Starting phenix.real_space_refine
on Tue Mar 26 01:32:59 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybw_10775/03_2024/6ybw_10775_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybw_10775/03_2024/6ybw_10775.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybw_10775/03_2024/6ybw_10775_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybw_10775/03_2024/6ybw_10775_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybw_10775/03_2024/6ybw_10775_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybw_10775/03_2024/6ybw_10775.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybw_10775/03_2024/6ybw_10775.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybw_10775/03_2024/6ybw_10775_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybw_10775/03_2024/6ybw_10775_updated.pdb"
  }
  resolution = 3.1
  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=   0.000 sd=   0.007
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P    1247      5.49       5
     Mg     60      5.21       5
     S     113      5.16       5
     C   28443      2.51       5
     N    9689      2.21       5
     O   13287      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "C ARG   11": "NH1" <-> "NH2"
    Residue "C ARG   49": "NH1" <-> "NH2"
    Residue "C ARG   68": "NH1" <-> "NH2"
    Residue "C ASP   88": "OD1" <-> "OD2"
    Residue "C GLU  117": "OE1" <-> "OE2"
    Residue "C PHE  130": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  151": "OD1" <-> "OD2"
    Residue "C ASP  158": "OD1" <-> "OD2"
    Residue "C ARG  191": "NH1" <-> "NH2"
    Residue "C ARG  198": "NH1" <-> "NH2"
    Residue "C ARG  221": "NH1" <-> "NH2"
    Residue "C GLU  251": "OE1" <-> "OE2"
    Residue "C ARG  252": "NH1" <-> "NH2"
    Residue "B GLU   49": "OE1" <-> "OE2"
    Residue "B GLU   52": "OE1" <-> "OE2"
    Residue "B ARG   97": "NH1" <-> "NH2"
    Residue "B ASP  119": "OD1" <-> "OD2"
    Residue "E ARG    5": "NH1" <-> "NH2"
    Residue "E ARG    8": "NH1" <-> "NH2"
    Residue "E ARG   17": "NH1" <-> "NH2"
    Residue "E GLU   58": "OE1" <-> "OE2"
    Residue "E ARG   67": "NH1" <-> "NH2"
    Residue "E ASP   98": "OD1" <-> "OD2"
    Residue "E GLU   99": "OE1" <-> "OE2"
    Residue "E ARG  107": "NH1" <-> "NH2"
    Residue "D ARG   17": "NH1" <-> "NH2"
    Residue "D ARG   18": "NH1" <-> "NH2"
    Residue "D GLU   21": "OE1" <-> "OE2"
    Residue "D ASP   26": "OD1" <-> "OD2"
    Residue "D ARG   54": "NH1" <-> "NH2"
    Residue "D ARG   69": "NH1" <-> "NH2"
    Residue "D GLU   73": "OE1" <-> "OE2"
    Residue "D ASP  104": "OD1" <-> "OD2"
    Residue "D GLU  107": "OE1" <-> "OE2"
    Residue "D ASP  158": "OD1" <-> "OD2"
    Residue "D ARG  169": "NH1" <-> "NH2"
    Residue "G GLU   29": "OE1" <-> "OE2"
    Residue "G ASP   35": "OD1" <-> "OD2"
    Residue "G GLU   42": "OE1" <-> "OE2"
    Residue "G ARG   57": "NH1" <-> "NH2"
    Residue "G ARG   78": "NH1" <-> "NH2"
    Residue "G ARG   81": "NH1" <-> "NH2"
    Residue "G ARG   99": "NH1" <-> "NH2"
    Residue "G ARG  106": "NH1" <-> "NH2"
    Residue "G GLU  131": "OE1" <-> "OE2"
    Residue "G GLU  138": "OE1" <-> "OE2"
    Residue "G ARG  143": "NH1" <-> "NH2"
    Residue "G ASP  159": "OD1" <-> "OD2"
    Residue "G GLU  167": "OE1" <-> "OE2"
    Residue "G GLU  171": "OE1" <-> "OE2"
    Residue "G ASP  184": "OD1" <-> "OD2"
    Residue "G GLU  188": "OE1" <-> "OE2"
    Residue "F ARG   31": "NH1" <-> "NH2"
    Residue "H GLU   13": "OE1" <-> "OE2"
    Residue "H GLU   14": "OE1" <-> "OE2"
    Residue "H GLU   75": "OE1" <-> "OE2"
    Residue "K ASP    4": "OD1" <-> "OD2"
    Residue "K ASP   67": "OD1" <-> "OD2"
    Residue "J ASP    9": "OD1" <-> "OD2"
    Residue "J GLU   18": "OE1" <-> "OE2"
    Residue "J GLU   49": "OE1" <-> "OE2"
    Residue "J ASP   85": "OD1" <-> "OD2"
    Residue "J ASP  112": "OD1" <-> "OD2"
    Residue "M ARG   81": "NH1" <-> "NH2"
    Residue "M GLU   87": "OE1" <-> "OE2"
    Residue "M GLU   94": "OE1" <-> "OE2"
    Residue "M PHE  128": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L GLU   79": "OE1" <-> "OE2"
    Residue "L PHE   96": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L GLU  105": "OE1" <-> "OE2"
    Residue "L ARG  123": "NH1" <-> "NH2"
    Residue "L GLU  146": "OE1" <-> "OE2"
    Residue "L ARG  166": "NH1" <-> "NH2"
    Residue "L ARG  167": "NH1" <-> "NH2"
    Residue "L ARG  200": "NH1" <-> "NH2"
    Residue "L ASP  221": "OD1" <-> "OD2"
    Residue "L ARG  227": "NH1" <-> "NH2"
    Residue "L ASP  242": "OD1" <-> "OD2"
    Residue "L GLU  258": "OE1" <-> "OE2"
    Residue "O PHE   39": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O GLU   68": "OE1" <-> "OE2"
    Residue "O ARG   82": "NH1" <-> "NH2"
    Residue "O GLU   89": "OE1" <-> "OE2"
    Residue "O ASP  104": "OD1" <-> "OD2"
    Residue "O ARG  151": "NH1" <-> "NH2"
    Residue "O ARG  162": "NH1" <-> "NH2"
    Residue "O ARG  165": "NH1" <-> "NH2"
    Residue "O ARG  213": "NH1" <-> "NH2"
    Residue "O PHE  223": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "O GLU  230": "OE1" <-> "OE2"
    Residue "N ASP    6": "OD1" <-> "OD2"
    Residue "N GLU   12": "OE1" <-> "OE2"
    Residue "N GLU   35": "OE1" <-> "OE2"
    Residue "N TYR   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N PHE  103": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "N GLU  118": "OE1" <-> "OE2"
    Residue "N ASP  126": "OD1" <-> "OD2"
    Residue "N GLU  181": "OE1" <-> "OE2"
    Residue "Q ARG   10": "NH1" <-> "NH2"
    Residue "Q GLU   46": "OE1" <-> "OE2"
    Residue "Q ARG   85": "NH1" <-> "NH2"
    Residue "Q ARG   87": "NH1" <-> "NH2"
    Residue "Q ARG   89": "NH1" <-> "NH2"
    Residue "Q ASP   94": "OD1" <-> "OD2"
    Residue "P GLU   25": "OE1" <-> "OE2"
    Residue "P ASP   80": "OD1" <-> "OD2"
    Residue "P ARG  117": "NH1" <-> "NH2"
    Residue "P ASP  131": "OD1" <-> "OD2"
    Residue "P ARG  141": "NH1" <-> "NH2"
    Residue "P ARG  150": "NH1" <-> "NH2"
    Residue "S ASP   19": "OD1" <-> "OD2"
    Residue "S GLU   44": "OE1" <-> "OE2"
    Residue "S ASP  126": "OD1" <-> "OD2"
    Residue "S ARG  131": "NH1" <-> "NH2"
    Residue "S ARG  132": "NH1" <-> "NH2"
    Residue "S GLU  150": "OE1" <-> "OE2"
    Residue "S GLU  165": "OE1" <-> "OE2"
    Residue "S ARG  178": "NH1" <-> "NH2"
    Residue "S GLU  204": "OE1" <-> "OE2"
    Residue "S GLU  205": "OE1" <-> "OE2"
    Residue "S GLU  219": "OE1" <-> "OE2"
    Residue "R ARG   25": "NH1" <-> "NH2"
    Residue "R ARG   41": "NH1" <-> "NH2"
    Residue "R ASP  105": "OD1" <-> "OD2"
    Residue "R GLU  114": "OE1" <-> "OE2"
    Residue "R GLU  133": "OE1" <-> "OE2"
    Residue "R GLU  135": "OE1" <-> "OE2"
    Residue "R GLU  151": "OE1" <-> "OE2"
    Residue "R GLU  164": "OE1" <-> "OE2"
    Residue "R GLU  196": "OE1" <-> "OE2"
    Residue "T PHE   12": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T ARG   20": "NH1" <-> "NH2"
    Residue "T ASP   26": "OD1" <-> "OD2"
    Residue "T ARG   41": "NH1" <-> "NH2"
    Residue "T ASP   53": "OD1" <-> "OD2"
    Residue "T ARG   61": "NH1" <-> "NH2"
    Residue "q ARG   24": "NH1" <-> "NH2"
    Residue "q ASP   31": "OD1" <-> "OD2"
    Residue "q GLU   34": "OE1" <-> "OE2"
    Residue "q ASP   83": "OD1" <-> "OD2"
    Residue "q ASP   90": "OD1" <-> "OD2"
    Residue "q GLU  108": "OE1" <-> "OE2"
    Residue "p ARG   38": "NH1" <-> "NH2"
    Residue "p ASP   52": "OD1" <-> "OD2"
    Residue "p ASP   53": "OD1" <-> "OD2"
    Residue "p GLU   81": "OE1" <-> "OE2"
    Residue "I GLU   86": "OE1" <-> "OE2"
    Residue "I GLU  103": "OE1" <-> "OE2"
    Residue "I ARG  104": "NH1" <-> "NH2"
    Residue "I ASP  110": "OD1" <-> "OD2"
    Residue "I ARG  114": "NH1" <-> "NH2"
    Residue "I ARG  121": "NH1" <-> "NH2"
    Residue "I GLU  142": "OE1" <-> "OE2"
    Residue "y ARG   56": "NH1" <-> "NH2"
    Residue "y GLU   58": "OE1" <-> "OE2"
    Residue "y GLU   59": "OE1" <-> "OE2"
    Residue "y ARG   74": "NH1" <-> "NH2"
    Residue "y GLU   84": "OE1" <-> "OE2"
    Residue "y TYR   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "y ARG  104": "NH1" <-> "NH2"
    Residue "y ARG  108": "NH1" <-> "NH2"
    Residue "y ASP  112": "OD1" <-> "OD2"
    Residue "y GLU  119": "OE1" <-> "OE2"
    Residue "y GLU  122": "OE1" <-> "OE2"
    Residue "y ARG  142": "NH1" <-> "NH2"
    Residue "y GLU  153": "OE1" <-> "OE2"
    Residue "9 ARG    2": "NH1" <-> "NH2"
    Residue "9 ARG   23": "NH1" <-> "NH2"
  Time to flip residues: 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib"
  Total number of atoms: 52840
  Number of models: 1
  Model: ""
    Number of chains: 30
    Chain: "C"
      Number of atoms: 2035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 2035
          Classifications: {'peptide': 256}
          Link IDs: {'PTRANS': 14, 'TRANS': 241}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "B"
      Number of atoms: 1166
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 1166
          Classifications: {'peptide': 142}
          Link IDs: {'PTRANS': 6, 'TRANS': 135}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1087
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1087
          Classifications: {'peptide': 140}
          Link IDs: {'PTRANS': 5, 'TRANS': 134}
    Chain: "D"
      Number of atoms: 1477
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 177, 1477
          Classifications: {'peptide': 177}
          Link IDs: {'PTRANS': 6, 'TRANS': 170}
    Chain: "G"
      Number of atoms: 1430
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 177, 1430
          Classifications: {'peptide': 177}
          Link IDs: {'PTRANS': 9, 'TRANS': 167}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 378
          Classifications: {'peptide': 47}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 44}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 631
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 631
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 5, 'TRANS': 75}
    Chain: "K"
      Number of atoms: 617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 617
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "J"
      Number of atoms: 1034
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 1034
          Classifications: {'peptide': 129}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 125}
    Chain: "M"
      Number of atoms: 432
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 432
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "L"
      Number of atoms: 1707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1707
          Classifications: {'peptide': 220}
          Link IDs: {'PTRANS': 12, 'TRANS': 207}
    Chain: "O"
      Number of atoms: 1715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1715
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 5, 'TRANS': 205}
    Chain: "N"
      Number of atoms: 1633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1633
          Classifications: {'peptide': 207}
          Link IDs: {'PTRANS': 12, 'TRANS': 194}
    Chain: "Q"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 792
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 6, 'TRANS': 92}
    Chain: "P"
      Number of atoms: 982
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 982
          Classifications: {'peptide': 131}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 125}
    Chain: "S"
      Number of atoms: 1862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1862
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 10, 'TRANS': 219}
    Chain: "R"
      Number of atoms: 1627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1627
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 6, 'TRANS': 191}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "T"
      Number of atoms: 1015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 1015
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 4, 'TRANS': 120}
    Chain: "q"
      Number of atoms: 714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 714
          Classifications: {'peptide': 88}
          Link IDs: {'TRANS': 87}
    Chain: "p"
      Number of atoms: 691
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 691
          Classifications: {'peptide': 85}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 83}
    Chain: "I"
      Number of atoms: 1208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 150, 1208
          Classifications: {'peptide': 150}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 141}
    Chain: "z"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 795
          Classifications: {'peptide': 160}
          Incomplete info: {'truncation_to_alanine': 148}
          Link IDs: {'PTRANS': 2, 'TRANS': 157}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 525
          Unresolved non-hydrogen angles: 642
          Unresolved non-hydrogen dihedrals: 432
          Unresolved non-hydrogen chiralities: 39
          Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 3, 'GLU:plan': 23, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 258
    Chain: "y"
      Number of atoms: 1145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 1145
          Classifications: {'peptide': 162}
          Incomplete info: {'truncation_to_alanine': 53}
          Link IDs: {'PTRANS': 2, 'TRANS': 159}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 207
          Unresolved non-hydrogen angles: 246
          Unresolved non-hydrogen dihedrals: 178
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASP:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 110
    Chain: "9"
      Number of atoms: 230
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 230
          Classifications: {'peptide': 24}
          Link IDs: {'TRANS': 23}
    Chain: "A"
      Number of atoms: 26040
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1220, 26040
          Classifications: {'DNA': 2, 'RNA': 1218}
          Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 107, 'rna2p_pyr': 83, 'rna3p': 17, 'rna3p_pur': 533, 'rna3p_pyr': 469}
          Link IDs: {'rna2p': 190, 'rna3p': 1029}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'  U:plan': 1, '  C:plan': 2, '  C:plan2': 2}
          Unresolved non-hydrogen planarities: 31
    Chain: "7"
      Number of atoms: 336
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 336
          Classifications: {'RNA': 28}
          Modifications used: {'rna3p_pur': 28}
          Link IDs: {'rna3p': 27}
          Unresolved non-hydrogen bonds: 336
          Unresolved non-hydrogen angles: 532
          Unresolved non-hydrogen dihedrals: 336
          Unresolved non-hydrogen chiralities: 28
          Planarities with less than four sites: {'  A%rna3p_pur:plan2': 28, '  A%rna3p_pur:plan': 28}
          Unresolved non-hydrogen planarities: 336
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "Q"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "S"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 58
          Unusual residues: {' MG': 58}
          Classifications: {'undetermined': 58}
          Link IDs: {None: 57}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  15541  SG  CYS Q  26     108.336  65.466  62.768  1.00 55.68           S
  ATOM  15943  SG  CYS Q  77     107.712  65.426  59.309  1.00 53.89           S

  Residues with excluded nonbonded symmetry interactions: 18
    residue:
      pdb=" P     A 7  10 " occ=0.00
      ... (10 atoms not shown)
      pdb=" C1'   A 7  10 " occ=0.00
    residue:
      pdb=" P     A 7  11 " occ=0.00
      ... (10 atoms not shown)
      pdb=" C1'   A 7  11 " occ=0.00
    residue:
      pdb=" P     A 7  12 " occ=0.00
      ... (10 atoms not shown)
      pdb=" C1'   A 7  12 " occ=0.00
    residue:
      pdb=" P     A 7  13 " occ=0.00
      ... (10 atoms not shown)
      pdb=" C1'   A 7  13 " occ=0.00
    residue:
      pdb=" P     A 7  14 " occ=0.00
      ... (10 atoms not shown)
      pdb=" C1'   A 7  14 " occ=0.00
    residue:
      pdb=" P     A 7  15 " occ=0.00
      ... (10 atoms not shown)
      pdb=" C1'   A 7  15 " occ=0.00
    residue:
      pdb=" P     A 7  16 " occ=0.00
      ... (10 atoms not shown)
      pdb=" C1'   A 7  16 " occ=0.00
    residue:
      pdb=" P     A 7  17 " occ=0.00
      ... (10 atoms not shown)
      pdb=" C1'   A 7  17 " occ=0.00
    residue:
      pdb=" P     A 7  18 " occ=0.00
      ... (10 atoms not shown)
      pdb=" C1'   A 7  18 " occ=0.00
    residue:
      pdb=" P     A 7  19 " occ=0.00
      ... (10 atoms not shown)
      pdb=" C1'   A 7  19 " occ=0.00
    residue:
      pdb=" P     A 7  20 " occ=0.00
      ... (10 atoms not shown)
      pdb=" C1'   A 7  20 " occ=0.00
    residue:
      pdb=" P     A 7  21 " occ=0.00
      ... (10 atoms not shown)
      pdb=" C1'   A 7  21 " occ=0.00
    ... (remaining 6 not shown)
  Time building chain proxies: 27.69, per 1000 atoms: 0.52
  Number of scatterers: 52840
  At special positions: 0
  Unit cell: (162.174, 207.282, 202.986, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S     113     16.00
     P    1247     15.00
     Mg     60     11.99
     O   13287      8.00
     N    9689      7.00
     C   28443      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: 26.67
  Conformation dependent library (CDL) restraints added in 5.7 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN Q 201 "
        pdb="ZN    ZN Q 201 " - pdb=" SG  CYS Q  26 "
        pdb="ZN    ZN Q 201 " - pdb=" SG  CYS Q  77 "


  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  6286

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      104 helices and 32 sheets defined
      31.0% alpha, 14.7% beta
      309 base pairs and 627 stacking pairs defined.
    Time for finding SS restraints: 27.69
  Creating SS restraints...
    Processing helix  chain 'C' and resid 11 through 13
      No H-bonds generated for 'chain 'C' and resid 11 through 13'
    Processing helix  chain 'C' and resid 16 through 18
      No H-bonds generated for 'chain 'C' and resid 16 through 18'
    Processing helix  chain 'C' and resid 44 through 49
    Processing helix  chain 'C' and resid 60 through 67
      removed outlier: 4.207A  pdb=" N   GLN C  67 " --> pdb=" O   LYS C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 224
      No H-bonds generated for 'chain 'C' and resid 222 through 224'
    Processing helix  chain 'C' and resid 248 through 255
    Processing helix  chain 'E' and resid 10 through 20
    Processing helix  chain 'E' and resid 25 through 31
    Processing helix  chain 'E' and resid 90 through 93
    Processing helix  chain 'E' and resid 130 through 134
    Processing helix  chain 'D' and resid 22 through 35
    Processing helix  chain 'D' and resid 41 through 62
      removed outlier: 4.117A  pdb=" N   VAL D  46 " --> pdb=" O   GLU D  42 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 68 through 84
    Processing helix  chain 'D' and resid 94 through 99
      removed outlier: 3.989A  pdb=" N   LEU D  98 " --> pdb=" O   LEU D  94 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   GLY D  99 " --> pdb=" O   ASP D  95 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 94 through 99'
    Processing helix  chain 'D' and resid 110 through 115
    Processing helix  chain 'D' and resid 123 through 131
      removed outlier: 3.720A  pdb=" N   ARG D 127 " --> pdb=" O   ILE D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 154 through 156
      No H-bonds generated for 'chain 'D' and resid 154 through 156'
    Processing helix  chain 'D' and resid 172 through 175
      No H-bonds generated for 'chain 'D' and resid 172 through 175'
    Processing helix  chain 'G' and resid 18 through 32
    Processing helix  chain 'G' and resid 66 through 74
      removed outlier: 5.085A  pdb=" N   LYS G  70 " --> pdb=" O   PRO G  67 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 76 through 86
      removed outlier: 4.216A  pdb=" N   LYS G  85 " --> pdb=" O   ARG G  81 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LYS G  86 " --> pdb=" O   GLU G  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 118 through 120
      No H-bonds generated for 'chain 'G' and resid 118 through 120'
    Processing helix  chain 'G' and resid 122 through 133
      removed outlier: 3.701A  pdb=" N   LEU G 130 " --> pdb=" O   HIS G 126 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 163 through 166
      No H-bonds generated for 'chain 'G' and resid 163 through 166'
    Processing helix  chain 'G' and resid 170 through 181
    Processing helix  chain 'F' and resid 12 through 15
      No H-bonds generated for 'chain 'F' and resid 12 through 15'
    Processing helix  chain 'F' and resid 31 through 42
    Processing helix  chain 'H' and resid 12 through 17
      removed outlier: 3.807A  pdb=" N   ARG H  17 " --> pdb=" O   GLU H  13 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 57 through 62
    Processing helix  chain 'K' and resid 66 through 75
    Processing helix  chain 'J' and resid 6 through 19
    Processing helix  chain 'J' and resid 32 through 44
      removed outlier: 3.901A  pdb=" N   HIS J  44 " --> pdb=" O   VAL J  40 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 86 through 93
    Processing helix  chain 'J' and resid 115 through 118
      No H-bonds generated for 'chain 'J' and resid 115 through 118'
    Processing helix  chain 'M' and resid 100 through 109
    Processing helix  chain 'L' and resid 65 through 71
    Processing helix  chain 'L' and resid 79 through 82
      No H-bonds generated for 'chain 'L' and resid 79 through 82'
    Processing helix  chain 'L' and resid 92 through 97
      removed outlier: 3.564A  pdb=" N   PHE L  97 " --> pdb=" O   ILE L  93 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 147 through 159
    Processing helix  chain 'L' and resid 208 through 216
      removed outlier: 3.671A  pdb=" N   LYS L 212 " --> pdb=" O   PRO L 208 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU L 213 " --> pdb=" O   VAL L 209 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 233 through 248
      removed outlier: 3.893A  pdb=" N   THR L 247 " --> pdb=" O   ALA L 243 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   TYR L 248 " --> pdb=" O   ILE L 244 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 265 through 268
      No H-bonds generated for 'chain 'L' and resid 265 through 268'
    Processing helix  chain 'L' and resid 270 through 273
      No H-bonds generated for 'chain 'L' and resid 270 through 273'
    Processing helix  chain 'O' and resid 24 through 26
      No H-bonds generated for 'chain 'O' and resid 24 through 26'
    Processing helix  chain 'O' and resid 59 through 62
      No H-bonds generated for 'chain 'O' and resid 59 through 62'
    Processing helix  chain 'O' and resid 71 through 75
    Processing helix  chain 'O' and resid 107 through 112
    Processing helix  chain 'O' and resid 158 through 177
    Processing helix  chain 'O' and resid 181 through 189
    Processing helix  chain 'O' and resid 192 through 202
      removed outlier: 3.873A  pdb=" N   GLN O 202 " --> pdb=" O   GLU O 198 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 226 through 231
    Processing helix  chain 'N' and resid 12 through 21
    Processing helix  chain 'N' and resid 34 through 37
    Processing helix  chain 'N' and resid 51 through 67
    Processing helix  chain 'N' and resid 71 through 73
      No H-bonds generated for 'chain 'N' and resid 71 through 73'
    Processing helix  chain 'N' and resid 82 through 93
      removed outlier: 4.324A  pdb=" N   ARG N  85 " --> pdb=" O   THR N  82 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   ALA N  86 " --> pdb=" O   GLY N  83 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   VAL N  87 " --> pdb=" O   GLN N  84 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU N  88 " --> pdb=" O   ARG N  85 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   PHE N  90 " --> pdb=" O   VAL N  87 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA N  91 " --> pdb=" O   LEU N  88 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 131 through 139
      removed outlier: 3.839A  pdb=" N   TYR N 139 " --> pdb=" O   THR N 135 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 168 through 186
    Processing helix  chain 'N' and resid 199 through 202
    Processing helix  chain 'Q' and resid 47 through 56
      removed outlier: 5.746A  pdb=" N   ARG Q  51 " --> pdb=" O   ALA Q  48 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ILE Q  53 " --> pdb=" O   VAL Q  50 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLU Q  55 " --> pdb=" O   ASP Q  52 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 75 through 80
    Processing helix  chain 'Q' and resid 91 through 93
      No H-bonds generated for 'chain 'Q' and resid 91 through 93'
    Processing helix  chain 'P' and resid 66 through 69
      removed outlier: 3.956A  pdb=" N   SER P  69 " --> pdb=" O   ARG P  66 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 66 through 69'
    Processing helix  chain 'P' and resid 71 through 88
    Processing helix  chain 'P' and resid 112 through 121
    Processing helix  chain 'S' and resid 122 through 125
      No H-bonds generated for 'chain 'S' and resid 122 through 125'
    Processing helix  chain 'S' and resid 138 through 144
    Processing helix  chain 'S' and resid 154 through 156
      No H-bonds generated for 'chain 'S' and resid 154 through 156'
    Processing helix  chain 'S' and resid 182 through 228
    Processing helix  chain 'R' and resid 89 through 93
    Processing helix  chain 'R' and resid 107 through 116
    Processing helix  chain 'R' and resid 143 through 154
      removed outlier: 3.519A  pdb=" N   LYS R 147 " --> pdb=" O   LYS R 143 " (cutoff:3.500A)
WARNING: missing atoms!
      removed outlier: 3.787A  pdb=" N   ARG R 152 " --> pdb=" O   LYS R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 160 through 168
      removed outlier: 3.574A  pdb=" N   GLN R 168 " --> pdb=" O   GLU R 164 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 193 through 205
    Processing helix  chain 'T' and resid 37 through 47
    Processing helix  chain 'T' and resid 52 through 54
      No H-bonds generated for 'chain 'T' and resid 52 through 54'
    Processing helix  chain 'T' and resid 79 through 85
    Processing helix  chain 'T' and resid 88 through 93
    Processing helix  chain 'T' and resid 104 through 114
    Processing helix  chain 'T' and resid 120 through 126
      removed outlier: 3.980A  pdb=" N   VAL T 125 " --> pdb=" O   LYS T 122 " (cutoff:3.500A)
    Processing helix  chain 'q' and resid 97 through 104
      removed outlier: 3.597A  pdb=" N   SER q 102 " --> pdb=" O   ASP q  98 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 56 through 67
      removed outlier: 3.536A  pdb=" N   LYS p  61 " --> pdb=" O   LYS p  57 " (cutoff:3.500A)
    Processing helix  chain 'p' and resid 90 through 97
      removed outlier: 3.971A  pdb=" N   CYS p  94 " --> pdb=" O   ARG p  90 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   GLN p  95 " --> pdb=" O   LYS p  91 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 30 through 42
    Processing helix  chain 'I' and resid 47 through 57
    Processing helix  chain 'I' and resid 63 through 67
    Processing helix  chain 'I' and resid 71 through 78
      removed outlier: 3.931A  pdb=" N   LYS I  78 " --> pdb=" O   ILE I  74 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 86 through 104
      removed outlier: 3.913A  pdb=" N   ARG I 104 " --> pdb=" O   LYS I 100 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 109 through 131
    Processing helix  chain 'z' and resid 55 through 64
    Processing helix  chain 'z' and resid 76 through 95
      removed outlier: 4.282A  pdb=" N   GLN z  87 " --> pdb=" O   GLU z  83 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   GLN z  88 " --> pdb=" O   LYS z  84 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 115 through 134
      removed outlier: 3.727A  pdb=" N   LYS z 133 " --> pdb=" O   LEU z 129 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 154 through 169
      removed outlier: 3.796A  pdb=" N   GLU z 158 " --> pdb=" O   ASP z 154 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 175 through 190
      removed outlier: 5.255A  pdb=" N   LEU z 180 " --> pdb=" O   TYR z 176 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ILE z 189 " --> pdb=" O   ARG z 185 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   SER z 190 " --> pdb=" O   ASP z 186 " (cutoff:3.500A)
    Processing helix  chain 'z' and resid 195 through 213
    Processing helix  chain 'y' and resid 52 through 73
    Processing helix  chain 'y' and resid 76 through 93
    Processing helix  chain 'y' and resid 96 through 100
      removed outlier: 3.784A  pdb=" N   LYS y  99 " --> pdb=" O   ILE y  96 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLU y 100 " --> pdb=" O   VAL y  97 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'y' and resid 96 through 100'
    Processing helix  chain 'y' and resid 104 through 120
    Processing helix  chain 'y' and resid 124 through 127
      No H-bonds generated for 'chain 'y' and resid 124 through 127'
    Processing helix  chain 'y' and resid 134 through 159
      removed outlier: 4.035A  pdb=" N   ARG y 150 " --> pdb=" O   ARG y 146 " (cutoff:3.500A)
      removed outlier: 5.550A  pdb=" N   ASP y 151 " --> pdb=" O   LYS y 147 " (cutoff:3.500A)
      removed outlier: 5.420A  pdb=" N   PHE y 152 " --> pdb=" O   TYR y 148 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLU y 153 " --> pdb=" O   ASN y 149 " (cutoff:3.500A)
      removed outlier: 5.699A  pdb=" N   SER y 154 " --> pdb=" O   ARG y 150 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   HIS y 155 " --> pdb=" O   ASP y 151 " (cutoff:3.500A)
    Processing helix  chain 'y' and resid 265 through 279
    Processing helix  chain 'y' and resid 288 through 295
      removed outlier: 4.011A  pdb=" N   GLU y 293 " --> pdb=" O   LEU y 289 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   GLU y 294 " --> pdb=" O   ASP y 290 " (cutoff:3.500A)
    Processing helix  chain '9' and resid 3 through 23
      removed outlier: 3.632A  pdb=" N   ARG 9  18 " --> pdb=" O   LYS 9  14 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   LYS 9  19 " --> pdb=" O   ARG 9  15 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   MET 9  20 " --> pdb=" O   LYS 9  16 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ARG 9  23 " --> pdb=" O   LYS 9  19 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'C' and resid 70 through 72
    Processing sheet with id=  B, first strand: chain 'C' and resid 121 through 125
      removed outlier: 3.854A  pdb=" N   ASP C 171 " --> pdb=" O   GLN C 161 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   ASP C 163 " --> pdb=" O   ILE C 169 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ILE C 169 " --> pdb=" O   ASP C 163 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'C' and resid 146 through 148
    Processing sheet with id=  D, first strand: chain 'C' and resid 225 through 229
      removed outlier: 6.571A  pdb=" N   LEU C 180 " --> pdb=" O   ILE C 228 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   HIS C 209 " --> pdb=" O   THR C 196 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   ARG C 198 " --> pdb=" O   VAL C 207 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL C 207 " --> pdb=" O   ARG C 198 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 101 through 112
      removed outlier: 3.552A  pdb=" N   ARG B 101 " --> pdb=" O   ILE B  96 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   ARG B  89 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 5.627A  pdb=" N   VAL B  77 " --> pdb=" O   ARG B  89 " (cutoff:3.500A)
      removed outlier: 8.194A  pdb=" N   ASP B  91 " --> pdb=" O   GLY B  75 " (cutoff:3.500A)
      removed outlier: 8.379A  pdb=" N   GLY B  75 " --> pdb=" O   ASP B  91 " (cutoff:3.500A)
      removed outlier: 15.435A  pdb=" N   LEU B  93 " --> pdb=" O   LEU B  73 " (cutoff:3.500A)
      removed outlier: 16.390A  pdb=" N   LEU B  73 " --> pdb=" O   LEU B  93 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   GLY B 129 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   VAL B 142 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'E' and resid 80 through 84
      removed outlier: 3.639A  pdb=" N   GLU E  53 " --> pdb=" O   ARG E  71 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   GLN E  73 " --> pdb=" O   VAL E  51 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   VAL E  51 " --> pdb=" O   GLN E  73 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   ALA E 103 " --> pdb=" O   VAL E 122 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   VAL E 122 " --> pdb=" O   ALA E 103 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'D' and resid 135 through 137
    Processing sheet with id=  H, first strand: chain 'G' and resid 47 through 53
      removed outlier: 3.500A  pdb=" N   ALA G  47 " --> pdb=" O   PHE G  63 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'G' and resid 185 through 189
      removed outlier: 8.444A  pdb=" N   ASN G 186 " --> pdb=" O   ARG G 152 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ILE G 154 " --> pdb=" O   ASN G 186 " (cutoff:3.500A)
      removed outlier: 7.558A  pdb=" N   GLU G 188 " --> pdb=" O   ILE G 154 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   VAL G 156 " --> pdb=" O   GLU G 188 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'H' and resid 44 through 47
    Processing sheet with id=  K, first strand: chain 'K' and resid 32 through 37
    Processing sheet with id=  L, first strand: chain 'J' and resid 24 through 27
    Processing sheet with id=  M, first strand: chain 'J' and resid 71 through 74
      removed outlier: 6.931A  pdb=" N   VAL J 103 " --> pdb=" O   LEU J 126 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   PHE J 128 " --> pdb=" O   PHE J 101 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   PHE J 101 " --> pdb=" O   PHE J 128 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'M' and resid 96 through 98
    Processing sheet with id=  O, first strand: chain 'L' and resid 137 through 144
      removed outlier: 3.596A  pdb=" N   LYS L 108 " --> pdb=" O   PHE L 127 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ALA L 129 " --> pdb=" O   VAL L 106 " (cutoff:3.500A)
      removed outlier: 5.358A  pdb=" N   VAL L 106 " --> pdb=" O   ALA L 129 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   GLY L 131 " --> pdb=" O   ASP L 104 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   ASP L 104 " --> pdb=" O   GLY L 131 " (cutoff:3.500A)
    Processing sheet with id=  P, first strand: chain 'L' and resid 184 through 188
    Processing sheet with id=  Q, first strand: chain 'O' and resid 95 through 97
      removed outlier: 8.317A  pdb=" N   CYS O  96 " --> pdb=" O   TRP O  30 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   ASP O  32 " --> pdb=" O   CYS O  96 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   GLY O  45 " --> pdb=" O   VAL O  33 " (cutoff:3.500A)
    Processing sheet with id=  R, first strand: chain 'O' and resid 66 through 70
      removed outlier: 5.440A  pdb=" N   ILE O  87 " --> pdb=" O   PHE O 100 " (cutoff:3.500A)
      removed outlier: 5.226A  pdb=" N   PHE O 100 " --> pdb=" O   ILE O  87 " (cutoff:3.500A)
      removed outlier: 13.784A  pdb=" N   ASN O  99 " --> pdb=" O   LYS O 219 " (cutoff:3.500A)
      removed outlier: 13.270A  pdb=" N   LYS O 219 " --> pdb=" O   ASN O  99 " (cutoff:3.500A)
      removed outlier: 8.353A  pdb=" N   HIS O 101 " --> pdb=" O   MET O 217 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   MET O 217 " --> pdb=" O   HIS O 101 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   LYS O 214 " --> pdb=" O   PHE O 138 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   LEU O 134 " --> pdb=" O   LEU O 218 " (cutoff:3.500A)
    Processing sheet with id=  S, first strand: chain 'N' and resid 97 through 100
      removed outlier: 6.662A  pdb=" N   LEU N 121 " --> pdb=" O   SER N  75 " (cutoff:3.500A)
      removed outlier: 7.688A  pdb=" N   ILE N  77 " --> pdb=" O   LEU N 121 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   VAL N 123 " --> pdb=" O   ILE N  77 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   VAL N 124 " --> pdb=" O   PRO N 143 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ILE N 145 " --> pdb=" O   VAL N 124 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ILE N 159 " --> pdb=" O   ALA N 146 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   CYS N 148 " --> pdb=" O   ILE N 159 " (cutoff:3.500A)
      removed outlier: 5.960A  pdb=" N   ILE N 161 " --> pdb=" O   CYS N 148 " (cutoff:3.500A)
    Processing sheet with id=  T, first strand: chain 'N' and resid 38 through 41
      removed outlier: 6.804A  pdb=" N   ILE N  48 " --> pdb=" O   TYR N  39 " (cutoff:3.500A)
    Processing sheet with id=  U, first strand: chain 'Q' and resid 36 through 43
    Processing sheet with id=  V, first strand: chain 'P' and resid 52 through 57
      removed outlier: 6.883A  pdb=" N   VAL P  44 " --> pdb=" O   ILE P  53 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ARG P  55 " --> pdb=" O   VAL P  42 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   VAL P  42 " --> pdb=" O   ARG P  55 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   THR P  57 " --> pdb=" O   THR P  40 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   THR P  40 " --> pdb=" O   THR P  57 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   HIS P  94 " --> pdb=" O   CYS P  31 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   ILE P  33 " --> pdb=" O   HIS P  94 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LYS P  96 " --> pdb=" O   ILE P  33 " (cutoff:3.500A)
      removed outlier: 7.843A  pdb=" N   ALA P  35 " --> pdb=" O   LYS P  96 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ARG P  98 " --> pdb=" O   ALA P  35 " (cutoff:3.500A)
    Processing sheet with id=  W, first strand: chain 'S' and resid 12 through 17
    Processing sheet with id=  X, first strand: chain 'S' and resid 35 through 37
      removed outlier: 5.906A  pdb=" N   ARG S  51 " --> pdb=" O   ILE S 113 " (cutoff:3.500A)
      removed outlier: 5.292A  pdb=" N   ILE S 113 " --> pdb=" O   ARG S  51 " (cutoff:3.500A)
    Processing sheet with id=  Y, first strand: chain 'S' and resid 73 through 77
    Processing sheet with id=  Z, first strand: chain 'R' and resid 72 through 77
      removed outlier: 3.853A  pdb=" N   ILE R 175 " --> pdb=" O   CYS R 100 " (cutoff:3.500A)
      removed outlier: 4.555A  pdb=" N   CYS R 100 " --> pdb=" O   ILE R 175 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   TYR R  83 " --> pdb=" O   ILE R 101 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   LEU R 103 " --> pdb=" O   VAL R  81 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   VAL R  81 " --> pdb=" O   LEU R 103 " (cutoff:3.500A)
    Processing sheet with id= AA, first strand: chain 'R' and resid 42 through 45
      removed outlier: 6.669A  pdb=" N   HIS R  44 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
      removed outlier: 5.257A  pdb=" N   ALA R  57 " --> pdb=" O   HIS R  44 " (cutoff:3.500A)
    Processing sheet with id= AB, first strand: chain 'T' and resid 5 through 10
    Processing sheet with id= AC, first strand: chain 'T' and resid 13 through 15
    Processing sheet with id= AD, first strand: chain 'q' and resid 47 through 50
    Processing sheet with id= AE, first strand: chain 'q' and resid 77 through 80
      removed outlier: 5.858A  pdb=" N   GLY q  80 " --> pdb=" O   VAL q  91 " (cutoff:3.500A)
      removed outlier: 5.211A  pdb=" N   VAL q  91 " --> pdb=" O   GLY q  80 " (cutoff:3.500A)
    Processing sheet with id= AF, first strand: chain 'p' and resid 33 through 37

    872 hydrogen bonds defined for protein.
    2475 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      780 hydrogen bonds
      1260 hydrogen bond angles
      0 basepair planarities
      309 basepair parallelities
      627 stacking parallelities
  Total time for adding SS restraints: 32.29

  Time building geometry restraints manager: 28.38 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 9491
        1.33 -     1.45: 20098
        1.45 -     1.58: 24049
        1.58 -     1.70: 2486
        1.70 -     1.82: 173
  Bond restraints: 56297
  Sorted by residual:
  bond pdb=" C4  5MU A 814 "
       pdb=" C5  5MU A 814 "
    ideal  model  delta    sigma   weight residual
    1.802  1.442  0.360 2.00e-02 2.50e+03 3.23e+02
  bond pdb=" N1  5MU A 814 "
       pdb=" C6  5MU A 814 "
    ideal  model  delta    sigma   weight residual
    1.635  1.386  0.249 2.00e-02 2.50e+03 1.54e+02
  bond pdb=" C2' A2M A 668 "
       pdb=" C1' A2M A 668 "
    ideal  model  delta    sigma   weight residual
    1.305  1.531 -0.226 2.00e-02 2.50e+03 1.28e+02
  bond pdb=" C2' A2M A 484 "
       pdb=" C1' A2M A 484 "
    ideal  model  delta    sigma   weight residual
    1.305  1.530 -0.225 2.00e-02 2.50e+03 1.27e+02
  bond pdb=" C2' A2M A1031 "
       pdb=" C1' A2M A1031 "
    ideal  model  delta    sigma   weight residual
    1.305  1.529 -0.224 2.00e-02 2.50e+03 1.25e+02
  ... (remaining 56292 not shown)

  Histogram of bond angle deviations from ideal:
       97.42 -   105.19: 5933
      105.19 -   112.97: 32637
      112.97 -   120.75: 25369
      120.75 -   128.52: 16378
      128.52 -   136.30: 1573
  Bond angle restraints: 81890
  Sorted by residual:
  angle pdb=" C1' A2M A  27 "
        pdb=" N9  A2M A  27 "
        pdb=" C8  A2M A  27 "
      ideal   model   delta    sigma   weight residual
      88.50  126.97  -38.47 3.00e+00 1.11e-01 1.64e+02
  angle pdb=" C1' A2M A 668 "
        pdb=" N9  A2M A 668 "
        pdb=" C8  A2M A 668 "
      ideal   model   delta    sigma   weight residual
      88.50  126.96  -38.46 3.00e+00 1.11e-01 1.64e+02
  angle pdb=" C1' A2M A 159 "
        pdb=" N9  A2M A 159 "
        pdb=" C8  A2M A 159 "
      ideal   model   delta    sigma   weight residual
      88.50  126.58  -38.08 3.00e+00 1.11e-01 1.61e+02
  angle pdb=" C1' A2M A 166 "
        pdb=" N9  A2M A 166 "
        pdb=" C8  A2M A 166 "
      ideal   model   delta    sigma   weight residual
      88.50  126.58  -38.08 3.00e+00 1.11e-01 1.61e+02
  angle pdb=" C1' A2M A 484 "
        pdb=" N9  A2M A 484 "
        pdb=" C8  A2M A 484 "
      ideal   model   delta    sigma   weight residual
      88.50  126.50  -38.00 3.00e+00 1.11e-01 1.60e+02
  ... (remaining 81885 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.89: 32298
       35.89 -    71.79: 3176
       71.79 -   107.68: 394
      107.68 -   143.57: 14
      143.57 -   179.47: 11
  Dihedral angle restraints: 35893
    sinusoidal: 26180
      harmonic: 9713
  Sorted by residual:
  dihedral pdb=" C4'   A 7   4 "
           pdb=" C3'   A 7   4 "
           pdb=" C2'   A 7   4 "
           pdb=" C1'   A 7   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.00  -28.74   64.74     1      8.00e+00 1.56e-02 8.60e+01
  dihedral pdb=" O4'   C A1139 "
           pdb=" C1'   C A1139 "
           pdb=" N1    C A1139 "
           pdb=" C2    C A1139 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   19.47 -179.47     1      1.50e+01 4.44e-03 8.53e+01
  dihedral pdb=" O4'   C A1752 "
           pdb=" C1'   C A1752 "
           pdb=" N1    C A1752 "
           pdb=" C2    C A1752 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   16.08 -176.08     1      1.50e+01 4.44e-03 8.52e+01
  ... (remaining 35890 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 9317
       0.086 -    0.172: 768
       0.172 -    0.257: 55
       0.257 -    0.343: 11
       0.343 -    0.429: 8
  Chirality restraints: 10159
  Sorted by residual:
  chirality pdb=" C2' A2M A 166 "
            pdb=" C3' A2M A 166 "
            pdb=" O2' A2M A 166 "
            pdb=" C1' A2M A 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.39   -2.82    0.43 2.00e-01 2.50e+01 4.60e+00
  chirality pdb=" C2' A2M A1031 "
            pdb=" C3' A2M A1031 "
            pdb=" O2' A2M A1031 "
            pdb=" C1' A2M A1031 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.39   -2.79    0.39 2.00e-01 2.50e+01 3.90e+00
  chirality pdb=" C1'   C A 537 "
            pdb=" O4'   C A 537 "
            pdb=" C2'   C A 537 "
            pdb=" N1    C A 537 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.10    0.37 2.00e-01 2.50e+01 3.43e+00
  ... (remaining 10156 not shown)

  Planarity restraints: 5822
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C5' OMG A 509 "   -0.065 2.00e-02 2.50e+03   6.21e-01 8.67e+03
        pdb=" C4' OMG A 509 "   -0.436 2.00e-02 2.50e+03
        pdb=" O4' OMG A 509 "   -0.689 2.00e-02 2.50e+03
        pdb=" C3' OMG A 509 "    0.609 2.00e-02 2.50e+03
        pdb=" O3' OMG A 509 "    0.663 2.00e-02 2.50e+03
        pdb=" C2' OMG A 509 "    0.177 2.00e-02 2.50e+03
        pdb=" O2' OMG A 509 "   -1.011 2.00e-02 2.50e+03
        pdb=" C1' OMG A 509 "   -0.196 2.00e-02 2.50e+03
        pdb=" N9  OMG A 509 "    0.948 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C5' OMG A 683 "   -0.108 2.00e-02 2.50e+03   6.16e-01 8.53e+03
        pdb=" C4' OMG A 683 "   -0.421 2.00e-02 2.50e+03
        pdb=" O4' OMG A 683 "   -0.595 2.00e-02 2.50e+03
        pdb=" C3' OMG A 683 "    0.619 2.00e-02 2.50e+03
        pdb=" O3' OMG A 683 "    0.696 2.00e-02 2.50e+03
        pdb=" C2' OMG A 683 "    0.150 2.00e-02 2.50e+03
        pdb=" O2' OMG A 683 "   -1.046 2.00e-02 2.50e+03
        pdb=" C1' OMG A 683 "   -0.212 2.00e-02 2.50e+03
        pdb=" N9  OMG A 683 "    0.917 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C5' 5MU A 814 "    0.075 2.00e-02 2.50e+03   6.00e-01 8.10e+03
        pdb=" C4' 5MU A 814 "    0.431 2.00e-02 2.50e+03
        pdb=" O4' 5MU A 814 "    0.598 2.00e-02 2.50e+03
        pdb=" C3' 5MU A 814 "   -0.604 2.00e-02 2.50e+03
        pdb=" O3' 5MU A 814 "   -0.669 2.00e-02 2.50e+03
        pdb=" C2' 5MU A 814 "   -0.171 2.00e-02 2.50e+03
        pdb=" O2' 5MU A 814 "    1.010 2.00e-02 2.50e+03
        pdb=" C1' 5MU A 814 "    0.216 2.00e-02 2.50e+03
        pdb=" N1  5MU A 814 "   -0.886 2.00e-02 2.50e+03
  ... (remaining 5819 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 2014
        2.66 -     3.22: 41845
        3.22 -     3.78: 96081
        3.78 -     4.34: 129285
        4.34 -     4.90: 185730
  Nonbonded interactions: 454955
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN S 177 "
            pdb="MG    MG S 301 "
     model   vdw
     2.097 2.170
  nonbonded pdb=" OP2   A A1082 "
            pdb="MG    MG A1941 "
     model   vdw
     2.103 2.170
  nonbonded pdb=" OP2   C A 409 "
            pdb="MG    MG A1949 "
     model   vdw
     2.106 2.170
  nonbonded pdb=" OP2   A A 449 "
            pdb="MG    MG A1904 "
     model   vdw
     2.111 2.170
  nonbonded pdb=" OP1   G A 684 "
            pdb="MG    MG A1956 "
     model   vdw
     2.111 2.170
  ... (remaining 454950 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=1.00
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:             10.310
  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:             0.060
  Extract box with map and model:          28.150
  Check model and map are aligned:         0.820
  Set scattering table:                    0.490
  Process input model:                     176.730
  Find NCS groups from input model:        1.500
  Set up NCS constraints:                  0.230
  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:3.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  221.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
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      :  0.008   0.360  56297  Z= 0.478
  Angle     :  1.059  38.472  81890  Z= 0.524
  Chirality :  0.049   0.429  10159
  Planarity :  0.021   0.621   5822
  Dihedral  : 22.636 179.466  29607
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 16.42 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.06 (0.13), residues: 3310
  helix: -0.57 (0.14), residues: 1083
  sheet: -1.58 (0.20), residues: 588
  loop : -1.80 (0.13), residues: 1639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP I  25 
 HIS   0.014   0.002   HIS R  22 
 PHE   0.038   0.002   PHE N 103 
 TYR   0.031   0.002   TYR p  54 
 ARG   0.017   0.001   ARG G  57 

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

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

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  779 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 83
    poor density    : 696
  time to evaluate  : 4.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS R 144 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 MET cc_start: 0.8798 (mtm) cc_final: 0.8572 (mtm)
REVERT: C   54 TYR cc_start: 0.9182 (m-80) cc_final: 0.8900 (m-80)
REVERT: C   62 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8587 (ttmm)
REVERT: C  158 ASP cc_start: 0.8335 (m-30) cc_final: 0.7920 (m-30)
REVERT: B  130 GLU cc_start: 0.8255 (tt0) cc_final: 0.8025 (tt0)
REVERT: E   95 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8051 (mm-30)
REVERT: D  107 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7442 (mm-30)
REVERT: D  154 GLN cc_start: 0.8871 (tt0) cc_final: 0.8231 (tt0)
REVERT: D  155 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7846 (tptp)
REVERT: G   81 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7913 (ttp80)
REVERT: G  138 GLU cc_start: 0.7637 (tt0) cc_final: 0.7421 (tt0)
REVERT: G  162 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7550 (mm-40)
REVERT: G  186 ASN cc_start: 0.8319 (m-40) cc_final: 0.7903 (m110)
REVERT: H   80 ARG cc_start: 0.8567 (ptt90) cc_final: 0.7267 (ptp90)
REVERT: J   68 ARG cc_start: 0.9187 (mtt180) cc_final: 0.8741 (mtt180)
REVERT: M   82 ASP cc_start: 0.8260 (t70) cc_final: 0.7884 (t0)
REVERT: M  118 GLN cc_start: 0.8527 (tp-100) cc_final: 0.8042 (tp-100)
REVERT: M  127 ASN cc_start: 0.8839 (p0) cc_final: 0.8313 (p0)
REVERT: L   57 ASP cc_start: 0.5234 (OUTLIER) cc_final: 0.4789 (t70)
REVERT: L   92 GLU cc_start: 0.8430 (mp0) cc_final: 0.8061 (mp0)
REVERT: O  211 PHE cc_start: 0.8765 (m-80) cc_final: 0.8560 (m-80)
REVERT: N   17 LYS cc_start: 0.8689 (mttm) cc_final: 0.8459 (mttp)
REVERT: N  166 LYS cc_start: 0.9128 (ttpp) cc_final: 0.8787 (ttmm)
REVERT: N  198 MET cc_start: 0.7432 (mtp) cc_final: 0.7078 (ttm)
REVERT: Q   42 ARG cc_start: 0.7776 (ptp90) cc_final: 0.7528 (ttp-170)
REVERT: Q   64 LEU cc_start: 0.8995 (tp) cc_final: 0.8776 (tp)
REVERT: Q   85 ARG cc_start: 0.5272 (tpt170) cc_final: 0.3479 (mtt-85)
REVERT: q   40 LYS cc_start: 0.5445 (OUTLIER) cc_final: 0.4620 (tppt)
REVERT: q   47 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.6119 (tp)
REVERT: q   50 MET cc_start: 0.1703 (ttm) cc_final: 0.1274 (tpp)
REVERT: q   99 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.6203 (pm20)
REVERT: p   84 GLN cc_start: 0.8338 (tt0) cc_final: 0.8051 (tt0)
REVERT: y  116 TYR cc_start: 0.4438 (OUTLIER) cc_final: 0.4134 (t80)
REVERT: 9   11 ARG cc_start: 0.8390 (mtt180) cc_final: 0.8150 (mtt90)
  outliers start: 83
  outliers final: 50
  residues processed: 762
  average time/residue: 0.7054
  time to fit residues: 855.9226
Evaluate side-chains
  637 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 581
  time to evaluate  : 3.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 VAL
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain E residue   61 GLN
Chi-restraints excluded: chain E residue  105 PHE
Chi-restraints excluded: chain E residue  125 VAL
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue  155 LYS
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   33 ASN
Chi-restraints excluded: chain G residue  119 SER
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   81 LYS
Chi-restraints excluded: chain J residue   30 CYS
Chi-restraints excluded: chain M residue   95 ILE
Chi-restraints excluded: chain M residue   99 ASP
Chi-restraints excluded: chain M residue  102 THR
Chi-restraints excluded: chain L residue   57 ASP
Chi-restraints excluded: chain L residue  225 SER
Chi-restraints excluded: chain L residue  259 THR
Chi-restraints excluded: chain L residue  262 THR
Chi-restraints excluded: chain O residue   55 THR
Chi-restraints excluded: chain O residue  129 THR
Chi-restraints excluded: chain N residue   15 VAL
Chi-restraints excluded: chain N residue   44 ASP
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain N residue  171 VAL
Chi-restraints excluded: chain N residue  188 THR
Chi-restraints excluded: chain Q residue   88 SER
Chi-restraints excluded: chain P residue   65 ASP
Chi-restraints excluded: chain P residue   81 VAL
Chi-restraints excluded: chain P residue  130 GLU
Chi-restraints excluded: chain S residue  158 VAL
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  145 ILE
Chi-restraints excluded: chain T residue   27 VAL
Chi-restraints excluded: chain T residue   80 ASP
Chi-restraints excluded: chain T residue  100 LYS
Chi-restraints excluded: chain q residue   39 ILE
Chi-restraints excluded: chain q residue   40 LYS
Chi-restraints excluded: chain q residue   47 LEU
Chi-restraints excluded: chain q residue   51 CYS
Chi-restraints excluded: chain q residue   55 VAL
Chi-restraints excluded: chain q residue   73 THR
Chi-restraints excluded: chain q residue   86 ASP
Chi-restraints excluded: chain q residue   99 GLU
Chi-restraints excluded: chain p residue   50 ILE
Chi-restraints excluded: chain p residue  108 LEU
Chi-restraints excluded: chain I residue   24 THR
Chi-restraints excluded: chain I residue   29 THR
Chi-restraints excluded: chain I residue   87 ASP
Chi-restraints excluded: chain y residue  102 VAL
Chi-restraints excluded: chain y residue  116 TYR
Chi-restraints excluded: chain y residue  140 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 452
   random chunks:
   chunk 381 optimal weight:    2.9990
   chunk 342 optimal weight:    0.6980
   chunk 190 optimal weight:    2.9990
   chunk 117 optimal weight:    2.9990
   chunk 231 optimal weight:    0.6980
   chunk 183 optimal weight:    0.5980
   chunk 354 optimal weight:    8.9990
   chunk 137 optimal weight:    0.9980
   chunk 215 optimal weight:    0.9980
   chunk 263 optimal weight:    8.9990
   chunk 410 optimal weight:    5.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C 157 ASN
B   5 GLN
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 121 GLN
E  20 GLN
E  46 HIS
E 110 HIS
D 134 HIS
D 140 GLN
G  68 GLN
G 114 GLN
G 157 HIS
G 168 HIS
F  15 GLN
H  26 GLN
H  49 HIS
** J  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  64 ASN
** J  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  93 GLN
M 116 ASN
M 118 GLN
L 235 ASN
O  40 ASN
O 232 HIS
N  29 ASN
Q  17 HIS
P  32 HIS
S 110 ASN
S 146 ASN
S 197 GLN
R 168 GLN
q  87 ASN
p  32 HIS
p  76 HIS
p  89 GLN
I  90 HIS
y 118 ASN

Total number of N/Q/H flips: 35

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.1050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  56297  Z= 0.185
  Angle     :  0.682  17.549  81890  Z= 0.356
  Chirality :  0.037   0.350  10159
  Planarity :  0.006   0.132   5822
  Dihedral  : 23.234 179.857  23070
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 19.54 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.07 (0.14), residues: 3310
  helix:  0.45 (0.15), residues: 1084
  sheet: -1.23 (0.21), residues: 568
  loop : -1.28 (0.14), residues: 1658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R   8 
 HIS   0.008   0.001   HIS J  56 
 PHE   0.015   0.001   PHE O  81 
 TYR   0.016   0.001   TYR C 103 
 ARG   0.006   0.000   ARG y  50 

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

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

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  711 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 84
    poor density    : 627
  time to evaluate  : 3.709 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS R 144 " (corrupted residue). Skipping it.
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 MET cc_start: 0.8706 (mtm) cc_final: 0.8504 (mtm)
REVERT: C   54 TYR cc_start: 0.9195 (m-10) cc_final: 0.8915 (m-80)
REVERT: B  130 GLU cc_start: 0.8251 (tt0) cc_final: 0.8045 (tt0)
REVERT: E   95 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7944 (mm-30)
REVERT: D  107 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7467 (mm-30)
REVERT: D  154 GLN cc_start: 0.8902 (tt0) cc_final: 0.8292 (tt0)
REVERT: G  162 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7508 (mm-40)
REVERT: G  186 ASN cc_start: 0.8282 (m-40) cc_final: 0.7799 (m110)
REVERT: H   80 ARG cc_start: 0.8597 (ptt90) cc_final: 0.7226 (ptp90)
REVERT: J   68 ARG cc_start: 0.9189 (mtt180) cc_final: 0.8748 (mtt180)
REVERT: J  112 ASP cc_start: 0.8268 (p0) cc_final: 0.7997 (p0)
REVERT: J  119 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.9054 (mttp)
REVERT: M   82 ASP cc_start: 0.8180 (t70) cc_final: 0.7740 (t0)
REVERT: M  118 GLN cc_start: 0.8476 (tp40) cc_final: 0.8063 (tp-100)
REVERT: M  127 ASN cc_start: 0.8849 (p0) cc_final: 0.8306 (p0)
REVERT: L   92 GLU cc_start: 0.8490 (mp0) cc_final: 0.7960 (mp0)
REVERT: L  117 ARG cc_start: 0.6899 (mmt-90) cc_final: 0.6192 (mpt180)
REVERT: O  183 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7762 (mm-30)
REVERT: O  211 PHE cc_start: 0.8762 (m-80) cc_final: 0.8480 (m-80)
REVERT: N   17 LYS cc_start: 0.8648 (mttm) cc_final: 0.8388 (mttp)
REVERT: N  166 LYS cc_start: 0.9138 (ttpp) cc_final: 0.8770 (ttmm)
REVERT: N  192 GLU cc_start: 0.8696 (pm20) cc_final: 0.8446 (pm20)
REVERT: Q   42 ARG cc_start: 0.7750 (ptp90) cc_final: 0.7543 (ttp-170)
REVERT: Q   85 ARG cc_start: 0.5258 (tpt170) cc_final: 0.3514 (mtt-85)
REVERT: P   52 THR cc_start: 0.8361 (m) cc_final: 0.8032 (m)
REVERT: T   19 GLN cc_start: 0.8549 (mp10) cc_final: 0.8347 (mp10)
REVERT: T   42 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7993 (mm-30)
REVERT: T   85 ASN cc_start: 0.9052 (m-40) cc_final: 0.8822 (m-40)
REVERT: T   86 GLU cc_start: 0.8240 (tp30) cc_final: 0.7516 (tp30)
REVERT: q   50 MET cc_start: 0.1628 (ttm) cc_final: 0.1273 (tpp)
REVERT: q   99 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6350 (pm20)
REVERT: p   64 LYS cc_start: 0.7276 (mtpt) cc_final: 0.7052 (mtmt)
REVERT: p   84 GLN cc_start: 0.8321 (tt0) cc_final: 0.8095 (tt0)
REVERT: I   32 ASP cc_start: 0.8345 (p0) cc_final: 0.8074 (p0)
REVERT: I   53 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8851 (mp)
  outliers start: 84
  outliers final: 52
  residues processed: 681
  average time/residue: 0.6641
  time to fit residues: 736.9753
Evaluate side-chains
  649 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 55
    poor density    : 594
  time to evaluate  : 3.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  223 SER
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue  105 PHE
Chi-restraints excluded: chain E residue  125 VAL
Chi-restraints excluded: chain G residue   33 ASN
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain G residue  159 ASP
Chi-restraints excluded: chain G residue  188 GLU
Chi-restraints excluded: chain H residue   40 CYS
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain K residue   81 LYS
Chi-restraints excluded: chain J residue    2 VAL
Chi-restraints excluded: chain J residue  119 LYS
Chi-restraints excluded: chain M residue   85 VAL
Chi-restraints excluded: chain M residue   93 GLN
Chi-restraints excluded: chain M residue   95 ILE
Chi-restraints excluded: chain M residue  102 THR
Chi-restraints excluded: chain M residue  130 THR
Chi-restraints excluded: chain L residue  259 THR
Chi-restraints excluded: chain O residue   55 THR
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue  188 THR
Chi-restraints excluded: chain Q residue   24 THR
Chi-restraints excluded: chain Q residue   44 ILE
Chi-restraints excluded: chain Q residue   57 SER
Chi-restraints excluded: chain Q residue   76 SER
Chi-restraints excluded: chain Q residue   90 GLU
Chi-restraints excluded: chain P residue   81 VAL
Chi-restraints excluded: chain S residue    6 SER
Chi-restraints excluded: chain S residue  139 SER
Chi-restraints excluded: chain S residue  158 VAL
Chi-restraints excluded: chain S residue  181 THR
Chi-restraints excluded: chain S residue  217 MET
Chi-restraints excluded: chain R residue   72 CYS
Chi-restraints excluded: chain R residue  107 THR
Chi-restraints excluded: chain R residue  138 ASN
Chi-restraints excluded: chain R residue  145 ILE
Chi-restraints excluded: chain R residue  154 LYS
Chi-restraints excluded: chain T residue   27 VAL
Chi-restraints excluded: chain T residue   80 ASP
Chi-restraints excluded: chain q residue   28 PHE
Chi-restraints excluded: chain q residue   39 ILE
Chi-restraints excluded: chain q residue   99 GLU
Chi-restraints excluded: chain p residue  108 LEU
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   24 THR
Chi-restraints excluded: chain I residue   29 THR
Chi-restraints excluded: chain I residue   35 GLU
Chi-restraints excluded: chain I residue   53 ILE
Chi-restraints excluded: chain I residue   67 THR
Chi-restraints excluded: chain I residue   87 ASP
Chi-restraints excluded: chain y residue   53 LYS
Chi-restraints excluded: chain y residue  102 VAL
Chi-restraints excluded: chain 9 residue   20 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 452
   random chunks:
   chunk 228 optimal weight:    1.9990
   chunk 127 optimal weight:    0.2980
   chunk 341 optimal weight:    6.9990
   chunk 279 optimal weight:    1.9990
   chunk 113 optimal weight:    0.0570
   chunk 411 optimal weight:    6.9990
   chunk 444 optimal weight:   10.0000
   chunk 366 optimal weight:    3.9990
   chunk 407 optimal weight:    3.9990
   chunk 140 optimal weight:    3.9990
   chunk 329 optimal weight:    2.9990
   overall best weight:    1.4704

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

Flipped N/Q/H residues before XYZ refinement:
C 157 ASN
C 197 ASN
B   5 GLN
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  61 GLN
E  63 ASN
** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  64 ASN
** J  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 168 GLN
I  13 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  56297  Z= 0.288
  Angle     :  0.684  17.528  81890  Z= 0.354
  Chirality :  0.038   0.360  10159
  Planarity :  0.006   0.134   5822
  Dihedral  : 23.136 179.699  23014
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 20.09 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.75 (0.14), residues: 3310
  helix:  0.77 (0.16), residues: 1080
  sheet: -1.08 (0.21), residues: 555
  loop : -1.10 (0.14), residues: 1675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP N 176 
 HIS   0.009   0.001   HIS J  56 
 PHE   0.014   0.001   PHE O  81 
 TYR   0.021   0.002   TYR C 103 
 ARG   0.007   0.000   ARG I 106 

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

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

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  704 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 106
    poor density    : 598
  time to evaluate  : 4.045 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS R 144 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: C   54 TYR cc_start: 0.9219 (m-10) cc_final: 0.8891 (m-80)
REVERT: C  121 TYR cc_start: 0.9153 (p90) cc_final: 0.8929 (p90)
REVERT: E   95 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7808 (mm-30)
REVERT: D  154 GLN cc_start: 0.8958 (tt0) cc_final: 0.8285 (tt0)
REVERT: D  155 LYS cc_start: 0.8456 (tptt) cc_final: 0.7835 (tptp)
REVERT: H   80 ARG cc_start: 0.8627 (ptt90) cc_final: 0.7233 (ptp90)
REVERT: J  112 ASP cc_start: 0.8275 (p0) cc_final: 0.8055 (p0)
REVERT: M   82 ASP cc_start: 0.8186 (t70) cc_final: 0.7731 (t0)
REVERT: M  118 GLN cc_start: 0.8551 (tp40) cc_final: 0.8100 (tp-100)
REVERT: M  127 ASN cc_start: 0.8863 (p0) cc_final: 0.8337 (p0)
REVERT: L  248 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.8533 (m-80)
REVERT: O  211 PHE cc_start: 0.8873 (m-80) cc_final: 0.8447 (m-80)
REVERT: N   17 LYS cc_start: 0.8650 (mttm) cc_final: 0.8374 (mttt)
REVERT: N  192 GLU cc_start: 0.8740 (pm20) cc_final: 0.8438 (pm20)
REVERT: Q   85 ARG cc_start: 0.5295 (tpt170) cc_final: 0.3513 (mtt-85)
REVERT: P   76 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8269 (mm)
REVERT: R  119 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.8007 (mm)
REVERT: R  146 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8281 (mm110)
REVERT: T   19 GLN cc_start: 0.8585 (mp10) cc_final: 0.8293 (mp10)
REVERT: T   86 GLU cc_start: 0.8264 (tp30) cc_final: 0.7528 (tp30)
REVERT: q   50 MET cc_start: 0.1550 (ttm) cc_final: 0.1296 (tpp)
REVERT: q   99 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6307 (pm20)
REVERT: p   84 GLN cc_start: 0.8318 (tt0) cc_final: 0.8115 (tt0)
REVERT: I   53 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8802 (mp)
REVERT: 9   16 LYS cc_start: 0.8426 (ttpt) cc_final: 0.8215 (ttpt)
  outliers start: 106
  outliers final: 77
  residues processed: 668
  average time/residue: 0.6457
  time to fit residues: 707.8799
Evaluate side-chains
  651 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 82
    poor density    : 569
  time to evaluate  : 3.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  223 SER
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue  105 PHE
Chi-restraints excluded: chain E residue  125 VAL
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   33 ASN
Chi-restraints excluded: chain G residue  107 LYS
Chi-restraints excluded: chain G residue  119 SER
Chi-restraints excluded: chain G residue  159 ASP
Chi-restraints excluded: chain G residue  170 VAL
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain H residue   62 VAL
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   81 LYS
Chi-restraints excluded: chain J residue    2 VAL
Chi-restraints excluded: chain J residue  119 LYS
Chi-restraints excluded: chain M residue   85 VAL
Chi-restraints excluded: chain M residue   95 ILE
Chi-restraints excluded: chain M residue  102 THR
Chi-restraints excluded: chain M residue  130 THR
Chi-restraints excluded: chain L residue  160 LEU
Chi-restraints excluded: chain L residue  248 TYR
Chi-restraints excluded: chain L residue  259 THR
Chi-restraints excluded: chain O residue   50 THR
Chi-restraints excluded: chain O residue   55 THR
Chi-restraints excluded: chain O residue   59 SER
Chi-restraints excluded: chain O residue  129 THR
Chi-restraints excluded: chain N residue   46 ILE
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue  183 LEU
Chi-restraints excluded: chain N residue  188 THR
Chi-restraints excluded: chain Q residue   24 THR
Chi-restraints excluded: chain Q residue   29 CYS
Chi-restraints excluded: chain Q residue   67 LEU
Chi-restraints excluded: chain Q residue   76 SER
Chi-restraints excluded: chain Q residue   81 SER
Chi-restraints excluded: chain Q residue   90 GLU
Chi-restraints excluded: chain P residue   45 THR
Chi-restraints excluded: chain P residue   69 SER
Chi-restraints excluded: chain P residue   76 LEU
Chi-restraints excluded: chain P residue   81 VAL
Chi-restraints excluded: chain P residue  114 SER
Chi-restraints excluded: chain S residue    6 SER
Chi-restraints excluded: chain S residue   50 VAL
Chi-restraints excluded: chain S residue  139 SER
Chi-restraints excluded: chain S residue  158 VAL
Chi-restraints excluded: chain S residue  181 THR
Chi-restraints excluded: chain S residue  217 MET
Chi-restraints excluded: chain R residue   72 CYS
Chi-restraints excluded: chain R residue  107 THR
Chi-restraints excluded: chain R residue  119 LEU
Chi-restraints excluded: chain R residue  145 ILE
Chi-restraints excluded: chain R residue  154 LYS
Chi-restraints excluded: chain T residue    5 VAL
Chi-restraints excluded: chain T residue   27 VAL
Chi-restraints excluded: chain T residue   80 ASP
Chi-restraints excluded: chain T residue  125 VAL
Chi-restraints excluded: chain q residue   28 PHE
Chi-restraints excluded: chain q residue   38 VAL
Chi-restraints excluded: chain q residue   39 ILE
Chi-restraints excluded: chain q residue   99 GLU
Chi-restraints excluded: chain p residue   98 VAL
Chi-restraints excluded: chain p residue  108 LEU
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   22 VAL
Chi-restraints excluded: chain I residue   29 THR
Chi-restraints excluded: chain I residue   35 GLU
Chi-restraints excluded: chain I residue   53 ILE
Chi-restraints excluded: chain I residue   67 THR
Chi-restraints excluded: chain I residue   87 ASP
Chi-restraints excluded: chain I residue  131 THR
Chi-restraints excluded: chain y residue   53 LYS
Chi-restraints excluded: chain y residue   82 GLU
Chi-restraints excluded: chain y residue  102 VAL
Chi-restraints excluded: chain y residue  157 THR
Chi-restraints excluded: chain 9 residue   20 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 452
   random chunks:
   chunk 406 optimal weight:    2.9990
   chunk 309 optimal weight:   30.0000
   chunk 213 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 196 optimal weight:    5.9990
   chunk 276 optimal weight:    1.9990
   chunk 412 optimal weight:    3.9990
   chunk 436 optimal weight:   10.0000
   chunk 215 optimal weight:    4.9990
   chunk 391 optimal weight:   20.0000
   chunk 117 optimal weight:    1.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
C 197 ASN
B   5 GLN
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  56 HIS
J  64 ASN
** J  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  81 ASN
R 181 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.1650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.093  56297  Z= 0.412
  Angle     :  0.724  17.172  81890  Z= 0.373
  Chirality :  0.041   0.403  10159
  Planarity :  0.006   0.134   5822
  Dihedral  : 23.176 179.918  23013
  Min Nonbonded Distance : 1.838

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 20.16 %
    Favored  : 74.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.72 (0.14), residues: 3310
  helix:  0.74 (0.16), residues: 1089
  sheet: -1.11 (0.21), residues: 564
  loop : -1.04 (0.15), residues: 1657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP N 176 
 HIS   0.010   0.001   HIS J  56 
 PHE   0.017   0.002   PHE D 147 
 TYR   0.025   0.002   TYR C 103 
 ARG   0.009   0.001   ARG G  41 

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

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

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  726 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 139
    poor density    : 587
  time to evaluate  : 3.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS R 144 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: C   19 MET cc_start: 0.8865 (mtm) cc_final: 0.8631 (mtm)
REVERT: C   54 TYR cc_start: 0.9237 (m-10) cc_final: 0.8894 (m-80)
REVERT: C  149 TYR cc_start: 0.9225 (m-80) cc_final: 0.8970 (m-80)
REVERT: E   95 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7999 (mm-30)
REVERT: D  154 GLN cc_start: 0.9005 (tt0) cc_final: 0.8302 (tt0)
REVERT: D  155 LYS cc_start: 0.8487 (tptt) cc_final: 0.7849 (tptp)
REVERT: D  172 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7197 (ptt-90)
REVERT: G  165 ASN cc_start: 0.8915 (t0) cc_final: 0.8486 (t0)
REVERT: H   80 ARG cc_start: 0.8600 (ptt90) cc_final: 0.7267 (ptp90)
REVERT: K    8 PHE cc_start: 0.9028 (m-80) cc_final: 0.8802 (m-10)
REVERT: J  112 ASP cc_start: 0.8268 (p0) cc_final: 0.8043 (p0)
REVERT: M   82 ASP cc_start: 0.8097 (t70) cc_final: 0.7635 (t0)
REVERT: M  127 ASN cc_start: 0.8910 (p0) cc_final: 0.8361 (p0)
REVERT: L  248 TYR cc_start: 0.9073 (OUTLIER) cc_final: 0.8438 (m-80)
REVERT: O   32 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8055 (p0)
REVERT: O  128 LYS cc_start: 0.8456 (tttt) cc_final: 0.8032 (ttmt)
REVERT: O  211 PHE cc_start: 0.8894 (m-80) cc_final: 0.8454 (m-80)
REVERT: N   17 LYS cc_start: 0.8648 (mttm) cc_final: 0.8334 (mttt)
REVERT: N   42 LYS cc_start: 0.9035 (mtmm) cc_final: 0.8584 (mtmm)
REVERT: Q   42 ARG cc_start: 0.8044 (ttp-170) cc_final: 0.7818 (ttm110)
REVERT: Q   60 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6739 (p0)
REVERT: Q   85 ARG cc_start: 0.5317 (tpt170) cc_final: 0.3555 (mtt-85)
REVERT: R  205 ARG cc_start: 0.8074 (mmm-85) cc_final: 0.7861 (mmm160)
REVERT: T   19 GLN cc_start: 0.8631 (mp10) cc_final: 0.8389 (mp10)
REVERT: T   42 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7982 (tp30)
REVERT: T   86 GLU cc_start: 0.8321 (tp30) cc_final: 0.7505 (tp30)
REVERT: T  104 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8433 (mtp-110)
REVERT: q   50 MET cc_start: 0.1514 (ttm) cc_final: 0.1246 (tpp)
REVERT: p   84 GLN cc_start: 0.8367 (tt0) cc_final: 0.8113 (tt0)
REVERT: I  103 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7909 (pp20)
REVERT: 9    8 LYS cc_start: 0.8769 (tttp) cc_final: 0.8531 (tttm)
  outliers start: 139
  outliers final: 101
  residues processed: 681
  average time/residue: 0.6288
  time to fit residues: 701.5113
Evaluate side-chains
  670 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 107
    poor density    : 563
  time to evaluate  : 3.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  105 THR
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  223 SER
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue  105 PHE
Chi-restraints excluded: chain E residue  125 VAL
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  172 ARG
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   33 ASN
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain G residue  107 LYS
Chi-restraints excluded: chain G residue  119 SER
Chi-restraints excluded: chain G residue  159 ASP
Chi-restraints excluded: chain G residue  170 VAL
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   24 LYS
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   81 LYS
Chi-restraints excluded: chain J residue    2 VAL
Chi-restraints excluded: chain J residue   31 SER
Chi-restraints excluded: chain J residue   80 ASP
Chi-restraints excluded: chain J residue  119 LYS
Chi-restraints excluded: chain M residue   85 VAL
Chi-restraints excluded: chain M residue   95 ILE
Chi-restraints excluded: chain M residue  102 THR
Chi-restraints excluded: chain M residue  130 THR
Chi-restraints excluded: chain L residue  160 LEU
Chi-restraints excluded: chain L residue  236 PHE
Chi-restraints excluded: chain L residue  248 TYR
Chi-restraints excluded: chain L residue  259 THR
Chi-restraints excluded: chain L residue  262 THR
Chi-restraints excluded: chain L residue  264 SER
Chi-restraints excluded: chain O residue   32 ASP
Chi-restraints excluded: chain O residue   50 THR
Chi-restraints excluded: chain O residue   55 THR
Chi-restraints excluded: chain O residue   59 SER
Chi-restraints excluded: chain O residue  126 ASP
Chi-restraints excluded: chain O residue  129 THR
Chi-restraints excluded: chain N residue   46 ILE
Chi-restraints excluded: chain N residue   79 SER
Chi-restraints excluded: chain N residue  183 LEU
Chi-restraints excluded: chain N residue  188 THR
Chi-restraints excluded: chain Q residue   24 THR
Chi-restraints excluded: chain Q residue   29 CYS
Chi-restraints excluded: chain Q residue   30 VAL
Chi-restraints excluded: chain Q residue   44 ILE
Chi-restraints excluded: chain Q residue   57 SER
Chi-restraints excluded: chain Q residue   60 ASP
Chi-restraints excluded: chain Q residue   67 LEU
Chi-restraints excluded: chain Q residue   76 SER
Chi-restraints excluded: chain Q residue   81 SER
Chi-restraints excluded: chain Q residue   90 GLU
Chi-restraints excluded: chain P residue   26 ASN
Chi-restraints excluded: chain P residue   45 THR
Chi-restraints excluded: chain P residue   69 SER
Chi-restraints excluded: chain P residue   81 VAL
Chi-restraints excluded: chain P residue  114 SER
Chi-restraints excluded: chain S residue    6 SER
Chi-restraints excluded: chain S residue   50 VAL
Chi-restraints excluded: chain S residue   53 SER
Chi-restraints excluded: chain S residue  120 ASP
Chi-restraints excluded: chain S residue  139 SER
Chi-restraints excluded: chain S residue  158 VAL
Chi-restraints excluded: chain S residue  181 THR
Chi-restraints excluded: chain S residue  217 MET
Chi-restraints excluded: chain R residue   72 CYS
Chi-restraints excluded: chain R residue   93 THR
Chi-restraints excluded: chain R residue  102 VAL
Chi-restraints excluded: chain R residue  107 THR
Chi-restraints excluded: chain R residue  145 ILE
Chi-restraints excluded: chain R residue  154 LYS
Chi-restraints excluded: chain R residue  155 ASN
Chi-restraints excluded: chain T residue    5 VAL
Chi-restraints excluded: chain T residue   27 VAL
Chi-restraints excluded: chain T residue   77 ASP
Chi-restraints excluded: chain T residue   80 ASP
Chi-restraints excluded: chain T residue  104 ARG
Chi-restraints excluded: chain T residue  125 VAL
Chi-restraints excluded: chain q residue   39 ILE
Chi-restraints excluded: chain q residue   51 CYS
Chi-restraints excluded: chain q residue   55 VAL
Chi-restraints excluded: chain q residue   73 THR
Chi-restraints excluded: chain q residue   99 GLU
Chi-restraints excluded: chain p residue   37 GLN
Chi-restraints excluded: chain p residue   98 VAL
Chi-restraints excluded: chain p residue  108 LEU
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   24 THR
Chi-restraints excluded: chain I residue   29 THR
Chi-restraints excluded: chain I residue   33 VAL
Chi-restraints excluded: chain I residue   35 GLU
Chi-restraints excluded: chain I residue   67 THR
Chi-restraints excluded: chain I residue   69 ASN
Chi-restraints excluded: chain I residue   87 ASP
Chi-restraints excluded: chain I residue  103 GLU
Chi-restraints excluded: chain I residue  131 THR
Chi-restraints excluded: chain y residue   76 VAL
Chi-restraints excluded: chain y residue   77 THR
Chi-restraints excluded: chain y residue   82 GLU
Chi-restraints excluded: chain y residue  102 VAL
Chi-restraints excluded: chain y residue  157 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 452
   random chunks:
   chunk 363 optimal weight:    2.9990
   chunk 248 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 325 optimal weight:    0.0170
   chunk 180 optimal weight:    0.9990
   chunk 372 optimal weight:    1.9990
   chunk 302 optimal weight:    5.9990
   chunk 0 optimal weight:    1.9990
   chunk 223 optimal weight:    1.9990
   chunk 392 optimal weight:   20.0000
   chunk 110 optimal weight:    0.5980
   overall best weight:    0.9022

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

Flipped N/Q/H residues before XYZ refinement:
C 142 HIS
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 197 ASN
B   5 GLN
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  77 ASN
** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  64 ASN
** J  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 113 GLN
L 272 HIS
** O  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  81 ASN
R 111 GLN
R 165 GLN
R 167 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.1654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  56297  Z= 0.197
  Angle     :  0.655  17.331  81890  Z= 0.341
  Chirality :  0.036   0.347  10159
  Planarity :  0.006   0.128   5822
  Dihedral  : 23.157 179.450  23011
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 21.81 %
    Favored  : 74.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.40 (0.14), residues: 3310
  helix:  1.05 (0.16), residues: 1085
  sheet: -0.98 (0.21), residues: 564
  loop : -0.85 (0.15), residues: 1661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R   8 
 HIS   0.004   0.001   HIS R  22 
 PHE   0.013   0.001   PHE D 147 
 TYR   0.019   0.001   TYR C 103 
 ARG   0.007   0.000   ARG J  36 

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

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

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  714 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 112
    poor density    : 602
  time to evaluate  : 3.825 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS R 144 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: C   19 MET cc_start: 0.8788 (mtm) cc_final: 0.8564 (mtm)
REVERT: C   54 TYR cc_start: 0.9211 (m-80) cc_final: 0.8951 (m-80)
REVERT: C  121 TYR cc_start: 0.9146 (p90) cc_final: 0.8912 (p90)
REVERT: C  149 TYR cc_start: 0.9235 (m-80) cc_final: 0.8959 (m-80)
REVERT: B   10 TYR cc_start: 0.9173 (t80) cc_final: 0.8774 (t80)
REVERT: E   95 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7752 (mm-30)
REVERT: D  154 GLN cc_start: 0.8935 (tt0) cc_final: 0.8262 (tt0)
REVERT: D  155 LYS cc_start: 0.8439 (tptt) cc_final: 0.7816 (tptp)
REVERT: D  172 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7044 (ptt-90)
REVERT: G  165 ASN cc_start: 0.8808 (t0) cc_final: 0.8399 (t0)
REVERT: G  186 ASN cc_start: 0.8436 (m110) cc_final: 0.8125 (m110)
REVERT: H   80 ARG cc_start: 0.8536 (ptt90) cc_final: 0.7185 (ptp90)
REVERT: K    8 PHE cc_start: 0.9037 (m-80) cc_final: 0.8765 (m-10)
REVERT: J   98 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8710 (mt0)
REVERT: M   82 ASP cc_start: 0.8081 (t70) cc_final: 0.7674 (t0)
REVERT: M  127 ASN cc_start: 0.8884 (p0) cc_final: 0.8394 (p0)
REVERT: L  248 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.8503 (m-80)
REVERT: O   32 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8058 (p0)
REVERT: O  128 LYS cc_start: 0.8418 (tttt) cc_final: 0.8000 (tppt)
REVERT: O  211 PHE cc_start: 0.8857 (m-80) cc_final: 0.8448 (m-80)
REVERT: N   17 LYS cc_start: 0.8643 (mttm) cc_final: 0.8314 (mttt)
REVERT: N  192 GLU cc_start: 0.8733 (pm20) cc_final: 0.8501 (pm20)
REVERT: Q   85 ARG cc_start: 0.5227 (tpt170) cc_final: 0.3605 (mtt-85)
REVERT: P  125 LYS cc_start: 0.8858 (mmtp) cc_final: 0.8309 (mmmt)
REVERT: T   19 GLN cc_start: 0.8563 (mp10) cc_final: 0.8255 (mp10)
REVERT: T   86 GLU cc_start: 0.8337 (tp30) cc_final: 0.7467 (tp30)
REVERT: q   50 MET cc_start: 0.1542 (ttm) cc_final: 0.1282 (tpp)
REVERT: p   59 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8220 (pp)
REVERT: p   84 GLN cc_start: 0.8400 (tt0) cc_final: 0.8126 (tt0)
  outliers start: 112
  outliers final: 86
  residues processed: 675
  average time/residue: 0.6266
  time to fit residues: 699.2090
Evaluate side-chains
  666 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 91
    poor density    : 575
  time to evaluate  : 3.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  223 SER
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   50 ILE
Chi-restraints excluded: chain E residue  105 PHE
Chi-restraints excluded: chain E residue  125 VAL
Chi-restraints excluded: chain D residue  172 ARG
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   33 ASN
Chi-restraints excluded: chain G residue  107 LYS
Chi-restraints excluded: chain G residue  119 SER
Chi-restraints excluded: chain G residue  159 ASP
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain H residue   40 CYS
Chi-restraints excluded: chain K residue   81 LYS
Chi-restraints excluded: chain J residue    2 VAL
Chi-restraints excluded: chain J residue   80 ASP
Chi-restraints excluded: chain J residue   98 GLN
Chi-restraints excluded: chain J residue  119 LYS
Chi-restraints excluded: chain M residue   85 VAL
Chi-restraints excluded: chain M residue   95 ILE
Chi-restraints excluded: chain M residue  102 THR
Chi-restraints excluded: chain M residue  117 LEU
Chi-restraints excluded: chain M residue  130 THR
Chi-restraints excluded: chain L residue  160 LEU
Chi-restraints excluded: chain L residue  248 TYR
Chi-restraints excluded: chain L residue  259 THR
Chi-restraints excluded: chain L residue  264 SER
Chi-restraints excluded: chain O residue   32 ASP
Chi-restraints excluded: chain O residue   55 THR
Chi-restraints excluded: chain O residue   59 SER
Chi-restraints excluded: chain O residue  129 THR
Chi-restraints excluded: chain O residue  228 LEU
Chi-restraints excluded: chain N residue   44 ASP
Chi-restraints excluded: chain N residue   46 ILE
Chi-restraints excluded: chain N residue   79 SER
Chi-restraints excluded: chain N residue  188 THR
Chi-restraints excluded: chain Q residue   24 THR
Chi-restraints excluded: chain Q residue   76 SER
Chi-restraints excluded: chain Q residue   81 SER
Chi-restraints excluded: chain Q residue   90 GLU
Chi-restraints excluded: chain P residue   26 ASN
Chi-restraints excluded: chain P residue   45 THR
Chi-restraints excluded: chain P residue   65 ASP
Chi-restraints excluded: chain P residue   69 SER
Chi-restraints excluded: chain P residue   81 VAL
Chi-restraints excluded: chain P residue  114 SER
Chi-restraints excluded: chain P residue  130 GLU
Chi-restraints excluded: chain S residue    6 SER
Chi-restraints excluded: chain S residue   39 ASP
Chi-restraints excluded: chain S residue   50 VAL
Chi-restraints excluded: chain S residue  139 SER
Chi-restraints excluded: chain S residue  158 VAL
Chi-restraints excluded: chain S residue  181 THR
Chi-restraints excluded: chain S residue  217 MET
Chi-restraints excluded: chain R residue   72 CYS
Chi-restraints excluded: chain R residue  107 THR
Chi-restraints excluded: chain R residue  136 ILE
Chi-restraints excluded: chain R residue  145 ILE
Chi-restraints excluded: chain R residue  154 LYS
Chi-restraints excluded: chain T residue   77 ASP
Chi-restraints excluded: chain T residue   80 ASP
Chi-restraints excluded: chain q residue   27 VAL
Chi-restraints excluded: chain q residue   28 PHE
Chi-restraints excluded: chain q residue   39 ILE
Chi-restraints excluded: chain q residue   99 GLU
Chi-restraints excluded: chain p residue   37 GLN
Chi-restraints excluded: chain p residue   59 LEU
Chi-restraints excluded: chain p residue   98 VAL
Chi-restraints excluded: chain p residue  108 LEU
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   29 THR
Chi-restraints excluded: chain I residue   32 ASP
Chi-restraints excluded: chain I residue   35 GLU
Chi-restraints excluded: chain I residue   63 VAL
Chi-restraints excluded: chain I residue   67 THR
Chi-restraints excluded: chain I residue   87 ASP
Chi-restraints excluded: chain I residue  116 ILE
Chi-restraints excluded: chain I residue  131 THR
Chi-restraints excluded: chain I residue  145 THR
Chi-restraints excluded: chain y residue   76 VAL
Chi-restraints excluded: chain y residue   77 THR
Chi-restraints excluded: chain y residue   82 GLU
Chi-restraints excluded: chain y residue  102 VAL
Chi-restraints excluded: chain y residue  157 THR
Chi-restraints excluded: chain 9 residue   20 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 452
   random chunks:
   chunk 146 optimal weight:    2.9990
   chunk 393 optimal weight:   10.0000
   chunk 86 optimal weight:    2.9990
   chunk 256 optimal weight:    0.7980
   chunk 107 optimal weight:    3.9990
   chunk 437 optimal weight:    5.9990
   chunk 363 optimal weight:    2.9990
   chunk 202 optimal weight:    0.4980
   chunk 36 optimal weight:    3.9990
   chunk 144 optimal weight:    0.8980
   chunk 229 optimal weight:    3.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 197 ASN
B   5 GLN
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  93 GLN
L 113 GLN
** O  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 111 GLN
R 165 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077  56297  Z= 0.313
  Angle     :  0.675  17.200  81890  Z= 0.350
  Chirality :  0.038   0.357  10159
  Planarity :  0.006   0.132   5822
  Dihedral  : 23.086 179.912  23010
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 21.66 %
    Favored  : 73.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.35 (0.14), residues: 3310
  helix:  1.08 (0.16), residues: 1085
  sheet: -0.95 (0.21), residues: 564
  loop : -0.81 (0.15), residues: 1661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP N 176 
 HIS   0.005   0.001   HIS R  22 
 PHE   0.014   0.001   PHE D 147 
 TYR   0.028   0.002   TYR C 103 
 ARG   0.006   0.000   ARG J  36 

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

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

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  689 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 123
    poor density    : 566
  time to evaluate  : 3.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS R 144 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: C   19 MET cc_start: 0.8798 (mtm) cc_final: 0.8556 (mtm)
REVERT: C   54 TYR cc_start: 0.9234 (m-80) cc_final: 0.8947 (m-80)
REVERT: C  121 TYR cc_start: 0.9154 (p90) cc_final: 0.8914 (p90)
REVERT: C  149 TYR cc_start: 0.9249 (m-80) cc_final: 0.9007 (m-80)
REVERT: B   10 TYR cc_start: 0.9190 (t80) cc_final: 0.8844 (t80)
REVERT: E   95 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7948 (mm-30)
REVERT: D  154 GLN cc_start: 0.8980 (tt0) cc_final: 0.8257 (tt0)
REVERT: D  155 LYS cc_start: 0.8454 (tptt) cc_final: 0.7849 (tptp)
REVERT: D  172 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7049 (ptt-90)
REVERT: G  165 ASN cc_start: 0.8864 (t0) cc_final: 0.8421 (t0)
REVERT: G  186 ASN cc_start: 0.8478 (m110) cc_final: 0.8168 (m110)
REVERT: H   75 GLU cc_start: 0.5489 (OUTLIER) cc_final: 0.4704 (pp20)
REVERT: H   80 ARG cc_start: 0.8556 (ptt90) cc_final: 0.7204 (ptp90)
REVERT: K    8 PHE cc_start: 0.9034 (m-80) cc_final: 0.8767 (m-10)
REVERT: M   82 ASP cc_start: 0.8037 (t70) cc_final: 0.7679 (t0)
REVERT: M  127 ASN cc_start: 0.8900 (p0) cc_final: 0.8368 (p0)
REVERT: L  248 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.8440 (m-80)
REVERT: O   32 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8084 (p0)
REVERT: O  128 LYS cc_start: 0.8467 (tttt) cc_final: 0.8050 (ttmt)
REVERT: O  211 PHE cc_start: 0.8901 (m-80) cc_final: 0.8481 (m-80)
REVERT: N   17 LYS cc_start: 0.8664 (mttm) cc_final: 0.8374 (mttp)
REVERT: N  192 GLU cc_start: 0.8764 (pm20) cc_final: 0.8502 (pm20)
REVERT: Q   85 ARG cc_start: 0.5248 (tpt170) cc_final: 0.3522 (mtt-85)
REVERT: P  125 LYS cc_start: 0.8844 (mmtp) cc_final: 0.8265 (mmmt)
REVERT: T   19 GLN cc_start: 0.8595 (mp10) cc_final: 0.8358 (mp10)
REVERT: T   86 GLU cc_start: 0.8336 (tp30) cc_final: 0.7478 (tp30)
REVERT: q   22 GLU cc_start: 0.4343 (OUTLIER) cc_final: 0.3237 (tp30)
REVERT: q   50 MET cc_start: 0.1658 (ttm) cc_final: 0.1298 (tpp)
REVERT: p   59 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8266 (pp)
REVERT: p   84 GLN cc_start: 0.8412 (tt0) cc_final: 0.8141 (tt0)
REVERT: y   58 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.5210 (tm-30)
REVERT: y  104 ARG cc_start: 0.5046 (mmm-85) cc_final: 0.4823 (mmm-85)
  outliers start: 123
  outliers final: 99
  residues processed: 651
  average time/residue: 0.5971
  time to fit residues: 640.1401
Evaluate side-chains
  666 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 106
    poor density    : 560
  time to evaluate  : 3.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  105 THR
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  223 SER
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   50 ILE
Chi-restraints excluded: chain E residue  105 PHE
Chi-restraints excluded: chain E residue  125 VAL
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue  172 ARG
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   33 ASN
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain G residue  107 LYS
Chi-restraints excluded: chain G residue  119 SER
Chi-restraints excluded: chain G residue  159 ASP
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain H residue   40 CYS
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   81 LYS
Chi-restraints excluded: chain J residue    2 VAL
Chi-restraints excluded: chain J residue   30 CYS
Chi-restraints excluded: chain J residue   80 ASP
Chi-restraints excluded: chain J residue  119 LYS
Chi-restraints excluded: chain M residue   85 VAL
Chi-restraints excluded: chain M residue   93 GLN
Chi-restraints excluded: chain M residue   95 ILE
Chi-restraints excluded: chain M residue  102 THR
Chi-restraints excluded: chain M residue  117 LEU
Chi-restraints excluded: chain M residue  130 THR
Chi-restraints excluded: chain L residue  160 LEU
Chi-restraints excluded: chain L residue  248 TYR
Chi-restraints excluded: chain L residue  259 THR
Chi-restraints excluded: chain L residue  264 SER
Chi-restraints excluded: chain O residue   32 ASP
Chi-restraints excluded: chain O residue   40 ASN
Chi-restraints excluded: chain O residue   50 THR
Chi-restraints excluded: chain O residue   55 THR
Chi-restraints excluded: chain O residue   59 SER
Chi-restraints excluded: chain O residue  126 ASP
Chi-restraints excluded: chain O residue  129 THR
Chi-restraints excluded: chain N residue   44 ASP
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   79 SER
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain N residue  183 LEU
Chi-restraints excluded: chain N residue  188 THR
Chi-restraints excluded: chain Q residue   24 THR
Chi-restraints excluded: chain Q residue   29 CYS
Chi-restraints excluded: chain Q residue   67 LEU
Chi-restraints excluded: chain Q residue   76 SER
Chi-restraints excluded: chain Q residue   81 SER
Chi-restraints excluded: chain Q residue   90 GLU
Chi-restraints excluded: chain P residue   26 ASN
Chi-restraints excluded: chain P residue   45 THR
Chi-restraints excluded: chain P residue   69 SER
Chi-restraints excluded: chain P residue  114 SER
Chi-restraints excluded: chain P residue  130 GLU
Chi-restraints excluded: chain S residue    6 SER
Chi-restraints excluded: chain S residue   39 ASP
Chi-restraints excluded: chain S residue   50 VAL
Chi-restraints excluded: chain S residue   53 SER
Chi-restraints excluded: chain S residue  139 SER
Chi-restraints excluded: chain S residue  158 VAL
Chi-restraints excluded: chain S residue  181 THR
Chi-restraints excluded: chain S residue  217 MET
Chi-restraints excluded: chain R residue   72 CYS
Chi-restraints excluded: chain R residue  107 THR
Chi-restraints excluded: chain R residue  145 ILE
Chi-restraints excluded: chain R residue  154 LYS
Chi-restraints excluded: chain T residue    5 VAL
Chi-restraints excluded: chain T residue   27 VAL
Chi-restraints excluded: chain T residue   35 VAL
Chi-restraints excluded: chain T residue   77 ASP
Chi-restraints excluded: chain T residue   80 ASP
Chi-restraints excluded: chain q residue   22 GLU
Chi-restraints excluded: chain q residue   27 VAL
Chi-restraints excluded: chain q residue   39 ILE
Chi-restraints excluded: chain q residue   51 CYS
Chi-restraints excluded: chain q residue   55 VAL
Chi-restraints excluded: chain q residue   99 GLU
Chi-restraints excluded: chain p residue   37 GLN
Chi-restraints excluded: chain p residue   59 LEU
Chi-restraints excluded: chain p residue   98 VAL
Chi-restraints excluded: chain p residue  108 LEU
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   22 VAL
Chi-restraints excluded: chain I residue   24 THR
Chi-restraints excluded: chain I residue   32 ASP
Chi-restraints excluded: chain I residue   35 GLU
Chi-restraints excluded: chain I residue   63 VAL
Chi-restraints excluded: chain I residue   67 THR
Chi-restraints excluded: chain I residue   87 ASP
Chi-restraints excluded: chain I residue  131 THR
Chi-restraints excluded: chain I residue  145 THR
Chi-restraints excluded: chain y residue   53 LYS
Chi-restraints excluded: chain y residue   58 GLU
Chi-restraints excluded: chain y residue   77 THR
Chi-restraints excluded: chain y residue   82 GLU
Chi-restraints excluded: chain y residue  102 VAL
Chi-restraints excluded: chain y residue  157 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 452
   random chunks:
   chunk 421 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 249 optimal weight:    0.9990
   chunk 319 optimal weight:    0.9980
   chunk 247 optimal weight:    0.9980
   chunk 368 optimal weight:    3.9990
   chunk 244 optimal weight:    5.9990
   chunk 435 optimal weight:    7.9990
   chunk 272 optimal weight:   10.0000
   chunk 265 optimal weight:    5.9990
   chunk 201 optimal weight:    0.8980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 197 ASN
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  81 ASN
R 111 GLN
T  85 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  56297  Z= 0.238
  Angle     :  0.654  17.277  81890  Z= 0.341
  Chirality :  0.036   0.343  10159
  Planarity :  0.006   0.130   5822
  Dihedral  : 23.065 179.989  23008
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 21.59 %
    Favored  : 73.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.22 (0.14), residues: 3310
  helix:  1.19 (0.16), residues: 1085
  sheet: -0.89 (0.21), residues: 564
  loop : -0.73 (0.15), residues: 1661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R   8 
 HIS   0.005   0.001   HIS R  22 
 PHE   0.013   0.001   PHE D 147 
 TYR   0.030   0.001   TYR C 103 
 ARG   0.006   0.000   ARG J  36 

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

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

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  699 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 126
    poor density    : 573
  time to evaluate  : 3.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS R 144 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: C   19 MET cc_start: 0.8771 (mtm) cc_final: 0.8547 (mtm)
REVERT: C   54 TYR cc_start: 0.9217 (m-80) cc_final: 0.8952 (m-80)
REVERT: C  121 TYR cc_start: 0.9139 (p90) cc_final: 0.8908 (p90)
REVERT: E   95 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7940 (mm-30)
REVERT: D  154 GLN cc_start: 0.8956 (tt0) cc_final: 0.8235 (tt0)
REVERT: D  155 LYS cc_start: 0.8420 (tptt) cc_final: 0.7822 (tptp)
REVERT: D  172 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7019 (ptt-90)
REVERT: G   57 ARG cc_start: 0.7722 (ttt90) cc_final: 0.7380 (ttt90)
REVERT: G  165 ASN cc_start: 0.8830 (t0) cc_final: 0.8412 (t0)
REVERT: G  186 ASN cc_start: 0.8463 (m110) cc_final: 0.8157 (m110)
REVERT: H   75 GLU cc_start: 0.5591 (OUTLIER) cc_final: 0.4833 (pp20)
REVERT: H   80 ARG cc_start: 0.8548 (ptt90) cc_final: 0.7142 (ptp90)
REVERT: K    8 PHE cc_start: 0.9028 (m-80) cc_final: 0.8756 (m-10)
REVERT: M   82 ASP cc_start: 0.8077 (t70) cc_final: 0.7738 (t0)
REVERT: M  127 ASN cc_start: 0.8882 (p0) cc_final: 0.8378 (p0)
REVERT: L  248 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8449 (m-80)
REVERT: O   32 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8108 (p0)
REVERT: O  122 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7362 (mt-10)
REVERT: O  128 LYS cc_start: 0.8438 (tttt) cc_final: 0.8029 (ttmt)
REVERT: O  211 PHE cc_start: 0.8901 (m-80) cc_final: 0.8461 (m-80)
REVERT: N   17 LYS cc_start: 0.8657 (mttm) cc_final: 0.8327 (mttt)
REVERT: N  192 GLU cc_start: 0.8757 (pm20) cc_final: 0.8552 (pm20)
REVERT: Q   85 ARG cc_start: 0.5216 (tpt170) cc_final: 0.3515 (mtt-85)
REVERT: P  124 MET cc_start: 0.8454 (mmp) cc_final: 0.8020 (mmp)
REVERT: T   19 GLN cc_start: 0.8590 (mp10) cc_final: 0.8342 (mp10)
REVERT: T   86 GLU cc_start: 0.8323 (tp30) cc_final: 0.7490 (tp30)
REVERT: q   22 GLU cc_start: 0.4340 (OUTLIER) cc_final: 0.3237 (tp30)
REVERT: q   50 MET cc_start: 0.1726 (ttm) cc_final: 0.1311 (tpp)
REVERT: q   99 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6311 (pm20)
REVERT: p   59 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8232 (pp)
REVERT: p   84 GLN cc_start: 0.8413 (tt0) cc_final: 0.8139 (tt0)
REVERT: y   58 GLU cc_start: 0.5707 (OUTLIER) cc_final: 0.5151 (tm-30)
  outliers start: 126
  outliers final: 100
  residues processed: 658
  average time/residue: 0.5685
  time to fit residues: 608.7888
Evaluate side-chains
  672 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 108
    poor density    : 564
  time to evaluate  : 3.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  105 THR
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  223 SER
Chi-restraints excluded: chain C residue  232 ASN
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   50 ILE
Chi-restraints excluded: chain E residue  105 PHE
Chi-restraints excluded: chain E residue  125 VAL
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue  172 ARG
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   33 ASN
Chi-restraints excluded: chain G residue  107 LYS
Chi-restraints excluded: chain G residue  119 SER
Chi-restraints excluded: chain G residue  159 ASP
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   24 LYS
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain H residue   40 CYS
Chi-restraints excluded: chain H residue   62 VAL
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   66 ASP
Chi-restraints excluded: chain K residue   81 LYS
Chi-restraints excluded: chain J residue    2 VAL
Chi-restraints excluded: chain J residue   80 ASP
Chi-restraints excluded: chain J residue  119 LYS
Chi-restraints excluded: chain M residue   85 VAL
Chi-restraints excluded: chain M residue   95 ILE
Chi-restraints excluded: chain M residue  102 THR
Chi-restraints excluded: chain M residue  117 LEU
Chi-restraints excluded: chain M residue  119 VAL
Chi-restraints excluded: chain M residue  130 THR
Chi-restraints excluded: chain L residue  160 LEU
Chi-restraints excluded: chain L residue  236 PHE
Chi-restraints excluded: chain L residue  248 TYR
Chi-restraints excluded: chain L residue  259 THR
Chi-restraints excluded: chain L residue  264 SER
Chi-restraints excluded: chain O residue   32 ASP
Chi-restraints excluded: chain O residue   40 ASN
Chi-restraints excluded: chain O residue   55 THR
Chi-restraints excluded: chain O residue   59 SER
Chi-restraints excluded: chain O residue  126 ASP
Chi-restraints excluded: chain O residue  129 THR
Chi-restraints excluded: chain N residue   44 ASP
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   79 SER
Chi-restraints excluded: chain N residue  183 LEU
Chi-restraints excluded: chain N residue  188 THR
Chi-restraints excluded: chain Q residue   24 THR
Chi-restraints excluded: chain Q residue   29 CYS
Chi-restraints excluded: chain Q residue   57 SER
Chi-restraints excluded: chain Q residue   67 LEU
Chi-restraints excluded: chain Q residue   76 SER
Chi-restraints excluded: chain Q residue   81 SER
Chi-restraints excluded: chain Q residue   90 GLU
Chi-restraints excluded: chain P residue   26 ASN
Chi-restraints excluded: chain P residue   45 THR
Chi-restraints excluded: chain P residue   69 SER
Chi-restraints excluded: chain P residue  114 SER
Chi-restraints excluded: chain P residue  130 GLU
Chi-restraints excluded: chain S residue    6 SER
Chi-restraints excluded: chain S residue   39 ASP
Chi-restraints excluded: chain S residue   50 VAL
Chi-restraints excluded: chain S residue  139 SER
Chi-restraints excluded: chain S residue  158 VAL
Chi-restraints excluded: chain S residue  181 THR
Chi-restraints excluded: chain S residue  217 MET
Chi-restraints excluded: chain R residue   19 LYS
Chi-restraints excluded: chain R residue   72 CYS
Chi-restraints excluded: chain R residue  107 THR
Chi-restraints excluded: chain R residue  145 ILE
Chi-restraints excluded: chain R residue  154 LYS
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain T residue   27 VAL
Chi-restraints excluded: chain T residue   35 VAL
Chi-restraints excluded: chain T residue   77 ASP
Chi-restraints excluded: chain T residue   80 ASP
Chi-restraints excluded: chain q residue   22 GLU
Chi-restraints excluded: chain q residue   27 VAL
Chi-restraints excluded: chain q residue   28 PHE
Chi-restraints excluded: chain q residue   39 ILE
Chi-restraints excluded: chain q residue   51 CYS
Chi-restraints excluded: chain q residue   55 VAL
Chi-restraints excluded: chain q residue   99 GLU
Chi-restraints excluded: chain p residue   37 GLN
Chi-restraints excluded: chain p residue   59 LEU
Chi-restraints excluded: chain p residue   98 VAL
Chi-restraints excluded: chain p residue  108 LEU
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   32 ASP
Chi-restraints excluded: chain I residue   35 GLU
Chi-restraints excluded: chain I residue   63 VAL
Chi-restraints excluded: chain I residue   67 THR
Chi-restraints excluded: chain I residue   69 ASN
Chi-restraints excluded: chain I residue   87 ASP
Chi-restraints excluded: chain I residue  131 THR
Chi-restraints excluded: chain I residue  145 THR
Chi-restraints excluded: chain y residue   53 LYS
Chi-restraints excluded: chain y residue   58 GLU
Chi-restraints excluded: chain y residue   76 VAL
Chi-restraints excluded: chain y residue   77 THR
Chi-restraints excluded: chain y residue   82 GLU
Chi-restraints excluded: chain y residue  102 VAL
Chi-restraints excluded: chain y residue  157 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 452
   random chunks:
   chunk 269 optimal weight:    5.9990
   chunk 173 optimal weight:    0.8980
   chunk 260 optimal weight:    5.9990
   chunk 131 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   chunk 276 optimal weight:    3.9990
   chunk 296 optimal weight:   20.0000
   chunk 215 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 342 optimal weight:    4.9990
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 197 ASN
B   5 GLN
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  81 ASN
R 111 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.118  56297  Z= 0.510
  Angle     :  0.759  17.430  81890  Z= 0.388
  Chirality :  0.043   0.411  10159
  Planarity :  0.007   0.139   5822
  Dihedral  : 23.120 179.620  23008
  Min Nonbonded Distance : 1.821

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 21.70 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.51 (0.14), residues: 3310
  helix:  0.93 (0.16), residues: 1078
  sheet: -1.07 (0.21), residues: 575
  loop : -0.86 (0.15), residues: 1657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP N 176 
 HIS   0.005   0.001   HIS R  22 
 PHE   0.018   0.002   PHE D 147 
 TYR   0.039   0.002   TYR C 103 
 ARG   0.007   0.001   ARG R  77 

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

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

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  695 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 128
    poor density    : 567
  time to evaluate  : 3.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS R 144 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: C   19 MET cc_start: 0.8812 (mtm) cc_final: 0.8592 (mtm)
REVERT: C   54 TYR cc_start: 0.9243 (m-80) cc_final: 0.8920 (m-80)
REVERT: C  121 TYR cc_start: 0.9137 (p90) cc_final: 0.8871 (p90)
REVERT: C  149 TYR cc_start: 0.9255 (m-80) cc_final: 0.8943 (m-80)
REVERT: E   95 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8019 (mm-30)
REVERT: D  155 LYS cc_start: 0.8463 (tptt) cc_final: 0.7846 (tptp)
REVERT: D  172 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7156 (ptt-90)
REVERT: G  165 ASN cc_start: 0.8940 (t0) cc_final: 0.8544 (t0)
REVERT: H   75 GLU cc_start: 0.5484 (OUTLIER) cc_final: 0.4648 (pp20)
REVERT: H   80 ARG cc_start: 0.8582 (ptt90) cc_final: 0.7240 (ptp90)
REVERT: M   82 ASP cc_start: 0.8108 (t70) cc_final: 0.7740 (t0)
REVERT: M  127 ASN cc_start: 0.8947 (p0) cc_final: 0.8634 (p0)
REVERT: L  117 ARG cc_start: 0.6568 (mmt-90) cc_final: 0.6251 (mmt-90)
REVERT: L  248 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8374 (m-80)
REVERT: O   32 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8101 (p0)
REVERT: O  104 ASP cc_start: 0.7763 (t0) cc_final: 0.7502 (t0)
REVERT: O  128 LYS cc_start: 0.8451 (tttt) cc_final: 0.8061 (ttmt)
REVERT: N   17 LYS cc_start: 0.8657 (mttm) cc_final: 0.8343 (mttp)
REVERT: N  192 GLU cc_start: 0.8793 (pm20) cc_final: 0.8571 (pm20)
REVERT: Q   60 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6685 (p0)
REVERT: Q   85 ARG cc_start: 0.5359 (tpt170) cc_final: 0.3529 (mtt-85)
REVERT: P   38 ASN cc_start: 0.8367 (m-40) cc_final: 0.8058 (m110)
REVERT: T   19 GLN cc_start: 0.8659 (mp10) cc_final: 0.8417 (mp10)
REVERT: T   86 GLU cc_start: 0.8379 (tp30) cc_final: 0.7553 (tp30)
REVERT: q   22 GLU cc_start: 0.4297 (OUTLIER) cc_final: 0.3211 (tp30)
REVERT: q   50 MET cc_start: 0.1720 (ttm) cc_final: 0.1311 (tpp)
REVERT: p   84 GLN cc_start: 0.8355 (tt0) cc_final: 0.8099 (tt0)
REVERT: y   58 GLU cc_start: 0.5804 (OUTLIER) cc_final: 0.5245 (tm-30)
REVERT: 9    8 LYS cc_start: 0.8773 (tttp) cc_final: 0.8559 (tttm)
  outliers start: 128
  outliers final: 112
  residues processed: 657
  average time/residue: 0.5323
  time to fit residues: 572.9215
Evaluate side-chains
  673 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 119
    poor density    : 554
  time to evaluate  : 3.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  105 THR
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  223 SER
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   50 ILE
Chi-restraints excluded: chain E residue  105 PHE
Chi-restraints excluded: chain E residue  125 VAL
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  172 ARG
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   33 ASN
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain G residue  107 LYS
Chi-restraints excluded: chain G residue  119 SER
Chi-restraints excluded: chain G residue  159 ASP
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   24 LYS
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain H residue   62 VAL
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   66 ASP
Chi-restraints excluded: chain K residue   81 LYS
Chi-restraints excluded: chain J residue    2 VAL
Chi-restraints excluded: chain J residue   30 CYS
Chi-restraints excluded: chain J residue   80 ASP
Chi-restraints excluded: chain J residue  119 LYS
Chi-restraints excluded: chain M residue   85 VAL
Chi-restraints excluded: chain M residue   95 ILE
Chi-restraints excluded: chain M residue  102 THR
Chi-restraints excluded: chain M residue  117 LEU
Chi-restraints excluded: chain M residue  119 VAL
Chi-restraints excluded: chain M residue  130 THR
Chi-restraints excluded: chain L residue  160 LEU
Chi-restraints excluded: chain L residue  236 PHE
Chi-restraints excluded: chain L residue  248 TYR
Chi-restraints excluded: chain L residue  259 THR
Chi-restraints excluded: chain L residue  262 THR
Chi-restraints excluded: chain L residue  264 SER
Chi-restraints excluded: chain O residue   32 ASP
Chi-restraints excluded: chain O residue   50 THR
Chi-restraints excluded: chain O residue   55 THR
Chi-restraints excluded: chain O residue   59 SER
Chi-restraints excluded: chain O residue  126 ASP
Chi-restraints excluded: chain O residue  129 THR
Chi-restraints excluded: chain N residue   44 ASP
Chi-restraints excluded: chain N residue   73 ASP
Chi-restraints excluded: chain N residue   79 SER
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain N residue  183 LEU
Chi-restraints excluded: chain N residue  188 THR
Chi-restraints excluded: chain Q residue   24 THR
Chi-restraints excluded: chain Q residue   29 CYS
Chi-restraints excluded: chain Q residue   57 SER
Chi-restraints excluded: chain Q residue   60 ASP
Chi-restraints excluded: chain Q residue   67 LEU
Chi-restraints excluded: chain Q residue   76 SER
Chi-restraints excluded: chain Q residue   81 SER
Chi-restraints excluded: chain Q residue   90 GLU
Chi-restraints excluded: chain P residue   26 ASN
Chi-restraints excluded: chain P residue   45 THR
Chi-restraints excluded: chain P residue   69 SER
Chi-restraints excluded: chain P residue  114 SER
Chi-restraints excluded: chain P residue  130 GLU
Chi-restraints excluded: chain S residue    6 SER
Chi-restraints excluded: chain S residue   39 ASP
Chi-restraints excluded: chain S residue   50 VAL
Chi-restraints excluded: chain S residue   53 SER
Chi-restraints excluded: chain S residue   82 SER
Chi-restraints excluded: chain S residue  139 SER
Chi-restraints excluded: chain S residue  158 VAL
Chi-restraints excluded: chain S residue  181 THR
Chi-restraints excluded: chain S residue  217 MET
Chi-restraints excluded: chain R residue   19 LYS
Chi-restraints excluded: chain R residue   52 ASN
Chi-restraints excluded: chain R residue   72 CYS
Chi-restraints excluded: chain R residue   93 THR
Chi-restraints excluded: chain R residue  107 THR
Chi-restraints excluded: chain R residue  145 ILE
Chi-restraints excluded: chain R residue  154 LYS
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain T residue    5 VAL
Chi-restraints excluded: chain T residue   27 VAL
Chi-restraints excluded: chain T residue   35 VAL
Chi-restraints excluded: chain T residue   77 ASP
Chi-restraints excluded: chain T residue   80 ASP
Chi-restraints excluded: chain q residue   22 GLU
Chi-restraints excluded: chain q residue   39 ILE
Chi-restraints excluded: chain q residue   51 CYS
Chi-restraints excluded: chain q residue   55 VAL
Chi-restraints excluded: chain q residue   73 THR
Chi-restraints excluded: chain q residue   99 GLU
Chi-restraints excluded: chain p residue   37 GLN
Chi-restraints excluded: chain p residue   41 ARG
Chi-restraints excluded: chain p residue   98 VAL
Chi-restraints excluded: chain p residue  108 LEU
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   22 VAL
Chi-restraints excluded: chain I residue   24 THR
Chi-restraints excluded: chain I residue   32 ASP
Chi-restraints excluded: chain I residue   35 GLU
Chi-restraints excluded: chain I residue   63 VAL
Chi-restraints excluded: chain I residue   67 THR
Chi-restraints excluded: chain I residue   69 ASN
Chi-restraints excluded: chain I residue   87 ASP
Chi-restraints excluded: chain I residue  131 THR
Chi-restraints excluded: chain I residue  145 THR
Chi-restraints excluded: chain y residue   53 LYS
Chi-restraints excluded: chain y residue   58 GLU
Chi-restraints excluded: chain y residue   76 VAL
Chi-restraints excluded: chain y residue   77 THR
Chi-restraints excluded: chain y residue   82 GLU
Chi-restraints excluded: chain y residue  102 VAL
Chi-restraints excluded: chain y residue  157 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 452
   random chunks:
   chunk 396 optimal weight:    2.9990
   chunk 417 optimal weight:    1.9990
   chunk 380 optimal weight:    3.9990
   chunk 405 optimal weight:    3.9990
   chunk 244 optimal weight:    4.9990
   chunk 176 optimal weight:    0.5980
   chunk 318 optimal weight:   10.0000
   chunk 124 optimal weight:    5.9990
   chunk 366 optimal weight:    1.9990
   chunk 383 optimal weight:    1.9990
   chunk 404 optimal weight:   10.0000
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 197 ASN
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  81 ASN
S 110 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.082  56297  Z= 0.363
  Angle     :  0.698  17.043  81890  Z= 0.361
  Chirality :  0.040   0.388  10159
  Planarity :  0.006   0.134   5822
  Dihedral  : 23.109 179.884  23008
  Min Nonbonded Distance : 1.849

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 21.74 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.42 (0.14), residues: 3310
  helix:  1.05 (0.16), residues: 1075
  sheet: -1.00 (0.21), residues: 565
  loop : -0.85 (0.15), residues: 1670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP N 176 
 HIS   0.005   0.001   HIS R  22 
 PHE   0.020   0.001   PHE G 135 
 TYR   0.030   0.002   TYR C 103 
 ARG   0.007   0.000   ARG R  77 

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

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

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  693 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 130
    poor density    : 563
  time to evaluate  : 3.033 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS R 144 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: C   19 MET cc_start: 0.8790 (mtm) cc_final: 0.8563 (mtm)
REVERT: C   54 TYR cc_start: 0.9236 (m-80) cc_final: 0.8949 (m-80)
REVERT: C  121 TYR cc_start: 0.9135 (p90) cc_final: 0.8868 (p90)
REVERT: C  149 TYR cc_start: 0.9242 (m-80) cc_final: 0.8992 (m-80)
REVERT: E   95 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7964 (mm-30)
REVERT: D   96 TYR cc_start: 0.8873 (m-80) cc_final: 0.8641 (m-10)
REVERT: D  154 GLN cc_start: 0.9004 (tt0) cc_final: 0.8289 (tt0)
REVERT: D  155 LYS cc_start: 0.8452 (tptt) cc_final: 0.7861 (tptp)
REVERT: D  172 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7049 (ptt-90)
REVERT: G  165 ASN cc_start: 0.8891 (t0) cc_final: 0.8442 (t0)
REVERT: H   75 GLU cc_start: 0.5404 (OUTLIER) cc_final: 0.4575 (pp20)
REVERT: H   80 ARG cc_start: 0.8560 (ptt90) cc_final: 0.7146 (ptp90)
REVERT: M   82 ASP cc_start: 0.8075 (t70) cc_final: 0.7720 (t0)
REVERT: M  127 ASN cc_start: 0.8908 (p0) cc_final: 0.8408 (p0)
REVERT: L  248 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8364 (m-80)
REVERT: O   32 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8119 (p0)
REVERT: O  128 LYS cc_start: 0.8481 (tttt) cc_final: 0.8081 (ttmt)
REVERT: N   17 LYS cc_start: 0.8658 (mttm) cc_final: 0.8315 (mttt)
REVERT: Q   85 ARG cc_start: 0.5364 (tpt170) cc_final: 0.3620 (mtt-85)
REVERT: T   86 GLU cc_start: 0.8385 (tp30) cc_final: 0.7497 (tp30)
REVERT: T   99 LYS cc_start: 0.8695 (tttt) cc_final: 0.8344 (ttmt)
REVERT: q   22 GLU cc_start: 0.4263 (OUTLIER) cc_final: 0.3185 (tp30)
REVERT: q   50 MET cc_start: 0.1667 (ttm) cc_final: 0.1277 (tpp)
REVERT: p   59 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8253 (pp)
REVERT: p   84 GLN cc_start: 0.8385 (tt0) cc_final: 0.8114 (tt0)
REVERT: I  103 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7900 (pp20)
REVERT: y   58 GLU cc_start: 0.5753 (OUTLIER) cc_final: 0.5198 (tm-30)
  outliers start: 130
  outliers final: 116
  residues processed: 651
  average time/residue: 0.5160
  time to fit residues: 549.7508
Evaluate side-chains
  681 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 124
    poor density    : 557
  time to evaluate  : 2.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  105 THR
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  223 SER
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   50 ILE
Chi-restraints excluded: chain E residue  105 PHE
Chi-restraints excluded: chain E residue  125 VAL
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   94 LEU
Chi-restraints excluded: chain D residue  172 ARG
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   33 ASN
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain G residue  107 LYS
Chi-restraints excluded: chain G residue  119 SER
Chi-restraints excluded: chain G residue  159 ASP
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   24 LYS
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain H residue   40 CYS
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   62 VAL
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   66 ASP
Chi-restraints excluded: chain K residue   81 LYS
Chi-restraints excluded: chain J residue    2 VAL
Chi-restraints excluded: chain J residue   30 CYS
Chi-restraints excluded: chain J residue   80 ASP
Chi-restraints excluded: chain J residue  119 LYS
Chi-restraints excluded: chain M residue   85 VAL
Chi-restraints excluded: chain M residue   95 ILE
Chi-restraints excluded: chain M residue  102 THR
Chi-restraints excluded: chain M residue  119 VAL
Chi-restraints excluded: chain M residue  130 THR
Chi-restraints excluded: chain L residue  160 LEU
Chi-restraints excluded: chain L residue  162 ILE
Chi-restraints excluded: chain L residue  236 PHE
Chi-restraints excluded: chain L residue  248 TYR
Chi-restraints excluded: chain L residue  259 THR
Chi-restraints excluded: chain L residue  262 THR
Chi-restraints excluded: chain L residue  264 SER
Chi-restraints excluded: chain O residue   32 ASP
Chi-restraints excluded: chain O residue   40 ASN
Chi-restraints excluded: chain O residue   50 THR
Chi-restraints excluded: chain O residue   55 THR
Chi-restraints excluded: chain O residue   59 SER
Chi-restraints excluded: chain O residue  126 ASP
Chi-restraints excluded: chain O residue  129 THR
Chi-restraints excluded: chain N residue   44 ASP
Chi-restraints excluded: chain N residue   79 SER
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain N residue  183 LEU
Chi-restraints excluded: chain N residue  188 THR
Chi-restraints excluded: chain Q residue   24 THR
Chi-restraints excluded: chain Q residue   26 CYS
Chi-restraints excluded: chain Q residue   29 CYS
Chi-restraints excluded: chain Q residue   57 SER
Chi-restraints excluded: chain Q residue   60 ASP
Chi-restraints excluded: chain Q residue   67 LEU
Chi-restraints excluded: chain Q residue   76 SER
Chi-restraints excluded: chain Q residue   81 SER
Chi-restraints excluded: chain Q residue   90 GLU
Chi-restraints excluded: chain P residue   26 ASN
Chi-restraints excluded: chain P residue   45 THR
Chi-restraints excluded: chain P residue   69 SER
Chi-restraints excluded: chain P residue  114 SER
Chi-restraints excluded: chain P residue  130 GLU
Chi-restraints excluded: chain S residue    6 SER
Chi-restraints excluded: chain S residue   39 ASP
Chi-restraints excluded: chain S residue   50 VAL
Chi-restraints excluded: chain S residue   82 SER
Chi-restraints excluded: chain S residue  139 SER
Chi-restraints excluded: chain S residue  158 VAL
Chi-restraints excluded: chain S residue  181 THR
Chi-restraints excluded: chain S residue  217 MET
Chi-restraints excluded: chain R residue   19 LYS
Chi-restraints excluded: chain R residue   52 ASN
Chi-restraints excluded: chain R residue   72 CYS
Chi-restraints excluded: chain R residue  107 THR
Chi-restraints excluded: chain R residue  145 ILE
Chi-restraints excluded: chain R residue  154 LYS
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain T residue    5 VAL
Chi-restraints excluded: chain T residue   27 VAL
Chi-restraints excluded: chain T residue   35 VAL
Chi-restraints excluded: chain T residue   77 ASP
Chi-restraints excluded: chain T residue   80 ASP
Chi-restraints excluded: chain q residue   22 GLU
Chi-restraints excluded: chain q residue   39 ILE
Chi-restraints excluded: chain q residue   51 CYS
Chi-restraints excluded: chain q residue   55 VAL
Chi-restraints excluded: chain q residue   73 THR
Chi-restraints excluded: chain q residue   99 GLU
Chi-restraints excluded: chain p residue   37 GLN
Chi-restraints excluded: chain p residue   41 ARG
Chi-restraints excluded: chain p residue   59 LEU
Chi-restraints excluded: chain p residue   98 VAL
Chi-restraints excluded: chain p residue  108 LEU
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   22 VAL
Chi-restraints excluded: chain I residue   24 THR
Chi-restraints excluded: chain I residue   32 ASP
Chi-restraints excluded: chain I residue   33 VAL
Chi-restraints excluded: chain I residue   35 GLU
Chi-restraints excluded: chain I residue   53 ILE
Chi-restraints excluded: chain I residue   63 VAL
Chi-restraints excluded: chain I residue   67 THR
Chi-restraints excluded: chain I residue   69 ASN
Chi-restraints excluded: chain I residue   87 ASP
Chi-restraints excluded: chain I residue  103 GLU
Chi-restraints excluded: chain I residue  131 THR
Chi-restraints excluded: chain I residue  145 THR
Chi-restraints excluded: chain y residue   53 LYS
Chi-restraints excluded: chain y residue   58 GLU
Chi-restraints excluded: chain y residue   76 VAL
Chi-restraints excluded: chain y residue   77 THR
Chi-restraints excluded: chain y residue   82 GLU
Chi-restraints excluded: chain y residue  102 VAL
Chi-restraints excluded: chain y residue  157 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 452
   random chunks:
   chunk 266 optimal weight:    8.9990
   chunk 429 optimal weight:    2.9990
   chunk 262 optimal weight:    0.9980
   chunk 203 optimal weight:    3.9990
   chunk 298 optimal weight:    5.9990
   chunk 450 optimal weight:   30.0000
   chunk 414 optimal weight:    3.9990
   chunk 358 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 276 optimal weight:    0.0970
   chunk 219 optimal weight:    0.9980
   overall best weight:    1.1780

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

Flipped N/Q/H residues before XYZ refinement:
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 197 ASN
B   5 GLN
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 113 GLN
** O  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  81 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.1915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  56297  Z= 0.237
  Angle     :  0.656  17.153  81890  Z= 0.342
  Chirality :  0.037   0.353  10159
  Planarity :  0.006   0.129   5822
  Dihedral  : 23.050 179.582  23008
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 22.69 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.25 (0.14), residues: 3310
  helix:  1.19 (0.16), residues: 1089
  sheet: -0.91 (0.22), residues: 563
  loop : -0.77 (0.15), residues: 1658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP N 176 
 HIS   0.005   0.001   HIS R  22 
 PHE   0.017   0.001   PHE G 135 
 TYR   0.028   0.001   TYR C 103 
 ARG   0.007   0.000   ARG R  77 

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

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

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6620 Ramachandran restraints generated.
    3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  682 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 113
    poor density    : 569
  time to evaluate  : 2.996 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
TARDY: cannot create tardy model for: "LYS R 144 " (corrupted residue). Skipping it.
   revert: symmetry clash
REVERT: C   19 MET cc_start: 0.8773 (mtm) cc_final: 0.8546 (mtm)
REVERT: C   54 TYR cc_start: 0.9213 (m-80) cc_final: 0.8955 (m-80)
REVERT: C  121 TYR cc_start: 0.9134 (p90) cc_final: 0.8903 (p90)
REVERT: C  149 TYR cc_start: 0.9216 (m-80) cc_final: 0.8939 (m-80)
REVERT: E   95 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7920 (mm-30)
REVERT: D  154 GLN cc_start: 0.8958 (tt0) cc_final: 0.8224 (tt0)
REVERT: D  172 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7020 (ptt-90)
REVERT: G   57 ARG cc_start: 0.7718 (ttt90) cc_final: 0.7423 (ttt90)
REVERT: G  165 ASN cc_start: 0.8838 (t0) cc_final: 0.8393 (t0)
REVERT: H   75 GLU cc_start: 0.5605 (OUTLIER) cc_final: 0.4844 (pp20)
REVERT: H   80 ARG cc_start: 0.8624 (ptt90) cc_final: 0.7184 (ptp90)
REVERT: K   41 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8705 (mtpp)
REVERT: M   82 ASP cc_start: 0.8021 (t70) cc_final: 0.7672 (t0)
REVERT: M  127 ASN cc_start: 0.8882 (p0) cc_final: 0.8398 (p0)
REVERT: L  248 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.8321 (m-80)
REVERT: O   32 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8129 (p0)
REVERT: O  128 LYS cc_start: 0.8448 (tttt) cc_final: 0.8065 (ttmt)
REVERT: O  211 PHE cc_start: 0.8915 (m-80) cc_final: 0.8498 (m-80)
REVERT: N   17 LYS cc_start: 0.8638 (mttm) cc_final: 0.8287 (mttt)
REVERT: Q   85 ARG cc_start: 0.5310 (tpt170) cc_final: 0.3599 (mtt-85)
REVERT: P   50 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7937 (ttmm)
REVERT: T   86 GLU cc_start: 0.8362 (tp30) cc_final: 0.7485 (tp30)
REVERT: T   99 LYS cc_start: 0.8723 (tttt) cc_final: 0.8352 (ttmt)
REVERT: q   50 MET cc_start: 0.1729 (ttm) cc_final: 0.1313 (tpp)
REVERT: p   59 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8248 (pp)
REVERT: p   84 GLN cc_start: 0.8394 (tt0) cc_final: 0.8125 (tt0)
REVERT: y   58 GLU cc_start: 0.5739 (OUTLIER) cc_final: 0.5188 (tm-30)
  outliers start: 113
  outliers final: 104
  residues processed: 648
  average time/residue: 0.5266
  time to fit residues: 557.1279
Evaluate side-chains
  668 residues out of total 2929 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 110
    poor density    : 558
  time to evaluate  : 2.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  105 THR
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  223 SER
Chi-restraints excluded: chain C residue  248 ILE
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain E residue   36 LEU
Chi-restraints excluded: chain E residue   50 ILE
Chi-restraints excluded: chain E residue  105 PHE
Chi-restraints excluded: chain E residue  125 VAL
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue  172 ARG
Chi-restraints excluded: chain G residue   30 LEU
Chi-restraints excluded: chain G residue   33 ASN
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain G residue  107 LYS
Chi-restraints excluded: chain G residue  119 SER
Chi-restraints excluded: chain G residue  159 ASP
Chi-restraints excluded: chain F residue   12 VAL
Chi-restraints excluded: chain F residue   24 LYS
Chi-restraints excluded: chain F residue   29 THR
Chi-restraints excluded: chain H residue   40 CYS
Chi-restraints excluded: chain H residue   57 VAL
Chi-restraints excluded: chain H residue   62 VAL
Chi-restraints excluded: chain H residue   75 GLU
Chi-restraints excluded: chain K residue   52 THR
Chi-restraints excluded: chain K residue   66 ASP
Chi-restraints excluded: chain K residue   81 LYS
Chi-restraints excluded: chain J residue    2 VAL
Chi-restraints excluded: chain J residue   30 CYS
Chi-restraints excluded: chain J residue   80 ASP
Chi-restraints excluded: chain J residue  119 LYS
Chi-restraints excluded: chain M residue   85 VAL
Chi-restraints excluded: chain M residue   95 ILE
Chi-restraints excluded: chain M residue  102 THR
Chi-restraints excluded: chain M residue  117 LEU
Chi-restraints excluded: chain M residue  119 VAL
Chi-restraints excluded: chain M residue  130 THR
Chi-restraints excluded: chain L residue  160 LEU
Chi-restraints excluded: chain L residue  236 PHE
Chi-restraints excluded: chain L residue  248 TYR
Chi-restraints excluded: chain L residue  259 THR
Chi-restraints excluded: chain L residue  264 SER
Chi-restraints excluded: chain O residue   32 ASP
Chi-restraints excluded: chain O residue   50 THR
Chi-restraints excluded: chain O residue   55 THR
Chi-restraints excluded: chain O residue   59 SER
Chi-restraints excluded: chain O residue  126 ASP
Chi-restraints excluded: chain O residue  129 THR
Chi-restraints excluded: chain N residue   44 ASP
Chi-restraints excluded: chain N residue   79 SER
Chi-restraints excluded: chain N residue  104 THR
Chi-restraints excluded: chain N residue  183 LEU
Chi-restraints excluded: chain N residue  188 THR
Chi-restraints excluded: chain Q residue   24 THR
Chi-restraints excluded: chain Q residue   29 CYS
Chi-restraints excluded: chain Q residue   57 SER
Chi-restraints excluded: chain Q residue   67 LEU
Chi-restraints excluded: chain Q residue   76 SER
Chi-restraints excluded: chain Q residue   81 SER
Chi-restraints excluded: chain Q residue   90 GLU
Chi-restraints excluded: chain P residue   26 ASN
Chi-restraints excluded: chain P residue   45 THR
Chi-restraints excluded: chain P residue   69 SER
Chi-restraints excluded: chain P residue  114 SER
Chi-restraints excluded: chain P residue  130 GLU
Chi-restraints excluded: chain S residue    6 SER
Chi-restraints excluded: chain S residue   39 ASP
Chi-restraints excluded: chain S residue   50 VAL
Chi-restraints excluded: chain S residue  139 SER
Chi-restraints excluded: chain S residue  158 VAL
Chi-restraints excluded: chain S residue  181 THR
Chi-restraints excluded: chain S residue  217 MET
Chi-restraints excluded: chain R residue   52 ASN
Chi-restraints excluded: chain R residue   62 VAL
Chi-restraints excluded: chain R residue   72 CYS
Chi-restraints excluded: chain R residue  145 ILE
Chi-restraints excluded: chain R residue  154 LYS
Chi-restraints excluded: chain R residue  182 CYS
Chi-restraints excluded: chain T residue   27 VAL
Chi-restraints excluded: chain T residue   35 VAL
Chi-restraints excluded: chain T residue   80 ASP
Chi-restraints excluded: chain q residue   39 ILE
Chi-restraints excluded: chain q residue   51 CYS
Chi-restraints excluded: chain q residue   55 VAL
Chi-restraints excluded: chain q residue   99 GLU
Chi-restraints excluded: chain p residue   37 GLN
Chi-restraints excluded: chain p residue   41 ARG
Chi-restraints excluded: chain p residue   59 LEU
Chi-restraints excluded: chain p residue   98 VAL
Chi-restraints excluded: chain p residue  108 LEU
Chi-restraints excluded: chain I residue   14 SER
Chi-restraints excluded: chain I residue   22 VAL
Chi-restraints excluded: chain I residue   24 THR
Chi-restraints excluded: chain I residue   32 ASP
Chi-restraints excluded: chain I residue   35 GLU
Chi-restraints excluded: chain I residue   63 VAL
Chi-restraints excluded: chain I residue   67 THR
Chi-restraints excluded: chain I residue   69 ASN
Chi-restraints excluded: chain I residue   87 ASP
Chi-restraints excluded: chain I residue  131 THR
Chi-restraints excluded: chain I residue  145 THR
Chi-restraints excluded: chain y residue   53 LYS
Chi-restraints excluded: chain y residue   58 GLU
Chi-restraints excluded: chain y residue   76 VAL
Chi-restraints excluded: chain y residue   77 THR
Chi-restraints excluded: chain y residue   82 GLU
Chi-restraints excluded: chain y residue  102 VAL
Chi-restraints excluded: chain y residue  157 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 452
   random chunks:
   chunk 284 optimal weight:    0.7980
   chunk 381 optimal weight:    2.9990
   chunk 109 optimal weight:    0.6980
   chunk 330 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 359 optimal weight:    3.9990
   chunk 150 optimal weight:    3.9990
   chunk 368 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 132 GLN
G  68 GLN
** O  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  81 ASN
T  85 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.127658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.082779 restraints weight = 82328.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 1.43
r_work: 0.2756 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2651 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  56297  Z= 0.187
  Angle     :  0.646  17.337  81890  Z= 0.338
  Chirality :  0.036   0.342  10159
  Planarity :  0.006   0.128   5822
  Dihedral  : 23.048 179.741  23008
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 23.02 %
    Favored  : 72.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.16 (0.15), residues: 3310
  helix:  1.26 (0.16), residues: 1089
  sheet: -0.84 (0.22), residues: 565
  loop : -0.71 (0.15), residues: 1656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP N 176 
 HIS   0.004   0.001   HIS R  22 
 PHE   0.022   0.001   PHE G 135 
 TYR   0.032   0.001   TYR C 103 
 ARG   0.007   0.000   ARG F  40 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12322.16 seconds
wall clock time: 219 minutes 49.56 seconds (13189.56 seconds total)