG  TYR L 134 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR L 134 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TYR L 134 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR L 134 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR L 134 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR L 134 "   -0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR L 134 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR G 134 "   -0.038 2.00e-02 2.50e+03   1.99e-02 7.93e+00
        pdb=" CG  TYR G 134 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR G 134 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 TYR G 134 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR G 134 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR G 134 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  TYR G 134 "   -0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR G 134 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 6477 not shown)

  Histogram of nonbonded interaction distances:
        0.00 -     0.98: 60
        0.98 -     1.96: 48
        1.96 -     2.94: 16140
        2.94 -     3.92: 107076
        3.92 -     4.90: 208788
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 332112
  Sorted by model distance:
  nonbonded pdb="FE    FE D 201 "
            pdb="FE    FE J 201 "
     model   vdw
     0.000 1.480
  nonbonded pdb="FE    FE D 201 "
            pdb="FE    FE M 201 "
     model   vdw
     0.000 1.480
  nonbonded pdb="FE    FE D 201 "
            pdb="FE    FE V 201 "
     model   vdw
     0.000 1.480
  nonbonded pdb="FE    FE J 201 "
            pdb="FE    FE M 201 "
     model   vdw
     0.000 1.480
  nonbonded pdb="FE    FE J 201 "
            pdb="FE    FE V 201 "
     model   vdw
     0.000 1.480
  ... (remaining 332107 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'B' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'C' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'D' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'E' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'F' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'G' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'H' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'I' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'J' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'K' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'L' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'M' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'N' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'O' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'P' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'Q' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'R' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'S' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'T' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'U' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'V' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'W' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
  selection = (chain 'X' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ 
 or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ 
sid 154 through 168 or resid 170 through 202))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.93
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.030
  Extract box with map and model:          5.930
  Check model and map are aligned:         0.640
  Set scattering table:                    0.350
  Process input model:                     116.480
  Find NCS groups from input model:        2.490
  Set up NCS constraints:                  0.210
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  138.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8805
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.015   0.083  36312  Z= 0.990
  Angle     :  1.547  10.740  49104  Z= 1.010
  Chirality :  0.070   0.261   5112
  Planarity :  0.007   0.040   6480
  Dihedral  : 19.276 179.750  14184
  Min Nonbonded Distance : 0.000

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  :  0.58 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 13.58 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.82 (0.11), residues: 4320
  helix: -1.81 (0.07), residues: 3384
  sheet:  None (None), residues: 0
  loop : -1.17 (0.22), residues: 936

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1536 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 192
    poor density    : 1344
  time to evaluate  : 4.165 
Fit side-chains
  outliers start: 192
  outliers final: 24
  residues processed: 1392
  average time/residue: 1.8529
  time to fit residues: 3007.0759
Evaluate side-chains
  978 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 954
  time to evaluate  : 4.348 
Switching outliers to nearest non-outliers
  outliers start: 24
  outliers final: 24
  residues processed: 0
  time to fit residues: 5.7722
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 576
   random chunks:
   chunk 486 optimal weight:    0.9980
   chunk 436 optimal weight:    8.9990
   chunk 242 optimal weight:    0.9980
   chunk 149 optimal weight:    0.0270
   chunk 294 optimal weight:    5.9990
   chunk 233 optimal weight:    4.9990
   chunk 451 optimal weight:   50.0000
   chunk 174 optimal weight:    0.8980
   chunk 274 optimal weight:    3.9990
   chunk 336 optimal weight:    5.9990
   chunk 523 optimal weight:   50.0000
   overall best weight:    1.3840

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
B  55 GLN
B  57 HIS
B  72 GLN
B  95 ASN
C  72 GLN
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  62 HIS
F  62 HIS
F  72 GLN
G  57 HIS
G  72 GLN
G 108 ASN
I  72 GLN
I 108 ASN
** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  55 GLN
K  72 GLN
K  95 ASN
L  72 GLN
M  55 GLN
M  95 ASN
M 108 ASN
N   8 ASN
N  57 HIS
N  62 HIS
O 108 ASN
P  72 GLN
Q  72 GLN
R  72 GLN
R 108 ASN
S  57 HIS
S  72 GLN
** S 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  55 GLN
T  57 HIS
T  72 GLN
U  57 HIS
U  72 GLN
U 151 ASN
V  72 GLN
W  57 HIS
W  95 ASN
X  72 GLN

Total number of N/Q/H flips: 41

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.290  36312  Z= 0.680
  Angle     :  1.968  40.348  49104  Z= 0.996
  Chirality :  0.076   0.723   5112
  Planarity :  0.017   0.175   6480
  Dihedral  : 13.696 179.984   4968
  Min Nonbonded Distance : 0.000

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.68 %
    Allowed  :  3.05 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  7.64 %
    Allowed  : 18.34 %
    Favored  : 74.02 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.11), residues: 4320
  helix: -0.67 (0.07), residues: 3384
  sheet:  None (None), residues: 0
  loop : -1.56 (0.20), residues: 936

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1359 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 265
    poor density    : 1094
  time to evaluate  : 3.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 265
  outliers final: 69
  residues processed: 1162
  average time/residue: 1.7628
  time to fit residues: 2413.4409
Evaluate side-chains
  1055 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 69
    poor density    : 986
  time to evaluate  : 4.517 
Switching outliers to nearest non-outliers
  outliers start: 69
  outliers final: 10
  residues processed: 59
  average time/residue: 0.9952
  time to fit residues: 82.3265
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 576
   random chunks:
   chunk 290 optimal weight:    0.8980
   chunk 162 optimal weight:   50.0000
   chunk 435 optimal weight:    2.9990
   chunk 356 optimal weight:   50.0000
   chunk 144 optimal weight:    0.8980
   chunk 524 optimal weight:   50.0000
   chunk 566 optimal weight:    0.9980
   chunk 466 optimal weight:    2.9990
   chunk 519 optimal weight:    6.9990
   chunk 178 optimal weight:    7.9990
   chunk 420 optimal weight:    1.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
A 108 ASN
C  72 GLN
C  95 ASN
D  55 GLN
D  95 ASN
D 109 GLN
E  55 GLN
E  72 GLN
F  95 ASN
G  95 ASN
G 108 ASN
H  72 GLN
I  55 GLN
I 108 ASN
J  55 GLN
K  72 GLN
L  55 GLN
L  72 GLN
M  10 HIS
M  22 ASN
M 108 ASN
** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  55 GLN
N 102 HIS
O  72 GLN
O 108 ASN
P  72 GLN
Q  72 GLN
R  72 GLN
R  95 ASN
R 108 ASN
R 115 HIS
S  55 GLN
S  72 GLN
S  95 ASN
T  72 GLN
T  95 ASN
U  72 GLN
U  95 ASN
U 108 ASN
V  72 GLN
V  95 ASN
W  72 GLN
X  72 GLN

Total number of N/Q/H flips: 44

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  36312  Z= 0.197
  Angle     :  0.551   7.371  49104  Z= 0.303
  Chirality :  0.039   0.140   5112
  Planarity :  0.004   0.055   6480
  Dihedral  : 13.007 179.974   4968
  Min Nonbonded Distance : 0.000

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  0.92 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 22.94 %
    Favored  : 73.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.02 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.29 (0.12), residues: 4320
  helix:  2.89 (0.08), residues: 3408
  sheet:  None (None), residues: 0
  loop : -0.78 (0.20), residues: 912

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1141 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 117
    poor density    : 1024
  time to evaluate  : 4.170 
Fit side-chains
  outliers start: 117
  outliers final: 32
  residues processed: 1062
  average time/residue: 1.6754
  time to fit residues: 2112.9612
Evaluate side-chains
  920 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 888
  time to evaluate  : 4.368 
Switching outliers to nearest non-outliers
  outliers start: 32
  outliers final: 26
  residues processed: 12
  average time/residue: 0.4740
  time to fit residues: 15.3025
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 576
   random chunks:
   chunk 517 optimal weight:    5.9990
   chunk 393 optimal weight:    3.9990
   chunk 271 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 250 optimal weight:    4.9990
   chunk 351 optimal weight:    3.9990
   chunk 525 optimal weight:   50.0000
   chunk 556 optimal weight:    0.9980
   chunk 274 optimal weight:    0.9980
   chunk 498 optimal weight:   50.0000
   chunk 150 optimal weight:    2.9990
   overall best weight:    1.9986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN
A  95 ASN
A 102 HIS
** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  95 ASN
B 102 HIS
C 102 HIS
** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   8 ASN
D 102 HIS
E  62 HIS
E  95 ASN
E 102 HIS
** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F   8 ASN
F  62 HIS
F 102 HIS
G   8 ASN
G 102 HIS
H   8 ASN
H  95 ASN
H 102 HIS
** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I   8 ASN
I 102 HIS
** I 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  95 ASN
J 102 HIS
K   8 ASN
** K 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 102 HIS
** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  10 HIS
M 102 HIS
** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  95 ASN
N 102 HIS
** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 102 HIS
O 108 ASN
P   8 ASN
P 102 HIS
** P 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 102 HIS
** Q 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 102 HIS
S 102 HIS
T   8 ASN
T 102 HIS
** T 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U   8 ASN
U 102 HIS
** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
V   8 ASN
V 102 HIS
** V 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
W 102 HIS
** W 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
X   8 ASN
X  95 ASN
X 102 HIS
** X 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 46

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  36312  Z= 0.212
  Angle     :  0.511   6.929  49104  Z= 0.280
  Chirality :  0.038   0.126   5112
  Planarity :  0.003   0.038   6480
  Dihedral  : 12.980 179.736   4968
  Min Nonbonded Distance : 0.000

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  :  1.07 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 25.31 %
    Favored  : 71.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.02 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.53 (0.12), residues: 4320
  helix:  3.78 (0.08), residues: 3432
  sheet:  None (None), residues: 0
  loop : -0.50 (0.20), residues: 888

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1031 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 93
    poor density    : 938
  time to evaluate  : 4.661 
Fit side-chains
  outliers start: 93
  outliers final: 53
  residues processed: 985
  average time/residue: 1.5995
  time to fit residues: 1890.9715
Evaluate side-chains
  954 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 901
  time to evaluate  : 4.393 
Switching outliers to nearest non-outliers
  outliers start: 53
  outliers final: 34
  residues processed: 24
  average time/residue: 0.6413
  time to fit residues: 29.1152
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 576
   random chunks:
   chunk 463 optimal weight:    6.9990
   chunk 316 optimal weight:   10.0000
   chunk 8 optimal weight:    0.0670
   chunk 414 optimal weight:    0.8980
   chunk 229 optimal weight:    0.9980
   chunk 475 optimal weight:   50.0000
   chunk 384 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 284 optimal weight:   50.0000
   chunk 499 optimal weight:   50.0000
   chunk 140 optimal weight:   50.0000
   overall best weight:    1.9920

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN
A 102 HIS
A 138 GLN
B 102 HIS
C 102 HIS
C 138 GLN
D   8 ASN
D  62 HIS
D 102 HIS
E  62 HIS
E 102 HIS
E 138 GLN
F   8 ASN
F 102 HIS
G   8 ASN
G  55 GLN
G 102 HIS
H   8 ASN
H 102 HIS
H 138 GLN
I   8 ASN
I  62 HIS
I 102 HIS
I 138 GLN
J 102 HIS
K   8 ASN
K 138 GLN
L 102 HIS
L 138 GLN
M 102 HIS
M 138 GLN
N 102 HIS
N 138 GLN
O   8 ASN
O  95 ASN
O 102 HIS
P   8 ASN
P 102 HIS
P 138 GLN
Q  95 ASN
Q 102 HIS
Q 138 GLN
R 102 HIS
S   8 ASN
S 102 HIS
T   8 ASN
T 102 HIS
T 138 GLN
U   8 ASN
U 102 HIS
U 138 GLN
V   8 ASN
V 102 HIS
** V 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
W 102 HIS
W 138 GLN
X   8 ASN
X 102 HIS
X 138 GLN

Total number of N/Q/H flips: 58

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021  36312  Z= 0.209
  Angle     :  0.496   6.590  49104  Z= 0.270
  Chirality :  0.038   0.120   5112
  Planarity :  0.003   0.034   6480
  Dihedral  : 12.989 179.825   4968
  Min Nonbonded Distance : 0.000

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  1.02 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 26.16 %
    Favored  : 70.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.02 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.98 (0.12), residues: 4320
  helix:  4.09 (0.08), residues: 3432
  sheet:  None (None), residues: 0
  loop : -0.36 (0.20), residues: 888

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1017 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 99
    poor density    : 918
  time to evaluate  : 4.349 
Fit side-chains
  outliers start: 99
  outliers final: 64
  residues processed: 966
  average time/residue: 1.5921
  time to fit residues: 1852.9278
Evaluate side-chains
  986 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 64
    poor density    : 922
  time to evaluate  : 4.504 
Switching outliers to nearest non-outliers
  outliers start: 64
  outliers final: 33
  residues processed: 32
  average time/residue: 0.9922
  time to fit residues: 48.0275
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 576
   random chunks:
   chunk 187 optimal weight:   50.0000
   chunk 501 optimal weight:   50.0000
   chunk 110 optimal weight:    4.9990
   chunk 326 optimal weight:    2.9990
   chunk 137 optimal weight:   10.0000
   chunk 557 optimal weight:    0.9990
   chunk 462 optimal weight:    6.9990
   chunk 258 optimal weight:   50.0000
   chunk 46 optimal weight:   50.0000
   chunk 184 optimal weight:    2.9990
   chunk 292 optimal weight:    0.8980
   overall best weight:    2.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN
A 102 HIS
B 102 HIS
C 102 HIS
D   8 ASN
D 102 HIS
E 102 HIS
F   8 ASN
F  62 HIS
F 102 HIS
** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G   8 ASN
G 102 HIS
H   8 ASN
H  55 GLN
H 102 HIS
I   8 ASN
I  62 HIS
I 102 HIS
J 102 HIS
K   8 ASN
L 102 HIS
M  95 ASN
M 102 HIS
N 102 HIS
O   8 ASN
O 102 HIS
P   8 ASN
P  55 GLN
P  95 ASN
P 102 HIS
Q 102 HIS
R  55 GLN
R 102 HIS
S   8 ASN
S  62 HIS
S 102 HIS
T   8 ASN
T 102 HIS
U   8 ASN
U 102 HIS
V   8 ASN
V 102 HIS
V 138 GLN
W  55 GLN
W  62 HIS
W 102 HIS
X   8 ASN
X  55 GLN
X 102 HIS

Total number of N/Q/H flips: 49

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.3351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026  36312  Z= 0.253
  Angle     :  0.515   6.571  49104  Z= 0.279
  Chirality :  0.039   0.124   5112
  Planarity :  0.003   0.032   6480
  Dihedral  : 13.019 179.952   4968
  Min Nonbonded Distance : 0.000

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  1.07 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 25.75 %
    Favored  : 70.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.02 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.96 (0.12), residues: 4320
  helix:  4.06 (0.08), residues: 3432
  sheet:  None (None), residues: 0
  loop : -0.28 (0.20), residues: 888

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1055 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 110
    poor density    : 945
  time to evaluate  : 4.369 
Fit side-chains
   revert: symmetry clash
  outliers start: 110
  outliers final: 61
  residues processed: 997
  average time/residue: 1.5958
  time to fit residues: 1904.4890
Evaluate side-chains
  1004 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 61
    poor density    : 943
  time to evaluate  : 4.106 
Switching outliers to nearest non-outliers
  outliers start: 61
  outliers final: 38
  residues processed: 24
  average time/residue: 1.2978
  time to fit residues: 43.9008
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 576
   random chunks:
   chunk 537 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 317 optimal weight:    0.9990
   chunk 406 optimal weight:   50.0000
   chunk 315 optimal weight:    5.9990
   chunk 469 optimal weight:    2.9990
   chunk 311 optimal weight:   50.0000
   chunk 555 optimal weight:    0.7980
   chunk 347 optimal weight:    7.9990
   chunk 338 optimal weight:    5.9990
   chunk 256 optimal weight:    1.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN
A 102 HIS
B 102 HIS
C 102 HIS
D   8 ASN
D 102 HIS
E 102 HIS
F   8 ASN
F  62 HIS
F 102 HIS
** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G   8 ASN
G 102 HIS
H   8 ASN
H 102 HIS
I   8 ASN
I  62 HIS
I 102 HIS
J  62 HIS
J 102 HIS
K   8 ASN
L   8 ASN
L 102 HIS
M 102 HIS
N 102 HIS
O   8 ASN
O 102 HIS
P   8 ASN
P 102 HIS
Q  55 GLN
Q 102 HIS
R 102 HIS
S   8 ASN
S 102 HIS
T   8 ASN
T 102 HIS
U   8 ASN
U  55 GLN
U 102 HIS
V   8 ASN
V 102 HIS
W  62 HIS
W 102 HIS
X   8 ASN
X 102 HIS

Total number of N/Q/H flips: 44

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
moved from start:          0.3520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  36312  Z= 0.193
  Angle     :  0.474   6.011  49104  Z= 0.259
  Chirality :  0.037   0.117   5112
  Planarity :  0.003   0.031   6480
  Dihedral  : 12.990 179.966   4968
  Min Nonbonded Distance : 0.000

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  1.19 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 25.93 %
    Favored  : 70.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.02 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.25 (0.12), residues: 4320
  helix:  4.27 (0.08), residues: 3432
  sheet:  None (None), residues: 0
  loop : -0.21 (0.20), residues: 888

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1060 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 112
    poor density    : 948
  time to evaluate  : 4.316 
Fit side-chains
   revert: symmetry clash
  outliers start: 112
  outliers final: 67
  residues processed: 998
  average time/residue: 1.6395
  time to fit residues: 1958.0557
Evaluate side-chains
  1002 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 935
  time to evaluate  : 4.121 
Switching outliers to nearest non-outliers
  outliers start: 67
  outliers final: 38
  residues processed: 30
  average time/residue: 0.8083
  time to fit residues: 39.2119
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 576
   random chunks:
   chunk 343 optimal weight:    4.9990
   chunk 221 optimal weight:    0.7980
   chunk 331 optimal weight:   50.0000
   chunk 167 optimal weight:   50.0000
   chunk 109 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 352 optimal weight:    2.9990
   chunk 378 optimal weight:   50.0000
   chunk 274 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 436 optimal weight:    7.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN
A 102 HIS
B 102 HIS
C 102 HIS
D   8 ASN
D 102 HIS
E 102 HIS
F   8 ASN
F  62 HIS
F 102 HIS
** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G   8 ASN
G 102 HIS
H   8 ASN
H 102 HIS
I   8 ASN
I  62 HIS
I 102 HIS
J 102 HIS
K   8 ASN
L   8 ASN
L 102 HIS
M 102 HIS
N 102 HIS
O   8 ASN
O 102 HIS
P   8 ASN
P 102 HIS
Q 102 HIS
R 102 HIS
S   8 ASN
S 102 HIS
T   8 ASN
T 102 HIS
U   8 ASN
U 102 HIS
V   8 ASN
V 102 HIS
W  62 HIS
W 102 HIS
X   8 ASN
X 102 HIS

Total number of N/Q/H flips: 41

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  36312  Z= 0.225
  Angle     :  0.497   6.127  49104  Z= 0.270
  Chirality :  0.038   0.120   5112
  Planarity :  0.003   0.031   6480
  Dihedral  : 12.999 179.958   4968
  Min Nonbonded Distance : 0.000

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  1.04 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 25.87 %
    Favored  : 70.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.02 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.18 (0.12), residues: 4320
  helix:  4.20 (0.08), residues: 3432
  sheet:  None (None), residues: 0
  loop : -0.15 (0.20), residues: 888

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1046 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 102
    poor density    : 944
  time to evaluate  : 4.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 102
  outliers final: 85
  residues processed: 991
  average time/residue: 1.6432
  time to fit residues: 1951.4236
Evaluate side-chains
  1034 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 85
    poor density    : 949
  time to evaluate  : 4.212 
Switching outliers to nearest non-outliers
  outliers start: 85
  outliers final: 40
  residues processed: 46
  average time/residue: 1.1067
  time to fit residues: 71.6659
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 576
   random chunks:
   chunk 505 optimal weight:    5.9990
   chunk 531 optimal weight:    0.6980
   chunk 485 optimal weight:    6.9990
   chunk 517 optimal weight:    4.9990
   chunk 311 optimal weight:   50.0000
   chunk 225 optimal weight:    0.7980
   chunk 406 optimal weight:   50.0000
   chunk 158 optimal weight:    0.9980
   chunk 467 optimal weight:    5.9990
   chunk 489 optimal weight:    0.6980
   chunk 515 optimal weight:    7.9990
   overall best weight:    1.6382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN
A 102 HIS
B 102 HIS
C 102 HIS
D   8 ASN
D 102 HIS
E 102 HIS
F   8 ASN
F  62 HIS
F 102 HIS
** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G   8 ASN
G 102 HIS
H   8 ASN
H 102 HIS
I   8 ASN
I  62 HIS
I 102 HIS
J 102 HIS
K   8 ASN
K 102 HIS
L   8 ASN
L 102 HIS
M 102 HIS
N   8 ASN
N 102 HIS
O   8 ASN
O  55 GLN
O 102 HIS
P   8 ASN
P 102 HIS
Q 102 HIS
R   8 ASN
R 102 HIS
S   8 ASN
S 102 HIS
T   8 ASN
T 102 HIS
U   8 ASN
U 102 HIS
V   8 ASN
V 102 HIS
W 102 HIS
X   8 ASN
X 102 HIS

Total number of N/Q/H flips: 44

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.3601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  36312  Z= 0.189
  Angle     :  0.470   5.797  49104  Z= 0.257
  Chirality :  0.036   0.116   5112
  Planarity :  0.003   0.031   6480
  Dihedral  : 12.987 179.986   4968
  Min Nonbonded Distance : 0.000

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  1.36 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 26.47 %
    Favored  : 70.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.02 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.37 (0.12), residues: 4320
  helix:  4.34 (0.08), residues: 3432
  sheet:  None (None), residues: 0
  loop : -0.08 (0.20), residues: 888

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1009 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 79
    poor density    : 930
  time to evaluate  : 4.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 79
  outliers final: 51
  residues processed: 973
  average time/residue: 1.6585
  time to fit residues: 1937.1229
Evaluate side-chains
  981 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 930
  time to evaluate  : 4.857 
Switching outliers to nearest non-outliers
  outliers start: 51
  outliers final: 39
  residues processed: 12
  average time/residue: 1.2694
  time to fit residues: 25.4063
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 576
   random chunks:
   chunk 339 optimal weight:    3.9990
   chunk 547 optimal weight:   50.0000
   chunk 333 optimal weight:   50.0000
   chunk 259 optimal weight:   50.0000
   chunk 380 optimal weight:   50.0000
   chunk 573 optimal weight:   50.0000
   chunk 528 optimal weight:    0.0270
   chunk 456 optimal weight:    6.9990
   chunk 47 optimal weight:   50.0000
   chunk 352 optimal weight:    2.9990
   chunk 280 optimal weight:    5.9990
   overall best weight:    4.0046

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN
A 102 HIS
B 102 HIS
C 102 HIS
D   8 ASN
D 102 HIS
E   8 ASN
E 102 HIS
F   8 ASN
F  62 HIS
F 102 HIS
** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G   8 ASN
G 102 HIS
H 102 HIS
I   8 ASN
I  62 HIS
I 102 HIS
J 102 HIS
K   8 ASN
K 102 HIS
L   8 ASN
L 102 HIS
M 102 HIS
N   8 ASN
N 102 HIS
O   8 ASN
O 102 HIS
P   8 ASN
P 102 HIS
Q 102 HIS
R   8 ASN
R 102 HIS
S   8 ASN
S 102 HIS
T   8 ASN
T 102 HIS
U   8 ASN
U 102 HIS
V   8 ASN
V 102 HIS
W 102 HIS
X   8 ASN
X 102 HIS

Total number of N/Q/H flips: 43

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  36312  Z= 0.364
  Angle     :  0.572   6.892  49104  Z= 0.309
  Chirality :  0.042   0.139   5112
  Planarity :  0.004   0.033   6480
  Dihedral  : 12.964 179.372   4968
  Min Nonbonded Distance : 0.000

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  1.74 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 26.13 %
    Favored  : 70.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.02 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.84 (0.12), residues: 4320
  helix:  3.93 (0.08), residues: 3432
  sheet:  None (None), residues: 0
  loop : -0.11 (0.20), residues: 888

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  8640 Ramachandran restraints generated.
    4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  1027 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 88
    poor density    : 939
  time to evaluate  : 4.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 88
  outliers final: 67
  residues processed: 983
  average time/residue: 1.6266
  time to fit residues: 1910.0639
Evaluate side-chains
  988 residues out of total 3504 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 67
    poor density    : 921
  time to evaluate  : 4.127 
Switching outliers to nearest non-outliers
  outliers start: 67
  outliers final: 31
  residues processed: 36
  average time/residue: 1.2241
  time to fit residues: 61.1597
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 576
   random chunks:
   chunk 362 optimal weight:    0.9980
   chunk 486 optimal weight:    0.7980
   chunk 139 optimal weight:   50.0000
   chunk 421 optimal weight:    0.9990
   chunk 67 optimal weight:   50.0000
   chunk 126 optimal weight:    3.9990
   chunk 457 optimal weight:    6.9990
   chunk 191 optimal weight:   50.0000
   chunk 469 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A   8 ASN
A 102 HIS
B 102 HIS
C 102 HIS
D   8 ASN
D 102 HIS
E 102 HIS
F   8 ASN
F 102 HIS
** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G   8 ASN
G 102 HIS
H 102 HIS
I   8 ASN
I  80 GLN
I 102 HIS
J 102 HIS
K   8 ASN
K 102 HIS
L   8 ASN
L 102 HIS
M 102 HIS
N   8 ASN
N 102 HIS
O   8 ASN
O 102 HIS
P   8 ASN
P 102 HIS
Q 102 HIS
R   8 ASN
R 102 HIS
S   8 ASN
S 102 HIS
T   8 ASN
T 102 HIS
U   8 ASN
U 102 HIS
V   8 ASN
V 102 HIS
W 102 HIS
X   8 ASN
X 102 HIS

Total number of N/Q/H flips: 41

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.112080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.089065 restraints weight = 304002.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 3.81
r_work: 0.2634 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2585 r_free = 0.2585    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1464 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2582 r_free = 0.2582    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:     1466 |
|-----------------------------------------------------------------------------|
r_final: 0.2582
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.3783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  36312  Z= 0.144
  Angle     :  0.459   5.539  49104  Z= 0.253
  Chirality :  0.036   0.116   5112
  Planarity :  0.003   0.039   6480
  Dihedral  : 12.897 179.635   4968
  Min Nonbonded Distance : 0.000

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  1.77 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 27.39 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 25.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.02 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.47 (0.12), residues: 4320
  helix:  4.41 (0.08), residues: 3432
  sheet:  None (None), residues: 0
  loop : -0.06 (0.20), residues: 888
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 24787.90 seconds
wall clock time: 440 minutes 5.50 seconds (26405.50 seconds total)