Starting phenix.real_space_refine
on Sat Feb 17 14:30:55 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj6_21690/02_2024/6wj6_21690_neut_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj6_21690/02_2024/6wj6_21690.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.58
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj6_21690/02_2024/6wj6_21690.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj6_21690/02_2024/6wj6_21690.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj6_21690/02_2024/6wj6_21690_neut_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wj6_21690/02_2024/6wj6_21690_neut_updated.pdb"
  }
  resolution = 2.58
  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=   0.008
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: 8
    Type Number    sf(0)   Gaussians
     Fe      2      7.16       5
     P       4      5.49       5
     Mg     35      5.21       5
     S      69      5.16       5
     Cl      1      4.86       5
     C   13000      2.51       5
     N    2603      2.21       5
     O    3170      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE   17": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR   29": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   33": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   52": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP   59": "OD1" <-> "OD2"
    Residue "A GLU   65": "OE1" <-> "OE2"
    Residue "A TYR   73": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE   93": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  103": "OD1" <-> "OD2"
    Residue "A GLU  104": "OE1" <-> "OE2"
    Residue "A TYR  112": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  117": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  119": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  124": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  126": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  136": "NH1" <-> "NH2"
    Residue "A TYR  147": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  158": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  186": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  254": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  255": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  285": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  295": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  300": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  302": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ARG  312": "NH1" <-> "NH2"
    Residue "B GLU   41": "OE1" <-> "OE2"
    Residue "B ASP   46": "OD1" <-> "OD2"
    Residue "B ASP   49": "OD1" <-> "OD2"
    Residue "B PHE   90": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  123": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  151": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  215": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  226": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  246": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  258": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  268": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  279": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  311": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ASP  313": "OD1" <-> "OD2"
    Residue "B PHE  325": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B ARG  352": "NH1" <-> "NH2"
    Residue "B PHE  363": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  364": "OE1" <-> "OE2"
    Residue "B ARG  378": "NH1" <-> "NH2"
    Residue "B ARG  385": "NH1" <-> "NH2"
    Residue "B PHE  401": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  411": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B GLU  435": "OE1" <-> "OE2"
    Residue "B PHE  451": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  462": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B PHE  475": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   49": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   57": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP   94": "OD1" <-> "OD2"
    Residue "C PHE   98": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU  129": "OE1" <-> "OE2"
    Residue "C TYR  130": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  133": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  173": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  174": "OD1" <-> "OD2"
    Residue "C ASP  182": "OD1" <-> "OD2"
    Residue "C PHE  197": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  205": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  279": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  284": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR  289": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  310": "NH1" <-> "NH2"
    Residue "C GLU  341": "OE1" <-> "OE2"
    Residue "C ARG  368": "NH1" <-> "NH2"
    Residue "C TYR  382": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  423": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE  424": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG  436": "NH1" <-> "NH2"
    Residue "C PHE  442": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ASP  447": "OD1" <-> "OD2"
    Residue "C ARG  448": "NH1" <-> "NH2"
    Residue "C GLU  449": "OE1" <-> "OE2"
    Residue "D ARG   12": "NH1" <-> "NH2"
    Residue "D PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP   19": "OD1" <-> "OD2"
    Residue "D PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   42": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   54": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   59": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU   69": "OE1" <-> "OE2"
    Residue "D ASP   83": "OD1" <-> "OD2"
    Residue "D PHE  125": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  130": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  131": "OE1" <-> "OE2"
    Residue "D TYR  141": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  153": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  168": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  181": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  188": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  219": "OE1" <-> "OE2"
    Residue "D GLU  224": "OE1" <-> "OE2"
    Residue "D GLU  227": "OE1" <-> "OE2"
    Residue "D PHE  232": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  235": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  242": "OE1" <-> "OE2"
    Residue "D PHE  252": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  257": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG  294": "NH1" <-> "NH2"
    Residue "D GLU  310": "OE1" <-> "OE2"
    Residue "D PHE  311": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE  314": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU  337": "OE1" <-> "OE2"
    Residue "D GLU  343": "OE1" <-> "OE2"
    Residue "E PHE   31": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E PHE   47": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG   60": "NH1" <-> "NH2"
    Residue "E GLU   62": "OE1" <-> "OE2"
    Residue "E GLU   68": "OE1" <-> "OE2"
    Residue "F PHE   31": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ARG    4": "NH1" <-> "NH2"
    Residue "H ARG    6": "NH1" <-> "NH2"
    Residue "H GLU   17": "OE1" <-> "OE2"
    Residue "H PHE   34": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR   49": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ASP   61": "OD1" <-> "OD2"
    Residue "I TYR    9": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I PHE   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "I ASP   27": "OD1" <-> "OD2"
    Residue "I ARG   30": "NH1" <-> "NH2"
    Residue "K PHE   30": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K PHE   31": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L ARG    9": "NH1" <-> "NH2"
    Residue "L GLU   13": "OE1" <-> "OE2"
    Residue "L ARG   16": "NH1" <-> "NH2"
    Residue "L PHE   33": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L TYR   36": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "L PHE   37": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M PHE    8": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "M PHE   26": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "T PHE   19": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "X PHE   29": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 18884
  Number of models: 1
  Model: ""
    Number of chains: 32
    Chain: "A"
      Number of atoms: 2357
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2357
          Classifications: {'peptide': 302}
          Link IDs: {'PTRANS': 13, 'TRANS': 288}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 478, 3751
          Classifications: {'peptide': 478}
          Link IDs: {'PTRANS': 26, 'TRANS': 451}
    Chain: "C"
      Number of atoms: 3259
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3259
          Classifications: {'peptide': 415}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 392}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 342, 2734
          Classifications: {'peptide': 342}
          Link IDs: {'PTRANS': 16, 'TRANS': 325}
    Chain: "E"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 603
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 4, 'TRANS': 67}
    Chain: "F"
      Number of atoms: 255
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 255
          Classifications: {'peptide': 32}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
    Chain: "H"
      Number of atoms: 494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 494
          Classifications: {'peptide': 63}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 59}
    Chain: "I"
      Number of atoms: 276
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 276
          Classifications: {'peptide': 35}
          Link IDs: {'PTRANS': 2, 'TRANS': 32}
    Chain: "K"
      Number of atoms: 278
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 278
          Classifications: {'peptide': 35}
          Link IDs: {'PTRANS': 4, 'TRANS': 30}
    Chain: "L"
      Number of atoms: 252
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 252
          Classifications: {'peptide': 31}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 29}
    Chain: "M"
      Number of atoms: 226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 226
          Classifications: {'peptide': 29}
          Link IDs: {'PTRANS': 1, 'TRANS': 27}
    Chain: "T"
      Number of atoms: 231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 231
          Classifications: {'peptide': 29}
          Link IDs: {'PTRANS': 2, 'TRANS': 26}
    Chain: "X"
      Number of atoms: 262
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 262
          Classifications: {'peptide': 35}
          Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 32}
    Chain: "A"
      Number of atoms: 392
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 392
          Unusual residues: {'BCR': 1, 'CLA': 3, 'FE2': 1, 'PHO': 1, 'PL9': 1, 'SQD': 2}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 71
          Unresolved non-hydrogen angles: 84
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 1301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 1301
          Unusual residues: {'BCR': 3, 'CLA': 16, 'LMG': 1, 'LMT': 2, 'SQD': 1}
          Classifications: {'undetermined': 23}
          Link IDs: {None: 22}
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 1102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 1102
          Unusual residues: {'BCR': 3, 'CLA': 13, 'DGD': 1, 'LMG': 1, 'SQD': 1}
          Classifications: {'undetermined': 19}
          Link IDs: {None: 18}
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'CLA:plan-5': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 554
          Unusual residues: {' CL': 1, 'BCR': 1, 'BCT': 1, 'CLA': 3, 'LHG': 3, 'LMG': 1, 'PHO': 1, 'PL9': 1}
          Classifications: {'undetermined': 12}
          Link IDs: {None: 11}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 7
    Chain: "E"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "H"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 62
          Unusual residues: {'DGD': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "I"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "L"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 49
          Unusual residues: {'LHG': 1}
          Classifications: {'undetermined': 1}
    Chain: "M"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "T"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 103
          Unusual residues: {'SQD': 2}
          Classifications: {'peptide': 1, 'undetermined': 2}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "X"
      Number of atoms: 82
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 82
          Unusual residues: {'BCR': 1, 'SQD': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
    Chain: "A"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 54
          Classifications: {'water': 54}
          Link IDs: {None: 53}
    Chain: "B"
      Number of atoms: 62
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 62
          Classifications: {'water': 62}
          Link IDs: {None: 61}
    Chain: "C"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 30
          Classifications: {'water': 30}
          Link IDs: {None: 29}
    Chain: "D"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 46
          Classifications: {'water': 46}
          Link IDs: {None: 45}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "T"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "X"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 10.71, per 1000 atoms: 0.57
  Number of scatterers: 18884
  At special positions: 0
  Unit cell: (108.675, 133.481, 107.494, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Fe      2     26.01
     Cl      1     17.00
     S      69     16.00
     P       4     15.00
     Mg     35     11.99
     O    3170      8.00
     N    2603      7.00
     C   13000      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=36, symmetry=0
  Number of additional bonds: simple=36, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 8.68
  Conformation dependent library (CDL) restraints added in 2.6 seconds
  

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3414

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      89 helices and 6 sheets defined
      59.2% alpha, 1.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 21
      removed outlier: 3.624A  pdb=" N   TRP A  20 " --> pdb=" O   GLN A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 54
      removed outlier: 3.877A  pdb=" N   LEU A  36 " --> pdb=" O   TRP A  32 " (cutoff:3.500A)
      Proline residue:  A  39  - end of helix
    Processing helix  chain 'A' and resid 71 through 73
      No H-bonds generated for 'chain 'A' and resid 71 through 73'
    Processing helix  chain 'A' and resid 96 through 98
      No H-bonds generated for 'chain 'A' and resid 96 through 98'
    Processing helix  chain 'A' and resid 102 through 107
    Processing helix  chain 'A' and resid 110 through 137
      removed outlier: 3.514A  pdb=" N   TRP A 131 " --> pdb=" O   MET A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 158
      removed outlier: 4.131A  pdb=" N   ALA A 149 " --> pdb=" O   VAL A 145 " (cutoff:3.500A)
      Proline residue:  A 150  - end of helix
      removed outlier: 3.588A  pdb=" N   VAL A 157 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 165
    Processing helix  chain 'A' and resid 168 through 170
      No H-bonds generated for 'chain 'A' and resid 168 through 170'
    Processing helix  chain 'A' and resid 176 through 190
    Processing helix  chain 'A' and resid 192 through 194
      No H-bonds generated for 'chain 'A' and resid 192 through 194'
    Processing helix  chain 'A' and resid 196 through 221
    Processing helix  chain 'A' and resid 250 through 258
      removed outlier: 3.637A  pdb=" N   ARG A 257 " --> pdb=" O   GLY A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 295
      Proline residue:  A 279  - end of helix
      removed outlier: 3.994A  pdb=" N   PHE A 295 " --> pdb=" O   SER A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 330
      removed outlier: 3.513A  pdb=" N   LEU A 321 " --> pdb=" O   TRP A 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 12
      removed outlier: 3.689A  pdb=" N   VAL B   8 " --> pdb=" O   TRP B   5 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   HIS B   9 " --> pdb=" O   TYR B   6 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   VAL B  11 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL B  12 " --> pdb=" O   HIS B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 44
    Processing helix  chain 'B' and resid 55 through 58
    Processing helix  chain 'B' and resid 63 through 69
      removed outlier: 4.008A  pdb=" N   LEU B  69 " --> pdb=" O   PHE B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 116
    Processing helix  chain 'B' and resid 135 through 156
    Processing helix  chain 'B' and resid 187 through 190
    Processing helix  chain 'B' and resid 195 through 218
      removed outlier: 3.721A  pdb=" N   VAL B 199 " --> pdb=" O   PRO B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 228
    Processing helix  chain 'B' and resid 234 through 258
      removed outlier: 3.704A  pdb=" N   SER B 239 " --> pdb=" O   THR B 236 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   SER B 241 " --> pdb=" O   LEU B 238 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ILE B 242 " --> pdb=" O   SER B 239 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE B 246 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   PHE B 247 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA B 249 " --> pdb=" O   PHE B 246 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL B 252 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ALA B 253 " --> pdb=" O   PHE B 250 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   THR B 255 " --> pdb=" O   VAL B 252 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   MET B 256 " --> pdb=" O   ALA B 253 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   TYR B 258 " --> pdb=" O   THR B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 268
      No H-bonds generated for 'chain 'B' and resid 265 through 268'
    Processing helix  chain 'B' and resid 272 through 276
    Processing helix  chain 'B' and resid 279 through 294
      removed outlier: 3.643A  pdb=" N   GLU B 283 " --> pdb=" O   TYR B 279 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   GLU B 294 " --> pdb=" O   SER B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 302
      removed outlier: 3.524A  pdb=" N   TRP B 302 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 298 through 302'
    Processing helix  chain 'B' and resid 307 through 312
    Processing helix  chain 'B' and resid 315 through 317
      No H-bonds generated for 'chain 'B' and resid 315 through 317'
    Processing helix  chain 'B' and resid 330 through 332
      No H-bonds generated for 'chain 'B' and resid 330 through 332'
    Processing helix  chain 'B' and resid 414 through 426
      removed outlier: 4.052A  pdb=" N   LEU B 426 " --> pdb=" O   ARG B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 474
      removed outlier: 3.803A  pdb=" N   PHE B 464 " --> pdb=" O   LEU B 460 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 22 through 29
      removed outlier: 6.015A  pdb=" N   ASN C  26 " --> pdb=" O   TRP C  23 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 60
      removed outlier: 3.773A  pdb=" N   THR C  55 " --> pdb=" O   ALA C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 68 through 71
      removed outlier: 3.696A  pdb=" N   GLN C  71 " --> pdb=" O   MET C  68 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 68 through 71'
    Processing helix  chain 'C' and resid 76 through 81
    Processing helix  chain 'C' and resid 96 through 121
      removed outlier: 3.603A  pdb=" N   LEU C 106 " --> pdb=" O   GLY C 102 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   SER C 108 " --> pdb=" O   LEU C 104 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 141 through 168
      removed outlier: 3.614A  pdb=" N   LEU C 154 " --> pdb=" O   TYR C 150 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU C 162 " --> pdb=" O   GLY C 158 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 193 through 196
      No H-bonds generated for 'chain 'C' and resid 193 through 196'
    Processing helix  chain 'C' and resid 199 through 201
      No H-bonds generated for 'chain 'C' and resid 199 through 201'
    Processing helix  chain 'C' and resid 217 through 239
      removed outlier: 3.699A  pdb=" N   ILE C 232 " --> pdb=" O   GLY C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 245 through 250
    Processing helix  chain 'C' and resid 255 through 279
      removed outlier: 3.672A  pdb=" N   TRP C 278 " --> pdb=" O   SER C 274 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 289
      No H-bonds generated for 'chain 'C' and resid 286 through 289'
    Processing helix  chain 'C' and resid 293 through 308
      removed outlier: 3.826A  pdb=" N   SER C 297 " --> pdb=" O   GLY C 293 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 341 through 345
      removed outlier: 3.995A  pdb=" N   ARG C 344 " --> pdb=" O   GLU C 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 351 through 354
      No H-bonds generated for 'chain 'C' and resid 351 through 354'
    Processing helix  chain 'C' and resid 366 through 369
      No H-bonds generated for 'chain 'C' and resid 366 through 369'
    Processing helix  chain 'C' and resid 373 through 385
      removed outlier: 3.904A  pdb=" N   MET C 383 " --> pdb=" O   ALA C 379 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   THR C 384 " --> pdb=" O   ALA C 380 " (cutoff:3.500A)
      removed outlier: 5.272A  pdb=" N   HIS C 385 " --> pdb=" O   GLU C 381 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 409 through 440
    Processing helix  chain 'C' and resid 452 through 455
      No H-bonds generated for 'chain 'C' and resid 452 through 455'
    Processing helix  chain 'D' and resid 14 through 22
    Processing helix  chain 'D' and resid 33 through 53
      removed outlier: 3.570A  pdb=" N   LEU D  37 " --> pdb=" O   GLY D  34 " (cutoff:3.500A)
      removed outlier: 5.456A  pdb=" N   PHE D  38 " --> pdb=" O   LEU D  35 " (cutoff:3.500A)
      Proline residue:  D  39  - end of helix
      removed outlier: 3.877A  pdb=" N   PHE D  42 " --> pdb=" O   PRO D  39 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   MET D  43 " --> pdb=" O   CYS D  40 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA D  44 " --> pdb=" O   ALA D  41 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LEU D  45 " --> pdb=" O   PHE D  42 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLY D  46 " --> pdb=" O   MET D  43 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY D  47 " --> pdb=" O   ALA D  44 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU D  49 " --> pdb=" O   GLY D  46 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   THR D  50 " --> pdb=" O   GLY D  47 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR D  53 " --> pdb=" O   THR D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 85
      No H-bonds generated for 'chain 'D' and resid 83 through 85'
    Processing helix  chain 'D' and resid 101 through 106
    Processing helix  chain 'D' and resid 109 through 136
      removed outlier: 3.512A  pdb=" N   PHE D 113 " --> pdb=" O   GLY D 109 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 141 through 157
      removed outlier: 4.403A  pdb=" N   GLY D 148 " --> pdb=" O   ILE D 144 " (cutoff:3.500A)
      Proline residue:  D 149  - end of helix
    Processing helix  chain 'D' and resid 159 through 163
    Processing helix  chain 'D' and resid 167 through 169
      No H-bonds generated for 'chain 'D' and resid 167 through 169'
    Processing helix  chain 'D' and resid 175 through 187
    Processing helix  chain 'D' and resid 191 through 193
      No H-bonds generated for 'chain 'D' and resid 191 through 193'
    Processing helix  chain 'D' and resid 195 through 220
    Processing helix  chain 'D' and resid 231 through 233
      No H-bonds generated for 'chain 'D' and resid 231 through 233'
    Processing helix  chain 'D' and resid 246 through 256
    Processing helix  chain 'D' and resid 264 through 291
      Proline residue:  D 275  - end of helix
      removed outlier: 3.780A  pdb=" N   LEU D 291 " --> pdb=" O   VAL D 287 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 299 through 307
    Processing helix  chain 'D' and resid 314 through 333
      Proline residue:  D 331  - end of helix
    Processing helix  chain 'D' and resid 335 through 337
      No H-bonds generated for 'chain 'D' and resid 335 through 337'
    Processing helix  chain 'D' and resid 343 through 345
      No H-bonds generated for 'chain 'D' and resid 343 through 345'
    Processing helix  chain 'D' and resid 349 through 351
      No H-bonds generated for 'chain 'D' and resid 349 through 351'
    Processing helix  chain 'E' and resid 11 through 14
      No H-bonds generated for 'chain 'E' and resid 11 through 14'
    Processing helix  chain 'E' and resid 18 through 22
      removed outlier: 4.041A  pdb=" N   ILE E  22 " --> pdb=" O   ARG E  18 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 18 through 22'
    Processing helix  chain 'E' and resid 27 through 39
      removed outlier: 3.520A  pdb=" N   GLY E  34 " --> pdb=" O   LEU E  30 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL E  38 " --> pdb=" O   GLY E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 42 through 47
    Processing helix  chain 'E' and resid 72 through 79
    Processing helix  chain 'F' and resid 17 through 41
      removed outlier: 4.059A  pdb=" N   LEU F  25 " --> pdb=" O   ALA F  21 " (cutoff:3.500A)
      Proline residue:  F  28  - end of helix
      removed outlier: 4.266A  pdb=" N   PHE F  41 " --> pdb=" O   ALA F  37 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 6 through 10
    Processing helix  chain 'H' and resid 12 through 15
    Processing helix  chain 'H' and resid 28 through 49
    Processing helix  chain 'I' and resid 3 through 24
      removed outlier: 3.688A  pdb=" N   SER I  17 " --> pdb=" O   GLY I  13 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 27 through 29
      No H-bonds generated for 'chain 'I' and resid 27 through 29'
    Processing helix  chain 'K' and resid 12 through 42
      removed outlier: 3.510A  pdb=" N   GLN K  15 " --> pdb=" O   GLU K  12 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   ILE K  16 " --> pdb=" O   ALA K  13 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASP K  18 " --> pdb=" O   GLN K  15 " (cutoff:3.500A)
      Proline residue:  K  19  - end of helix
      removed outlier: 3.568A  pdb=" N   ASP K  22 " --> pdb=" O   PRO K  19 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU K  24 " --> pdb=" O   VAL K  21 " (cutoff:3.500A)
      Proline residue:  K  25  - end of helix
      Proline residue:  K  28  - end of helix
      removed outlier: 4.002A  pdb=" N   PHE K  31 " --> pdb=" O   PRO K  28 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ALA K  33 " --> pdb=" O   PHE K  30 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU K  34 " --> pdb=" O   PHE K  31 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ALA K  35 " --> pdb=" O   LEU K  32 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   PHE K  36 " --> pdb=" O   ALA K  33 " (cutoff:3.500A)
      removed outlier: 5.493A  pdb=" N   GLN K  39 " --> pdb=" O   PHE K  36 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ALA K  40 " --> pdb=" O   VAL K  37 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ALA K  41 " --> pdb=" O   TRP K  38 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL K  42 " --> pdb=" O   GLN K  39 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 16 through 38
      removed outlier: 4.747A  pdb=" N   SER L  35 " --> pdb=" O   ILE L  31 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   TYR L  36 " --> pdb=" O   LEU L  32 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 5 through 29
      removed outlier: 4.189A  pdb=" N   PHE M   8 " --> pdb=" O   ASN M   5 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ALA M  10 " --> pdb=" O   GLY M   7 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ILE M  12 " --> pdb=" O   ILE M   9 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   LEU M  13 " --> pdb=" O   ALA M  10 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   PHE M  14 " --> pdb=" O   SER M  11 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU M  16 " --> pdb=" O   LEU M  13 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   VAL M  17 " --> pdb=" O   PHE M  14 " (cutoff:3.500A)
      Proline residue:  M  18  - end of helix
      removed outlier: 3.652A  pdb=" N   ILE M  24 " --> pdb=" O   PHE M  21 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   ILE M  27 " --> pdb=" O   ILE M  24 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   GLN M  28 " --> pdb=" O   LEU M  25 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   THR M  29 " --> pdb=" O   PHE M  26 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 3 through 22
    Processing helix  chain 'X' and resid 3 through 15
    Processing helix  chain 'X' and resid 24 through 33
    Processing sheet with id=  A, first strand: chain 'B' and resid 166 through 169
    Processing sheet with id=  B, first strand: chain 'B' and resid 343 through 347
    Processing sheet with id=  C, first strand: chain 'B' and resid 336 through 340
      removed outlier: 6.622A  pdb=" N   ASP B 431 " --> pdb=" O   GLN B 338 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 369 through 371
    Processing sheet with id=  E, first strand: chain 'C' and resid 172 through 174
    Processing sheet with id=  F, first strand: chain 'C' and resid 328 through 330

    689 hydrogen bonds defined for protein.
    1938 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.08

  Time building geometry restraints manager: 9.00 seconds

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

  Histogram of bond lengths:
        1.17 -     1.39: 7306
        1.39 -     1.60: 11874
        1.60 -     1.81: 150
        1.81 -     2.03: 35
        2.03 -     2.24: 109
  Bond restraints: 19474
  Sorted by residual:
  bond pdb=" C10 BCR C 519 "
       pdb=" C11 BCR C 519 "
    ideal  model  delta    sigma   weight residual
    1.436  1.172  0.264 2.00e-02 2.50e+03 1.74e+02
  bond pdb=" C10 BCR X 102 "
       pdb=" C11 BCR X 102 "
    ideal  model  delta    sigma   weight residual
    1.436  1.175  0.261 2.00e-02 2.50e+03 1.70e+02
  bond pdb=" C10 BCR B 618 "
       pdb=" C11 BCR B 618 "
    ideal  model  delta    sigma   weight residual
    1.436  1.177  0.259 2.00e-02 2.50e+03 1.68e+02
  bond pdb=" C10 BCR B 617 "
       pdb=" C11 BCR B 617 "
    ideal  model  delta    sigma   weight residual
    1.436  1.178  0.258 2.00e-02 2.50e+03 1.66e+02
  bond pdb=" C10 BCR C 516 "
       pdb=" C11 BCR C 516 "
    ideal  model  delta    sigma   weight residual
    1.436  1.179  0.257 2.00e-02 2.50e+03 1.65e+02
  ... (remaining 19469 not shown)

  Histogram of bond angle deviations from ideal:
       82.94 -   102.34: 388
      102.34 -   121.74: 21553
      121.74 -   141.14: 4777
      141.14 -   160.54: 63
      160.54 -   179.94: 98
  Bond angle restraints: 26879
  Sorted by residual:
  angle pdb=" C10 BCR X 102 "
        pdb=" C11 BCR X 102 "
        pdb=" C12 BCR X 102 "
      ideal   model   delta    sigma   weight residual
     122.66  179.94  -57.28 3.00e+00 1.11e-01 3.65e+02
  angle pdb=" C10 BCR D 407 "
        pdb=" C11 BCR D 407 "
        pdb=" C12 BCR D 407 "
      ideal   model   delta    sigma   weight residual
     122.66  177.86  -55.20 3.00e+00 1.11e-01 3.39e+02
  angle pdb=" C10 BCR B 618 "
        pdb=" C11 BCR B 618 "
        pdb=" C12 BCR B 618 "
      ideal   model   delta    sigma   weight residual
     122.66  177.61  -54.95 3.00e+00 1.11e-01 3.35e+02
  angle pdb=" C10 BCR B 619 "
        pdb=" C11 BCR B 619 "
        pdb=" C12 BCR B 619 "
      ideal   model   delta    sigma   weight residual
     122.66  177.34  -54.68 3.00e+00 1.11e-01 3.32e+02
  angle pdb=" C10 BCR C 516 "
        pdb=" C11 BCR C 516 "
        pdb=" C12 BCR C 516 "
      ideal   model   delta    sigma   weight residual
     122.66  177.23  -54.57 3.00e+00 1.11e-01 3.31e+02
  ... (remaining 26874 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.70: 9309
       24.70 -    49.41: 766
       49.41 -    74.11: 201
       74.11 -    98.82: 20
       98.82 -   123.52: 6
  Dihedral angle restraints: 10302
    sinusoidal: 4953
      harmonic: 5349
  Sorted by residual:
  dihedral pdb=" CA  PHE A 260 "
           pdb=" C   PHE A 260 "
           pdb=" N   GLN A 261 "
           pdb=" CA  GLN A 261 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.02   31.98     0      5.00e+00 4.00e-02 4.09e+01
  dihedral pdb=" CA  ASP C 365 "
           pdb=" C   ASP C 365 "
           pdb=" N   LYS C 366 "
           pdb=" CA  LYS C 366 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.95   25.05     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" CA  GLY C 209 "
           pdb=" C   GLY C 209 "
           pdb=" N   TRP C 210 "
           pdb=" CA  TRP C 210 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.85  -23.15     0      5.00e+00 4.00e-02 2.14e+01
  ... (remaining 10299 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.157: 2464
       0.157 -    0.314: 51
       0.314 -    0.471: 10
       0.471 -    0.628: 19
       0.628 -    0.785: 9
  Chirality restraints: 2553
  Sorted by residual:
  chirality pdb=" C3A CLA B 604 "
            pdb=" C2A CLA B 604 "
            pdb=" C4A CLA B 604 "
            pdb=" CMA CLA B 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.76   -1.98   -0.79 2.00e-01 2.50e+01 1.54e+01
  chirality pdb=" C3A CLA C 512 "
            pdb=" C2A CLA C 512 "
            pdb=" C4A CLA C 512 "
            pdb=" CMA CLA C 512 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.76   -2.04   -0.72 2.00e-01 2.50e+01 1.31e+01
  chirality pdb=" C3A CLA C 504 "
            pdb=" C2A CLA C 504 "
            pdb=" C4A CLA C 504 "
            pdb=" CMA CLA C 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.76   -2.04   -0.72 2.00e-01 2.50e+01 1.30e+01
  ... (remaining 2550 not shown)

  Planarity restraints: 3326
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 BCR C 519 "   -0.290 2.00e-02 2.50e+03   1.68e-01 3.51e+02
        pdb=" C11 BCR C 519 "    0.200 2.00e-02 2.50e+03
        pdb=" C34 BCR C 519 "    0.064 2.00e-02 2.50e+03
        pdb=" C8  BCR C 519 "    0.089 2.00e-02 2.50e+03
        pdb=" C9  BCR C 519 "   -0.062 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 BCR B 619 "    0.280 2.00e-02 2.50e+03   1.61e-01 3.22e+02
        pdb=" C11 BCR B 619 "   -0.192 2.00e-02 2.50e+03
        pdb=" C34 BCR B 619 "   -0.069 2.00e-02 2.50e+03
        pdb=" C8  BCR B 619 "   -0.077 2.00e-02 2.50e+03
        pdb=" C9  BCR B 619 "    0.058 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 BCR C 515 "    0.269 2.00e-02 2.50e+03   1.53e-01 2.92e+02
        pdb=" C11 BCR C 515 "   -0.182 2.00e-02 2.50e+03
        pdb=" C34 BCR C 515 "   -0.038 2.00e-02 2.50e+03
        pdb=" C8  BCR C 515 "   -0.091 2.00e-02 2.50e+03
        pdb=" C9  BCR C 515 "    0.042 2.00e-02 2.50e+03
  ... (remaining 3323 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 355
        2.65 -     3.21: 16428
        3.21 -     3.77: 31659
        3.77 -     4.34: 48803
        4.34 -     4.90: 74475
  Nonbonded interactions: 171720
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN C 298 "
            pdb=" OG1 THR C 342 "
     model   vdw
     2.082 2.440
  nonbonded pdb=" O   TYR C 258 "
            pdb=" O   HOH C 601 "
     model   vdw
     2.143 2.440
  nonbonded pdb=" O   LEU M  25 "
            pdb=" OG1 THR M  29 "
     model   vdw
     2.153 2.440
  nonbonded pdb=" O   ASN B 191 "
            pdb=" O   HOH B 701 "
     model   vdw
     2.159 2.440
  nonbonded pdb=" O   HOH A 502 "
            pdb=" O   HOH A 552 "
     model   vdw
     2.175 2.440
  ... (remaining 171715 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=1.00 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:             0.710
  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:             0.020
  Extract box with map and model:          4.710
  Check model and map are aligned:         0.270
  Set scattering table:                    0.170
  Process input model:                     51.280
  Find NCS groups from input model:        0.530
  Set up NCS constraints:                  0.080
  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:13.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   70.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
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      :  0.025   0.264  19474  Z= 1.323
  Angle     :  2.555  57.283  26879  Z= 0.883
  Chirality :  0.087   0.785   2553
  Planarity :  0.011   0.168   3326
  Dihedral  : 18.425 123.523   6888
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.14 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.58 (0.16), residues: 1866
  helix: -2.86 (0.11), residues: 1087
  sheet: -2.78 (0.65), residues: 49
  loop : -1.20 (0.22), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 131 
 HIS   0.006   0.001   HIS C 417 
 PHE   0.030   0.002   PHE B 246 
 TYR   0.016   0.002   TYR H  49 
 ARG   0.006   0.001   ARG D 294 

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

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

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 1.750 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.7123 (t0) cc_final: 0.6740 (t0)
REVERT: A   86 SER cc_start: 0.8798 (t) cc_final: 0.8577 (t)
REVERT: A   87 ASN cc_start: 0.8292 (t0) cc_final: 0.8076 (t0)
REVERT: A  214 MET cc_start: 0.7978 (tpt) cc_final: 0.7757 (mmm)
REVERT: A  293 MET cc_start: 0.7648 (mtm) cc_final: 0.7440 (mtp)
REVERT: B  231 MET cc_start: 0.9135 (mtt) cc_final: 0.8777 (mtt)
REVERT: B  347 LYS cc_start: 0.8174 (mttm) cc_final: 0.7946 (mttm)
REVERT: B  349 LYS cc_start: 0.7357 (pttm) cc_final: 0.6802 (pttp)
REVERT: B  359 MET cc_start: 0.8785 (ttm) cc_final: 0.8579 (ttp)
REVERT: B  422 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7755 (mtt-85)
REVERT: C   65 GLU cc_start: 0.7149 (pm20) cc_final: 0.6891 (pm20)
REVERT: C   91 GLU cc_start: 0.7722 (mp0) cc_final: 0.7328 (mp0)
REVERT: C  169 PHE cc_start: 0.6989 (m-80) cc_final: 0.6761 (m-80)
REVERT: D  317 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8321 (mtpt)
REVERT: D  343 GLU cc_start: 0.6856 (tp30) cc_final: 0.6583 (tp30)
REVERT: D  348 ARG cc_start: 0.7605 (ptp90) cc_final: 0.6921 (ptp-110)
REVERT: F   40 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8611 (mm-40)
REVERT: H    9 ASP cc_start: 0.7929 (m-30) cc_final: 0.7499 (m-30)
REVERT: I   30 ARG cc_start: 0.7207 (mtt-85) cc_final: 0.6747 (mmt90)
REVERT: L   23 LEU cc_start: 0.8320 (mt) cc_final: 0.8090 (OUTLIER)
REVERT: X   32 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7457 (mm110)
  outliers start: 0
  outliers final: 2
  residues processed: 269
  average time/residue: 1.3728
  time to fit residues: 414.3021
Evaluate side-chains
  210 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 209
  time to evaluate  : 1.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  356 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 155 optimal weight:    5.9990
   chunk 139 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 94 optimal weight:    8.9990
   chunk 74 optimal weight:    4.9990
   chunk 144 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 107 optimal weight:    1.9990
   chunk 167 optimal weight:    7.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 HIS
A 332 HIS
B  76 ASN
B 281 GLN
B 331 ASN
B 413 ASN
B 438 ASN
C 142 ASN
C 300 GLN
C 309 GLN
C 385 HIS
D 142 ASN
D 263 ASN
E  67 GLN
H   3 GLN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  19474  Z= 0.245
  Angle     :  0.669   8.693  26879  Z= 0.305
  Chirality :  0.044   0.198   2553
  Planarity :  0.006   0.049   3326
  Dihedral  : 18.716 106.065   3655
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.57 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  7.65 %
    Favored  : 90.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    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: -1.18 (0.18), residues: 1866
  helix: -0.60 (0.15), residues: 1096
  sheet: -2.44 (0.66), residues: 49
  loop : -0.70 (0.23), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 131 
 HIS   0.010   0.002   HIS B 114 
 PHE   0.023   0.002   PHE B 246 
 TYR   0.014   0.002   TYR B 172 
 ARG   0.007   0.000   ARG C 122 

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

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

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 220
  time to evaluate  : 1.842 
Fit side-chains
REVERT: A   59 ASP cc_start: 0.7177 (t0) cc_final: 0.6747 (t0)
REVERT: A   86 SER cc_start: 0.8733 (t) cc_final: 0.8473 (t)
REVERT: A   87 ASN cc_start: 0.8300 (t0) cc_final: 0.7945 (t0)
REVERT: A  322 ASN cc_start: 0.8279 (t0) cc_final: 0.8076 (t0)
REVERT: B   22 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8761 (m)
REVERT: B  231 MET cc_start: 0.9157 (mtt) cc_final: 0.8802 (mtt)
REVERT: B  347 LYS cc_start: 0.8243 (mttm) cc_final: 0.7974 (mttm)
REVERT: B  349 LYS cc_start: 0.7652 (pttm) cc_final: 0.7097 (pttp)
REVERT: B  350 GLU cc_start: 0.7100 (mp0) cc_final: 0.6804 (mp0)
REVERT: B  359 MET cc_start: 0.8840 (ttm) cc_final: 0.8626 (ttp)
REVERT: B  370 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8426 (mtm)
REVERT: B  374 ASP cc_start: 0.6116 (t0) cc_final: 0.5907 (t0)
REVERT: B  387 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6223 (mm-30)
REVERT: C  169 PHE cc_start: 0.7060 (m-80) cc_final: 0.6821 (m-80)
REVERT: C  229 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8213 (mm)
REVERT: C  330 ARG cc_start: 0.6960 (mtt-85) cc_final: 0.6749 (mtt-85)
REVERT: D  343 GLU cc_start: 0.6778 (tp30) cc_final: 0.6476 (tp30)
REVERT: D  348 ARG cc_start: 0.7593 (ptp90) cc_final: 0.7242 (ptt-90)
REVERT: H    9 ASP cc_start: 0.7774 (m-30) cc_final: 0.7386 (m-30)
REVERT: H   31 MET cc_start: 0.8653 (ttp) cc_final: 0.8235 (ttp)
REVERT: I   30 ARG cc_start: 0.7225 (mtt-85) cc_final: 0.6711 (mmt90)
REVERT: L   23 LEU cc_start: 0.8269 (mt) cc_final: 0.8034 (mp)
REVERT: X   32 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7487 (mm110)
  outliers start: 26
  outliers final: 10
  residues processed: 229
  average time/residue: 1.3407
  time to fit residues: 347.4737
Evaluate side-chains
  218 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 204
  time to evaluate  : 1.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  290 SER
Chi-restraints excluded: chain B residue  334 ASP
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  387 GLU
Chi-restraints excluded: chain B residue  388 SER
Chi-restraints excluded: chain C residue  201 LEU
Chi-restraints excluded: chain C residue  229 LEU
Chi-restraints excluded: chain C residue  230 ILE
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain H residue   16 SER
Chi-restraints excluded: chain I residue   11 VAL
Chi-restraints excluded: chain X residue    2 THR
Chi-restraints excluded: chain X residue   19 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 92 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 139 optimal weight:    8.9990
   chunk 113 optimal weight:    7.9990
   chunk 46 optimal weight:    3.9990
   chunk 167 optimal weight:    1.9990
   chunk 180 optimal weight:    3.9990
   chunk 149 optimal weight:    3.9990
   chunk 165 optimal weight:    4.9990
   chunk 57 optimal weight:    5.9990
   chunk 134 optimal weight:    0.9980
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  76 ASN
B 413 ASN
B 438 ASN
D 263 ASN
E  67 GLN
H   3 GLN
M   5 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  19474  Z= 0.339
  Angle     :  0.698   8.257  26879  Z= 0.319
  Chirality :  0.048   0.217   2553
  Planarity :  0.006   0.052   3326
  Dihedral  : 18.229 103.707   3653
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.68 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  9.59 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    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 (0.19), residues: 1866
  helix:  0.08 (0.15), residues: 1103
  sheet: -2.08 (0.68), residues: 49
  loop : -0.51 (0.23), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 131 
 HIS   0.008   0.002   HIS B 466 
 PHE   0.027   0.002   PHE B 246 
 TYR   0.017   0.002   TYR B 172 
 ARG   0.009   0.001   ARG E  60 

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

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

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 207
  time to evaluate  : 1.926 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.7192 (t0) cc_final: 0.6211 (p0)
REVERT: A   86 SER cc_start: 0.8710 (t) cc_final: 0.8155 (t)
REVERT: A  322 ASN cc_start: 0.8208 (t0) cc_final: 0.7983 (t0)
REVERT: B  149 LEU cc_start: 0.8791 (tp) cc_final: 0.8569 (tp)
REVERT: B  231 MET cc_start: 0.9164 (mtt) cc_final: 0.8820 (mtt)
REVERT: B  347 LYS cc_start: 0.8209 (mttm) cc_final: 0.7952 (mttm)
REVERT: B  349 LYS cc_start: 0.7642 (pttm) cc_final: 0.7168 (pttp)
REVERT: B  350 GLU cc_start: 0.7002 (mp0) cc_final: 0.6636 (mp0)
REVERT: B  370 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8420 (mtm)
REVERT: B  372 ASP cc_start: 0.7531 (p0) cc_final: 0.7323 (p0)
REVERT: B  387 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6269 (mm-30)
REVERT: C  169 PHE cc_start: 0.7060 (m-80) cc_final: 0.6804 (m-80)
REVERT: C  366 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7754 (mttp)
REVERT: H    9 ASP cc_start: 0.7722 (m-30) cc_final: 0.7421 (m-30)
REVERT: H   31 MET cc_start: 0.8583 (ttp) cc_final: 0.8231 (ttp)
REVERT: I   30 ARG cc_start: 0.7227 (mtt-85) cc_final: 0.6725 (mmt90)
REVERT: L   23 LEU cc_start: 0.8282 (mt) cc_final: 0.8053 (mp)
  outliers start: 32
  outliers final: 21
  residues processed: 224
  average time/residue: 1.4532
  time to fit residues: 365.5724
Evaluate side-chains
  230 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 207
  time to evaluate  : 1.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  290 SER
Chi-restraints excluded: chain B residue  294 GLU
Chi-restraints excluded: chain B residue  334 ASP
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  387 GLU
Chi-restraints excluded: chain B residue  412 SER
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain C residue  201 LEU
Chi-restraints excluded: chain C residue  230 ILE
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain D residue  150 ILE
Chi-restraints excluded: chain E residue   72 ILE
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain H residue   12 ARG
Chi-restraints excluded: chain H residue   16 SER
Chi-restraints excluded: chain I residue   11 VAL
Chi-restraints excluded: chain K residue   23 VAL
Chi-restraints excluded: chain X residue    2 THR
Chi-restraints excluded: chain X residue   19 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 165 optimal weight:    2.9990
   chunk 125 optimal weight:    3.9990
   chunk 86 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 112 optimal weight:    9.9990
   chunk 167 optimal weight:    2.9990
   chunk 177 optimal weight:    9.9990
   chunk 87 optimal weight:    0.0770
   chunk 159 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    1.8144

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  76 ASN
B 413 ASN
B 438 ASN
D 263 ASN
E  67 GLN
H   3 GLN
M   5 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8149
moved from start:          0.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  19474  Z= 0.232
  Angle     :  0.606   8.535  26879  Z= 0.278
  Chirality :  0.044   0.197   2553
  Planarity :  0.005   0.052   3326
  Dihedral  : 17.557 106.141   3653
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.20 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 10.56 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    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 (0.19), residues: 1866
  helix:  0.57 (0.16), residues: 1095
  sheet: -1.70 (0.72), residues: 49
  loop : -0.32 (0.23), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 131 
 HIS   0.007   0.002   HIS C 417 
 PHE   0.023   0.002   PHE B 246 
 TYR   0.013   0.001   TYR B 172 
 ARG   0.005   0.000   ARG E  60 

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

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

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 35
    poor density    : 208
  time to evaluate  : 1.849 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.7183 (t0) cc_final: 0.6221 (p0)
REVERT: A   86 SER cc_start: 0.8685 (t) cc_final: 0.8142 (t)
REVERT: B  231 MET cc_start: 0.9149 (mtt) cc_final: 0.8809 (mtt)
REVERT: B  347 LYS cc_start: 0.8172 (mttm) cc_final: 0.7923 (mttm)
REVERT: B  349 LYS cc_start: 0.7708 (pttm) cc_final: 0.7254 (pttt)
REVERT: B  370 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8405 (mtm)
REVERT: B  387 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6363 (mm-30)
REVERT: C  169 PHE cc_start: 0.7011 (m-80) cc_final: 0.6766 (m-80)
REVERT: C  366 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7741 (mttp)
REVERT: C  368 ARG cc_start: 0.6226 (mmt-90) cc_final: 0.5648 (mmp80)
REVERT: D  343 GLU cc_start: 0.6731 (tp30) cc_final: 0.6437 (tp30)
REVERT: F   39 MET cc_start: 0.9105 (mtt) cc_final: 0.8695 (mtm)
REVERT: H    9 ASP cc_start: 0.7703 (m-30) cc_final: 0.7316 (m-30)
REVERT: H   31 MET cc_start: 0.8546 (ttp) cc_final: 0.8200 (ttp)
REVERT: I   30 ARG cc_start: 0.7231 (mtt-85) cc_final: 0.6749 (mmt90)
REVERT: L   23 LEU cc_start: 0.8211 (mt) cc_final: 0.8010 (mp)
  outliers start: 35
  outliers final: 21
  residues processed: 222
  average time/residue: 1.3074
  time to fit residues: 326.6669
Evaluate side-chains
  219 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 196
  time to evaluate  : 1.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  290 SER
Chi-restraints excluded: chain B residue  334 ASP
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  387 GLU
Chi-restraints excluded: chain B residue  412 SER
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain C residue  201 LEU
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  230 ILE
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain D residue  144 ILE
Chi-restraints excluded: chain D residue  150 ILE
Chi-restraints excluded: chain F residue   40 GLN
Chi-restraints excluded: chain H residue   12 ARG
Chi-restraints excluded: chain I residue   11 VAL
Chi-restraints excluded: chain K residue   23 VAL
Chi-restraints excluded: chain X residue    2 THR
Chi-restraints excluded: chain X residue   19 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 148 optimal weight:    3.9990
   chunk 100 optimal weight:    7.9990
   chunk 2 optimal weight:    0.0770
   chunk 132 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 151 optimal weight:    0.0870
   chunk 122 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 90 optimal weight:    1.9990
   chunk 159 optimal weight:    5.9990
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.7918

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  76 ASN
B 413 ASN
B 438 ASN
C 372 GLN
C 375 GLN
E  67 GLN
H   3 GLN
M   5 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  19474  Z= 0.152
  Angle     :  0.537   8.550  26879  Z= 0.246
  Chirality :  0.041   0.187   2553
  Planarity :  0.004   0.051   3326
  Dihedral  : 16.615 105.058   3653
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 11.67 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    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:  0.70 (0.20), residues: 1866
  helix:  1.04 (0.16), residues: 1091
  sheet: -1.51 (0.68), residues: 54
  loop : -0.12 (0.23), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 131 
 HIS   0.006   0.001   HIS C 417 
 PHE   0.021   0.001   PHE X  29 
 TYR   0.010   0.001   TYR B 172 
 ARG   0.004   0.000   ARG C 122 

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

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

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 213
  time to evaluate  : 1.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.7152 (t0) cc_final: 0.6786 (t0)
REVERT: A   86 SER cc_start: 0.8642 (t) cc_final: 0.8233 (t)
REVERT: B  231 MET cc_start: 0.9120 (mtt) cc_final: 0.8775 (mtt)
REVERT: B  347 LYS cc_start: 0.7985 (mttm) cc_final: 0.7741 (mttm)
REVERT: B  349 LYS cc_start: 0.7680 (pttm) cc_final: 0.7322 (pttp)
REVERT: B  350 GLU cc_start: 0.7113 (mp0) cc_final: 0.6803 (mp0)
REVERT: B  370 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8370 (mtm)
REVERT: B  387 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6563 (mm-30)
REVERT: C  169 PHE cc_start: 0.7014 (m-80) cc_final: 0.6784 (m-80)
REVERT: C  215 ASN cc_start: 0.8461 (p0) cc_final: 0.8258 (p0)
REVERT: C  366 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7688 (mttp)
REVERT: C  368 ARG cc_start: 0.6142 (mmt-90) cc_final: 0.5566 (mmp80)
REVERT: D   45 LEU cc_start: 0.8349 (mp) cc_final: 0.8063 (mt)
REVERT: D  343 GLU cc_start: 0.6747 (tp30) cc_final: 0.6453 (tp30)
REVERT: F   39 MET cc_start: 0.9076 (mtt) cc_final: 0.8670 (mtm)
REVERT: H    9 ASP cc_start: 0.7675 (m-30) cc_final: 0.7349 (m-30)
REVERT: H   31 MET cc_start: 0.8529 (ttp) cc_final: 0.8182 (ttp)
REVERT: I   30 ARG cc_start: 0.7165 (mtt-85) cc_final: 0.6698 (mmt90)
REVERT: L   23 LEU cc_start: 0.8230 (mt) cc_final: 0.8027 (mp)
REVERT: M   21 PHE cc_start: 0.7260 (t80) cc_final: 0.6958 (t80)
REVERT: T   16 VAL cc_start: 0.7943 (t) cc_final: 0.7429 (p)
  outliers start: 30
  outliers final: 15
  residues processed: 227
  average time/residue: 1.3335
  time to fit residues: 341.5079
Evaluate side-chains
  216 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 200
  time to evaluate  : 1.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  290 SER
Chi-restraints excluded: chain B residue  334 ASP
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  230 ILE
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain D residue  150 ILE
Chi-restraints excluded: chain F residue   40 GLN
Chi-restraints excluded: chain H residue   12 ARG
Chi-restraints excluded: chain K residue   23 VAL
Chi-restraints excluded: chain X residue   19 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 160 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 104 optimal weight:    5.9990
   chunk 43 optimal weight:    0.2980
   chunk 178 optimal weight:    5.9990
   chunk 147 optimal weight:   10.0000
   chunk 82 optimal weight:    5.9990
   chunk 14 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  76 ASN
B 413 ASN
B 438 ASN
E  67 GLN
F  40 GLN
H   3 GLN
M   5 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  19474  Z= 0.145
  Angle     :  0.526   8.281  26879  Z= 0.241
  Chirality :  0.040   0.185   2553
  Planarity :  0.004   0.050   3326
  Dihedral  : 16.084 104.289   3653
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.31 %
    Favored  : 85.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    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:  0.99 (0.20), residues: 1866
  helix:  1.26 (0.16), residues: 1094
  sheet: -1.27 (0.69), residues: 54
  loop : -0.01 (0.24), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 131 
 HIS   0.006   0.001   HIS D 214 
 PHE   0.018   0.001   PHE B 246 
 TYR   0.011   0.001   TYR B 172 
 ARG   0.006   0.000   ARG C 122 

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

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

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 208
  time to evaluate  : 1.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.7136 (t0) cc_final: 0.6791 (t0)
REVERT: A   86 SER cc_start: 0.8645 (t) cc_final: 0.8262 (t)
REVERT: B   22 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8676 (m)
REVERT: B  231 MET cc_start: 0.9113 (mtt) cc_final: 0.8794 (mtt)
REVERT: B  347 LYS cc_start: 0.7917 (mttm) cc_final: 0.7669 (mttm)
REVERT: B  370 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8328 (mtm)
REVERT: C  366 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7666 (mttp)
REVERT: C  368 ARG cc_start: 0.6159 (mmt-90) cc_final: 0.5587 (mmp80)
REVERT: D   45 LEU cc_start: 0.8345 (mp) cc_final: 0.8061 (mt)
REVERT: D  343 GLU cc_start: 0.6735 (tp30) cc_final: 0.6429 (tp30)
REVERT: H    9 ASP cc_start: 0.7702 (m-30) cc_final: 0.7400 (m-30)
REVERT: H   31 MET cc_start: 0.8590 (ttp) cc_final: 0.8246 (ttp)
REVERT: I   30 ARG cc_start: 0.7124 (mtt-85) cc_final: 0.6670 (mmt90)
REVERT: M   21 PHE cc_start: 0.7285 (t80) cc_final: 0.6971 (t80)
REVERT: T   16 VAL cc_start: 0.7950 (t) cc_final: 0.7445 (p)
  outliers start: 29
  outliers final: 15
  residues processed: 223
  average time/residue: 1.2822
  time to fit residues: 322.5819
Evaluate side-chains
  213 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 196
  time to evaluate  : 1.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  290 SER
Chi-restraints excluded: chain B residue  334 ASP
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  230 ILE
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain H residue   12 ARG
Chi-restraints excluded: chain K residue   23 VAL
Chi-restraints excluded: chain X residue    2 THR
Chi-restraints excluded: chain X residue    4 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 171 optimal weight:    0.0170
   chunk 20 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   chunk 130 optimal weight:    0.8980
   chunk 100 optimal weight:    4.9990
   chunk 149 optimal weight:    5.9990
   chunk 99 optimal weight:    7.9990
   chunk 177 optimal weight:    0.4980
   chunk 110 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9980
   chunk 81 optimal weight:    0.0070
   overall best weight:    0.4836

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  76 ASN
C 360 ASN
E  67 GLN
F  40 GLN
H   3 GLN
M   5 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  19474  Z= 0.129
  Angle     :  0.505   8.214  26879  Z= 0.233
  Chirality :  0.039   0.175   2553
  Planarity :  0.004   0.049   3326
  Dihedral  : 15.523 104.326   3653
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.09 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    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:  1.21 (0.20), residues: 1866
  helix:  1.45 (0.16), residues: 1092
  sheet: -1.01 (0.69), residues: 54
  loop :  0.07 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  33 
 HIS   0.007   0.001   HIS B 201 
 PHE   0.014   0.001   PHE B 246 
 TYR   0.010   0.001   TYR B 172 
 ARG   0.006   0.000   ARG C 122 

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

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

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 209
  time to evaluate  : 1.673 
Fit side-chains
REVERT: A   59 ASP cc_start: 0.7024 (t0) cc_final: 0.6669 (t0)
REVERT: A   86 SER cc_start: 0.8652 (t) cc_final: 0.8262 (t)
REVERT: B   76 ASN cc_start: 0.8160 (m-40) cc_final: 0.7892 (m110)
REVERT: B  217 LEU cc_start: 0.8227 (mt) cc_final: 0.7935 (mt)
REVERT: B  231 MET cc_start: 0.9107 (mtt) cc_final: 0.8798 (mtt)
REVERT: B  347 LYS cc_start: 0.7928 (mttm) cc_final: 0.7669 (mttm)
REVERT: B  370 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8333 (mtm)
REVERT: C  169 PHE cc_start: 0.6920 (m-80) cc_final: 0.6661 (m-10)
REVERT: C  366 LYS cc_start: 0.7944 (mtpt) cc_final: 0.7692 (mttp)
REVERT: D   45 LEU cc_start: 0.8386 (mp) cc_final: 0.8102 (mt)
REVERT: D  343 GLU cc_start: 0.6710 (tp30) cc_final: 0.6402 (tp30)
REVERT: F   39 MET cc_start: 0.9036 (mtt) cc_final: 0.8685 (mtm)
REVERT: H    9 ASP cc_start: 0.7707 (m-30) cc_final: 0.7364 (m-30)
REVERT: H   12 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.5565 (tpm170)
REVERT: H   31 MET cc_start: 0.8592 (ttp) cc_final: 0.8251 (ttp)
REVERT: I   30 ARG cc_start: 0.7202 (mtt-85) cc_final: 0.6781 (mmt90)
REVERT: M   21 PHE cc_start: 0.7225 (t80) cc_final: 0.6907 (t80)
REVERT: T   16 VAL cc_start: 0.7934 (t) cc_final: 0.7428 (p)
  outliers start: 25
  outliers final: 12
  residues processed: 221
  average time/residue: 1.3823
  time to fit residues: 344.7797
Evaluate side-chains
  214 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 200
  time to evaluate  : 1.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  290 SER
Chi-restraints excluded: chain B residue  334 ASP
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain F residue   40 GLN
Chi-restraints excluded: chain H residue   12 ARG
Chi-restraints excluded: chain K residue   23 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 105 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 112 optimal weight:    0.9980
   chunk 120 optimal weight:    3.9990
   chunk 87 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 139 optimal weight:    0.0270
   chunk 161 optimal weight:    6.9990
   overall best weight:    0.9240

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   3 GLN
M   5 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  19474  Z= 0.156
  Angle     :  0.521   7.996  26879  Z= 0.240
  Chirality :  0.040   0.180   2553
  Planarity :  0.004   0.049   3326
  Dihedral  : 15.440 103.098   3653
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 13.16 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    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:  1.25 (0.20), residues: 1866
  helix:  1.48 (0.16), residues: 1088
  sheet: -0.96 (0.69), residues: 54
  loop :  0.08 (0.24), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  33 
 HIS   0.008   0.001   HIS B 201 
 PHE   0.022   0.001   PHE X  29 
 TYR   0.011   0.001   TYR B 172 
 ARG   0.006   0.000   ARG C 122 

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

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

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 198
  time to evaluate  : 1.855 
Fit side-chains
REVERT: A   59 ASP cc_start: 0.6982 (t0) cc_final: 0.6629 (t0)
REVERT: A   86 SER cc_start: 0.8659 (t) cc_final: 0.8276 (t)
REVERT: B   22 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8689 (m)
REVERT: B   76 ASN cc_start: 0.8152 (m-40) cc_final: 0.7873 (m110)
REVERT: B  217 LEU cc_start: 0.8282 (mt) cc_final: 0.7985 (mt)
REVERT: B  231 MET cc_start: 0.9104 (mtt) cc_final: 0.8784 (mtt)
REVERT: B  347 LYS cc_start: 0.7927 (mttm) cc_final: 0.7685 (mttm)
REVERT: B  370 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8309 (mtm)
REVERT: C  366 LYS cc_start: 0.7964 (mtpt) cc_final: 0.7712 (mttp)
REVERT: D  343 GLU cc_start: 0.6742 (tp30) cc_final: 0.6419 (tp30)
REVERT: F   39 MET cc_start: 0.9090 (mtt) cc_final: 0.8766 (mtm)
REVERT: H    9 ASP cc_start: 0.7692 (m-30) cc_final: 0.7436 (m-30)
REVERT: H   12 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.5597 (tpm170)
REVERT: H   31 MET cc_start: 0.8607 (ttp) cc_final: 0.8205 (ttp)
REVERT: I   30 ARG cc_start: 0.7208 (mtt-85) cc_final: 0.6793 (mmt90)
REVERT: M   21 PHE cc_start: 0.7239 (t80) cc_final: 0.6927 (t80)
REVERT: T   16 VAL cc_start: 0.7967 (t) cc_final: 0.7465 (p)
  outliers start: 29
  outliers final: 12
  residues processed: 215
  average time/residue: 1.3572
  time to fit residues: 328.9173
Evaluate side-chains
  212 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 197
  time to evaluate  : 1.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   36 SER
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  334 ASP
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  230 ILE
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain H residue   12 ARG
Chi-restraints excluded: chain K residue   23 VAL
Chi-restraints excluded: chain X residue    2 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 169 optimal weight:    4.9990
   chunk 155 optimal weight:    5.9990
   chunk 165 optimal weight:    3.9990
   chunk 99 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 129 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 149 optimal weight:    1.9990
   chunk 156 optimal weight:    1.9990
   chunk 164 optimal weight:    0.4980
   chunk 108 optimal weight:    0.8980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 263 ASN
M   5 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  19474  Z= 0.185
  Angle     :  0.542   8.097  26879  Z= 0.251
  Chirality :  0.042   0.244   2553
  Planarity :  0.005   0.049   3326
  Dihedral  : 15.466 101.869   3653
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.87 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    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:  1.22 (0.20), residues: 1866
  helix:  1.44 (0.16), residues: 1092
  sheet: -0.94 (0.68), residues: 54
  loop :  0.10 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 131 
 HIS   0.011   0.002   HIS B 201 
 PHE   0.026   0.001   PHE B 246 
 TYR   0.012   0.001   TYR B 172 
 ARG   0.006   0.000   ARG C 122 

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

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

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 197
  time to evaluate  : 1.756 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.6989 (t0) cc_final: 0.6634 (t0)
REVERT: A   86 SER cc_start: 0.8681 (t) cc_final: 0.8296 (t)
REVERT: B   76 ASN cc_start: 0.8108 (m-40) cc_final: 0.7841 (m110)
REVERT: B  217 LEU cc_start: 0.8312 (mt) cc_final: 0.8071 (mt)
REVERT: B  231 MET cc_start: 0.9091 (mtt) cc_final: 0.8780 (mtt)
REVERT: B  347 LYS cc_start: 0.7941 (mttm) cc_final: 0.7696 (mttm)
REVERT: B  370 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8340 (mtm)
REVERT: C  366 LYS cc_start: 0.7965 (mtpt) cc_final: 0.7732 (mttp)
REVERT: D  343 GLU cc_start: 0.6755 (tp30) cc_final: 0.6437 (tp30)
REVERT: F   39 MET cc_start: 0.9056 (mtt) cc_final: 0.8662 (mtm)
REVERT: H    9 ASP cc_start: 0.7717 (m-30) cc_final: 0.7483 (m-30)
REVERT: H   31 MET cc_start: 0.8576 (ttp) cc_final: 0.8142 (ttp)
REVERT: I   30 ARG cc_start: 0.7212 (mtt-85) cc_final: 0.6803 (mmt90)
REVERT: M   24 ILE cc_start: 0.8863 (mt) cc_final: 0.8643 (mp)
REVERT: T   16 VAL cc_start: 0.7996 (t) cc_final: 0.7489 (p)
  outliers start: 25
  outliers final: 16
  residues processed: 212
  average time/residue: 1.3451
  time to fit residues: 320.7586
Evaluate side-chains
  213 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 196
  time to evaluate  : 1.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   36 SER
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  334 ASP
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  425 GLN
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  230 ILE
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain H residue   12 ARG
Chi-restraints excluded: chain K residue   23 VAL
Chi-restraints excluded: chain L residue   23 LEU
Chi-restraints excluded: chain X residue    2 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 174 optimal weight:    4.9990
   chunk 106 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9990
   chunk 121 optimal weight:    1.9990
   chunk 183 optimal weight:    6.9990
   chunk 168 optimal weight:    3.9990
   chunk 145 optimal weight:    6.9990
   chunk 15 optimal weight:    0.7980
   chunk 112 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 115 optimal weight:    7.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  67 GLN
H   3 GLN
M   5 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  19474  Z= 0.278
  Angle     :  0.617   7.842  26879  Z= 0.285
  Chirality :  0.045   0.231   2553
  Planarity :  0.005   0.048   3326
  Dihedral  : 15.977  99.317   3653
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 14.00 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    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:  0.95 (0.20), residues: 1866
  helix:  1.18 (0.16), residues: 1096
  sheet: -1.16 (0.67), residues: 54
  loop :  0.07 (0.24), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 131 
 HIS   0.014   0.002   HIS B 201 
 PHE   0.031   0.002   PHE B 246 
 TYR   0.016   0.002   TYR B 172 
 ARG   0.006   0.001   ARG E  60 

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

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

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3732 Ramachandran restraints generated.
    1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 199
  time to evaluate  : 1.870 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 ASP cc_start: 0.7010 (t0) cc_final: 0.6650 (t0)
REVERT: A   86 SER cc_start: 0.8697 (t) cc_final: 0.8309 (t)
REVERT: A  172 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8701 (ttt)
REVERT: B  149 LEU cc_start: 0.8761 (tp) cc_final: 0.8542 (tp)
REVERT: B  231 MET cc_start: 0.9123 (mtt) cc_final: 0.8771 (mtt)
REVERT: B  347 LYS cc_start: 0.8000 (mttm) cc_final: 0.7757 (mttm)
REVERT: B  370 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8342 (mtm)
REVERT: C  366 LYS cc_start: 0.7985 (mtpt) cc_final: 0.7774 (mttp)
REVERT: C  368 ARG cc_start: 0.6874 (mmt180) cc_final: 0.6674 (mmt180)
REVERT: D  343 GLU cc_start: 0.6817 (tp30) cc_final: 0.6506 (tp30)
REVERT: F   39 MET cc_start: 0.9113 (mtt) cc_final: 0.8723 (mtm)
REVERT: H    9 ASP cc_start: 0.7716 (m-30) cc_final: 0.7501 (m-30)
REVERT: H   31 MET cc_start: 0.8578 (ttp) cc_final: 0.8180 (ttp)
REVERT: I   30 ARG cc_start: 0.7127 (mtt-85) cc_final: 0.6713 (mmt90)
REVERT: T   16 VAL cc_start: 0.8030 (t) cc_final: 0.7510 (p)
  outliers start: 21
  outliers final: 14
  residues processed: 211
  average time/residue: 1.4488
  time to fit residues: 345.2286
Evaluate side-chains
  210 residues out of total 1543 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 194
  time to evaluate  : 1.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  172 MET
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  334 ASP
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain C residue  187 THR
Chi-restraints excluded: chain C residue  230 ILE
Chi-restraints excluded: chain C residue  233 SER
Chi-restraints excluded: chain C residue  356 LEU
Chi-restraints excluded: chain H residue   12 ARG
Chi-restraints excluded: chain K residue   23 VAL
Chi-restraints excluded: chain L residue   23 LEU
Chi-restraints excluded: chain X residue    2 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 184
   random chunks:
   chunk 155 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 134 optimal weight:    5.9990
   chunk 21 optimal weight:   10.0000
   chunk 40 optimal weight:    4.9990
   chunk 146 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 150 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 128 optimal weight:    2.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  76 ASN
D 336 HIS
H   3 GLN
M   5 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.129826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.105181 restraints weight = 22191.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 1.48
r_work: 0.3010 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  19474  Z= 0.194
  Angle     :  0.558   8.135  26879  Z= 0.259
  Chirality :  0.042   0.244   2553
  Planarity :  0.005   0.049   3326
  Dihedral  : 15.678 102.597   3653
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 14.32 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.03 %
    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:  1.08 (0.20), residues: 1866
  helix:  1.32 (0.16), residues: 1092
  sheet: -1.15 (0.67), residues: 54
  loop :  0.08 (0.24), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 131 
 HIS   0.010   0.002   HIS B 201 
 PHE   0.025   0.001   PHE B 246 
 TYR   0.013   0.001   TYR B 172 
 ARG   0.008   0.000   ARG C 122 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6103.31 seconds
wall clock time: 109 minutes 46.07 seconds (6586.07 seconds total)